Methods for detection of genetic disorders

[0001] This application is a continuation of International Application No. PCT/US2004/006337, filed Mar. 1, 2004, which is a continuation-in-part of International Application No. PCT/US03/06198, filed Feb. 28, 2003, which claims the priority benefit of U.S. Provisional Application Ser. No. 60/378,354, filed May 8, 2002, the contents of each of which are hereby incorporated by reference herein in their entirety. The contents of each of the following applications are also hereby incorporated by reference in their entirety herein: U.S. patent application Ser. No. 10/093,618, filed Mar. 11, 2002, and U.S. Provisional Application Ser. No. 60/360,232, filed Mar. 1, 2002.

[0002] 1. Field of the Invention

[0003] The present invention is directed to a method for the detection of genetic disorders including chromosomal abnormalities and mutations. The present invention provides a rapid, non-invasive method for determining the sequence of DNA from a fetus. The method is especially useful for detection of chromosomal abnormalities in a fetus including translocations, transversions, monosomies, trisomies, and other aneuplodies, deletions, additions, amplifications, translocations and rearrangements.

[0004] 2. Background Art

[0005] Chromosomal abnormalities are responsible for a significant portion of genetic defects in liveborn humans. The nucleus of a human cell contains forty-six (46) chromosomes, which contain the genetic instructions, and determine the operations of the cell. Half of the forty-six chromosomes originate from each parent. Except for the sex chromosomes, which are quite different from each other in normal males, the chromosomes from the mother and the chromosomes from the father make a matched set. The pairs were combined when the egg was fertilized by the sperm. Occasionally, an error occurs in either the formation or combination of chromosomes, and the fertilized egg is formed with too many or too few chromosomes, or with chromosomes that are mixed in some way. Because each chromosome contains many genes, chromosomal abnormalities are likely to cause serious birth defects, affecting many body systems and often including developmental disability (e.g., mental retardation).

[0006] Cells mistakenly can rejoin broken ends of chromosomes, both spontaneously and after exposure to chemical compounds, carcinogens, and irradiation. When rejoining occurs within a chromosome, a chromosome segment between the two breakpoints becomes inverted and is classified as an inversion. With inversions, there is no loss of genetic material; however, inversions can cause disruption of a critical gene, or create a fusion gene that induces a disease related condition.

[0007] In a reciprocal translocation, two non-homologous chromosomes break and exchange fragments. In this scenario, two abnormal chromosomes result: each consists of a part derived from the other chromosome and lacks a part of itself. If the translocation is of a balanced type, the individual will display no abnormal phenotypes. However, during germ-cell formation in the translocation-bearing individuals, the proper distribution of chromosomes in the egg or sperm occasionally fails, resulting in miscarriage, malformation, or mental retardation of the offspring.

[0008] In a Robertsonian translocation, the centromeres of two acrocentric (a chromosome with a non-centrally located centromere) chromosomes fuse to generate one large metacentric chromosome. The karyotype of an individual with a centric fusion has one less than the normal diploid number of chromosomes.

[0009] Errors that generate too many or too few chromosomes can also lead to disease phenotypes. For example, a missing copy of chromosome X (monosomy X) results in Turner's Syndrome, while an additional copy of chromosome 21 results in Down's Syndrome. Other diseases such as Edward's Syndrome, and Patau Syndrome are caused by an additional copy of chromosome 18, and chromosome 13, respectively.

[0010] One of the most common chromosome abnormalities is known as Down syndrome. The estimated incidence of Down's syndrome is between 1 in 1,000 to 1 in 1,100 live births. Each year approximately 3,000 to 5,000 children are born in the U.S. with this chromosomal disorder. The vast majority of children with Down syndrome (approximately 95 percent) have an extra chromosome 21. Most often, the extra chromosome originates from the mother. However, in about 3-4 percent of people with Down syndrome, a translocation between chromosome 21 and either 14 or 22 is responsible for the genetic abnormality. Finally, another chromosome problem, called mosaicism, is noted in about 1 percent of individuals with Down's syndrome. In this case, some cells have 47 chromosomes and others have 46 chromosomes. Mosiacism is thought to be the result of an error in cell division soon after conception.

[0011] Chromosomal abnormalities are congenital, and therefore, prenatal diagnosis can be used to determine the health and condition of an unborn fetus. Without knowledge gained by prenatal diagnosis, there could be an untoward outcome for the fetus or the mother or both. Congenital anomalies account for 20 to 25% of perinatal deaths. Specifically, prenatal diagnosis is helpful for managing the remaining term of the pregnancy, planning for possible complications with the birth process, preparing for problems that can occur in the newborn infant, and finding conditions that may affect future pregnancies.

[0012] There are a variety of non-invasive and invasive techniques available for prenatal diagnosis including ultrasonography, amniocentesis, chorionic villus sampling (CVS), fetal blood cells in maternal blood, maternal serum alpha-fetoprotein, maternal serum beta-HCG, and maternal serum estriol. However, the techniques that are non-invasive are less specific, and the techniques with high specificity and high sensitivity are highly invasive. Furthermore, most techniques can be applied only during specific time periods during pregnancy for greatest utility.

Ultrasonography

[0013] This is a harmless, non-invasive procedure. High frequency sound waves are used to generate visible images from the pattern of the echoes made by different tissues and organs, including the fetus in the amniotic cavity. The developing embryo can be visualized at about 6 weeks of gestation. The major internal organs and extremities can be assessed to determine if any are abnormal at about 16 to 20 weeks gestation.

[0014] An ultrasound examination can be useful to determine the size and position of the fetus, the amount of amniotic fluid, and the appearance of fetal anatomy; however, there are limitations to this procedure. Subtle abnormalities, such as Down syndrome, where the morphologic abnormalities are often not marked, but only subtle, may not be detected at all.

Amniocentesis

[0015] This is a highly invasive procedure in which a needle is passed through the mother's lower abdomen into the amniotic cavity inside the uterus. This procedure can be performed at about 14 weeks gestation. For prenatal diagnosis, most amniocenteses are performed between 14 and 20 weeks gestation. However, an ultrasound examination is performed, prior to amniocentesis, to determine gestational age, position of the fetus and placenta, and determine if enough amniotic fluid is present. Within the amniotic fluid are fetal cells (mostly derived from fetal skin) which can be grown in culture for chromosomal, biochemical, and molecular biologic analyses.

[0016] Large chromosomal abnormalities, such as extra or missing chromosomes or chromosome fragments, can be detected by karyotyping, which involves the identification and analysis of all 46 chromosomes from a cell and arranges them in their matched pairs, based on subtle differences in size and structure. In this systematic display, abnormalities in chromosome number and structure are apparent. This procedure typically takes 7-10 days for completion.

[0017] While amniocentesis can be used to provide direct genetic information, risks are associated with the procedure including fetal loss and maternal Rh sensitization. The increased risk for fetal mortality following amniocentesis is about 0.5% above what would normally be expected. Rh negative mothers can be treated with RhoGam.

Chorionic Villus Sampling (CVS)

[0018] In this procedure, a catheter is passed via the vagina through the cervix and into the uterus to the developing placenta with ultrasound guidance. The introduction of the catheter allows cells from the placental chorionic villi to be obtained and analyzed by a variety of techniques, including chromosome analysis to determine the karyotype of the fetus. The cells can also be cultured for biochemical or molecular biologic analysis. Typically, CVS is performed between 9.5 and 12.5 weeks gestation.

[0019] CVS has the disadvantage of being an invasive procedure, and it has a low but significant rate of morbidity for the fetus; this loss rate is about 0.5 to 1% higher than for women undergoing amniocentesis. Rarely, CVS can be associated with limb defects in the fetus. Also, the possibility of maternal Rh sensitization is present. Furthermore, there is also the possibility that maternal blood cells in the developing placenta will be sampled instead of fetal cells and confound chromosome analysis.

Maternal Serum Alpha-Fetoprotein (MSAFP)

[0020] The developing fetus has two major blood proteins—albumin and alpha-fetoprotein (AFP). The mother typically has only albumin in her blood, and thus, the MSAFP test can be utilized to determine the levels of AFP from the fetus. Ordinarily, only a small amount of AFP gains access to the amniotic fluid and crosses the placenta to mother's blood. However, if the fetus has a neural tube defect, then more AFP escapes into the amniotic fluid. Neural tube defects include anencephaly (failure of closure at the cranial end of the neural tube) and spina bifida (failure of closure at the caudal end of the neural tube). The incidence of such defects is about 1 to 2 births per 1000 in the United States. Also, if there are defects in the fetal abdominal wall, the AFP from the fetus will end up in maternal blood in higher amounts.

[0021] The amount of MSAFP increases with gestational age, and thus for the MSAFP test to provide accurate results, the gestational age must be known with certainty. Also, the race of the mother and presence of gestational diabetes can influence the level of MSAFP that is to be considered normal. The MSAFP is typically reported as multiples of the mean (MoM). The greater the MoM, the more likely a defect is present. The MSAFP test has the greatest sensitivity between 16 and 18 weeks gestation, but can be used between 15 and 22 weeks gestation. The MSAFP tends to be lower when Down's Syndrome or other chromosomal abnormalities is present.

[0022] While the MSAFP test is non-invasive, the MSAFP is not 100% specific. MSAFP can be elevated for a variety of reasons that are not related to fetal neural tube or abdominal wall defects. The most common cause for an elevated MSAFP is a wrong estimation of the gestational age of the fetus. Therefore, results from an MSAFP test are never considered definitive and conclusive.

Maternal Serum Beta-HCG

[0023] Beginning at about a week following conception and implantation of the developing embryo into the uterus, the trophoblast will produce detectable beta-HCG (the beta subunit of human chorionic gonadotropin), which can be used to diagnose pregnancy. The beta-HCG also can be quantified in maternal serum, and this can be useful early in pregnancy when threatened abortion or ectopic pregnancy is suspected, because the amount of beta-HCG will be lower than normal.

[0024] In the middle to late second trimester, the beta-HCG can be used in conjunction with the MSAFP to screen for chromosomal abnormalities, in particular for Down syndrome. An elevated beta-HCG coupled with a decreased MSAFP suggests Down syndrome. High levels of HCG suggest trophoblastic disease (molar pregnancy). The absence of a fetus on ultrasonography along with an elevated HCG suggests a hydatidiform mole.

Maternal Serum Estriol

[0025] The amount of estriol in maternal serum is dependent upon a viable fetus, a properly functioning placenta, and maternal well-being. Dehydroepiandrosterone (DHEA) is made by the fetal adrenal glands, and is metabolized in the placenta to estriol. The estriol enters the maternal circulation and is excreted by the maternal kidney in urine or by the maternal liver in the bile. Normal levels of estriol, measured in the third trimester, will give an indication of general well-being of the fetus. If the estriol level drops, then the fetus is threatened and an immediate delivery may be necessary. Estriol tends to be lower when Down syndrome is present and when there is adrenal hypoplasia with anencephaly.

The Triple Screen Test

[0026] The triple screen test comprises analysis of maternal serum alpha-feto-protein (MSAFP), human chorionic gonadotrophin (hCG), and unconjugated estriol (uE3). The blood test is usually performed 16-18 weeks after the last menstrual period. While the triple screen test is non-invasive, abnormal test results are not indicative of a birth defect. Rather, the test only indicates an increased risk and suggests that further testing is needed. For example, 100 out of 1,000 women will have an abnormal result from the triple screen test. However, only 2-3 of the 100 women will have a fetus with a birth defect. This high incidence of false positives causes tremendous stress and unnecessary anxiety to the expectant mother.

Fetal Cells Isolated from Maternal Blood

[0027] The presence of fetal nucleated cells in maternal blood makes it possible to use these cells for noninvasive prenatal diagnosis (Walknowska, et al., Lancet 1:1119-1122, 1969; Lo et al., Lancet 2:1363-65, 1989; Lo et al., Blood 88:4390-95, 1996). The fetal cells can be sorted and analyzed by a variety of techniques to look for particular DNA sequences (Bianchi et al., Am. J. Hum. Genet. 61:822-29, (1997); Bianchi et al., PNAS 93:705-08, (1996)). Fluorescence in-situ hybridization (FISH) is one technique that can be applied to identify particular chromosomes of the fetal cells recovered from maternal blood and diagnose aneuploid conditions such as trisomies and monosomy X. Also, it has been reported that the number of fetal cells in maternal blood increases in aneuploid pregnancies.

[0028] The method of FISH uses DNA probes labeled with colored fluorescent tags that allow detection of specific chromosomes or genes under a microscope. Using FISH, subtle genetic abnormalities that cannot be detected by standard karyotyping are readily identifiable. This procedure typically takes 24-48 hours to complete. Additionally, using a panel of multi-colored DNA FISH probes, abnormal chromosome copy numbers can be seen.

[0029] While improvements have been made for the isolation and enrichment of fetal cells, it is still difficult to get many fetal blood cells. There may not be enough to reliably determine anomalies of the fetal karyotype or assay for other abnormalities. Furthermore, most techniques are time consuming, require high-inputs of labor, and are difficult to implement for a high throughput fashion.

Fetal DNA from Maternal Blood

[0030] Fetal DNA has been detected and quantitated in maternal plasma and serum (Lo et al., Lancet 350:485-487 (1997); Lo et al., Am. J. hum. Genet. 62:768-775 (1998)). Multiple fetal cell types occur in the maternal circulation, including fetal granulocytes, lymphocytes, nucleated red blood cells, and trophoblast cells (Pertl, and Bianchi, Obstetrics and Gynecology 98: 483-490 (2001)). Fetal DNA can be detected in the serum at the seventh week of gestation, and increases with the term of the pregnancy. The fetal DNA present in the maternal serum and plasma is comparable to the concentration of DNA obtained from fetal cell isolation protocols.

[0031] Circulating fetal DNA has been used to determine the sex of the fetus (Lo et al., Am. J. hum. Genet. 62:768-775 (1998)). Also, fetal rhesus D genotype has been detected using fetal DNA. However, the diagnostic and clinical applications of circulating fetal DNA is limited to genes that are present in the fetus but not in the mother (Pertl and Bianchi, Obstetrics and Gynecology 98: 483-490 (2001)). Thus, a need still exists for a non-invasive method that can determine the sequence of fetal DNA and provide definitive diagnosis of chromosomal abnormalities in a fetus.

[0032] The invention is directed to a method for detection of genetic disorders including mutations and chromosomal abnormalities. In a preferred embodiment, the present invention is used to detect mutations, and chromosomal abnormalities including but not limited to translocation, transversion, monosomy, trisomy, and other aneuploidies, deletion, addition, amplification, fragment, translocation, and rearrangement. Numerous abnormalities can be detected simultaneously. The present invention also provides a non-invasive method to determine the sequence of fetal DNA from a sample of a pregnant female. The present invention can be used to detect any alternation in gene sequence as compared to the wild type sequence including but not limited to point mutation, reading frame shift, transition, transversion, addition, insertion, deletion, addition-deletion, frame-shift, missense, reverse mutation, and microsatellite alteration. The present invention also provides a method for isolating free nucleic acid from a sample containing nucleic acid.

[0033] In one embodiment, the present invention is directed to a method for detecting chromosomal abnormalities said method comprising: (a) determining the sequence of alleles of a locus of interest on template DNA, and (b) quantitating a ratio for the alleles at a heterozygous locus of interest that was identified from the locus of interest of (a), wherein said ratio indicates the presence or absence of a chromosomal abnormality.

[0034] In another embodiment, the present invention provides a non-invasive method for determining the sequence of a locus of interest on fetal DNA, said method comprising: (a) obtaining a sample from a pregnant female; (b) adding a cell lysis inhibitor, a cell membrane stabilizer, or a cross-linker to the sample of (a); (c) obtaining template DNA from the sample of (b), wherein said template DNA comprises fetal DNA and maternal DNA; and (d) determining the sequence of a locus of interest on template DNA.

[0035] In another embodiment, the template DNA is obtained from a sample including but not limited to a cell, tissue, blood, serum, plasma, saliva, urine, tears, vaginal secretion, sweat, umbilical cord blood, chorionic villi, amniotic fluid, embryonic tissue, embryo, a two-celled embryo, a four-celled embryo, an eight-celled embryo, a 16-celled embryo, a 32-celled embryo, a 64-celled embryo, a 128-celled embryo, a 256-celled embryo, a 512-celled embryo, a 1024-celled embryo, lymph fluid, cerebrospinal fluid, mucosa secretion, peritoneal fluid, ascitic fluid, fecal matter, or body exudate.

[0036] In one embodiment, the template DNA is obtained from a sample from a pregnant female. In a preferred embodiment, the template DNA is obtained from a pregnant human female.

[0037] In another embodiment, the template DNA is obtained from an embryo. In a preferred embodiment, the template DNA is obtained from a single cell from an embryo.

[0038] In another embodiment, a cell lysis inhibitor is added to the sample including but not limited to formaldehyde, and derivatives of formaldehyde, formalin, glutaraldehyde, and derivatives of glutaraldehyde, crosslinkers, primary amine reactive crosslinkers, sulfhydryl reactive crosslinkers, sulfhydryl addition or disulfide reduction, carbohydrate reactive crosslinkers, carboxyl reactive crosslinkers, photoreactive crosslinkers, cleavable crosslinkers, AEDP, APG, BASED, BM(PEO)₃, BM(PEO)₄, BMB, BMDB, BMH, BMOE, BS3, BSOCOES, DFDNB, DMA, DMP, DMS, DPDPB, DSG, DSP, DSS, DST, DTBP, DTME, DTSSP, EGS, HBVS, sulfo-BSOCOES, Sulfo-DST, Sulfo-EGS or compounds listed in Table XXIII. In a preferred embodiment, formalin is present in the sample at a percentage including but not limited to 0.0001-0.03%, 0.03-0.05%, 0.05-0.08%, 0.08-0.1%, 0.1-0.3%, 0.3-0.5%, 0.5-0.7%, 0.7-0.9%, 0.9-1.2%, 1.2-1.5%, 1.5-2%, 2-3%, 3-5%, and greater than 5%.

[0039] An agent that stabilizes cell membranes may be added to the maternal blood sample to reduce maternal cell lysis including but not limited to aldehydes, urea formaldehyde, phenol formaldehyde, DMAE (dimethylaminoethanol), cholesterol, cholesterol derivatives, high concentrations of magnesium, vitamin E, and vitamin E derivatives, calcium, calcium gluconate, taurine, niacin, hydroxylamine derivatives, bimoclomol, sucrose, astaxanthin, glucose, amitriptyline, isomer A hopane tetral phenylacetate, isomer B hopane tetral phenylacetate, citicoline, inositol, vitamin B, vitamin B complex, cholesterol hemisuccinate, sorbitol, calcium, coenzyme Q, ubiquinone, vitamin K, vitamin K complex, menaquinone, zonegran, zinc, ginkgo biloba extract, diphenylhydantoin, perftoran, polyvinylpyrrolidone, phosphatidylserine, tegretol, PABA, disodium cromglycate, nedocromil sodium, phenyloin, zinc citrate, mexitil, dilantin, sodium hyaluronate, or polaxamer 188.

[0040] In another embodiment, an agent that prevents DNA destruction is added to the sample including but not limited to DNase inhibitors, zinc chloride, ethylenediaminetetraacetic acid, guanidine-HCl, guanidine isothiocyanate, N-lauroylsarcosine, and Na-dodecylsulphate.

[0041] In a preferred embodiment, template DNA is obtained from the plasma of the blood from a pregnant female. In another embodiment, the template DNA is obtained from the serum of the blood from a pregnant female.

[0042] In another embodiment, template DNA comprises fetal DNA and maternal DNA.

[0043] In another embodiment, the locus of interest on the template DNA is selected from a maternal homozygous locus of interest. In another embodiment, the locus of interest on the template DNA is selected from a maternal heterozygous locus of interest.

[0044] In another embodiment, the locus of interest on the template DNA is selected from a paternal homozygous locus of interest. In another embodiment, the locus of interest on the template DNA is selected from a paternal heterozygous locus of interest.

[0045] In one embodiment, the sequence of alleles of multiple loci of interest on a single chromosome is determined. In a preferred embodiment, the sequence of alleles of multiple loci of interest on multiple chromosomes is determined.

[0046] In another embodiment, determining the sequence of alleles of a locus of interest comprises a method including but not limited to allele specific PCR, gel electrophoresis, ELISA, mass spectrometry, hybridization, primer extension, fluorescence polarization, fluorescence detection, fluorescence resonance energy transfer (FRET), sequencing, DNA microarray, SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend, MassCleave™ (hMC) method, southern blot, slot blot, dot blot, and MALDI-TOF mass spectrometry.

[0047] In a preferred embodiment, determining the sequence of alleles of a locus of interest comprises (a) amplifying the locus of interest using a first and second primers, wherein the second primer contains a recognition site for a restriction enzyme that generates a 5′ overhang containing the locus of interest; (b) digesting the amplified DNA with the restriction enzyme that recognizes the recognition site on the second primer; (c) incorporating a nucleotide into the digested DNA of (b) by using the 5′ overhang containing the locus of interest as a template; and (d) determining the sequence of the locus of interest by determining the sequence of the DNA of (c).

[0048] In one embodiment, the amplification can comprise polymerase chain reaction (PCR). In a further embodiment, the annealing temperature for cycle 1 of PCR can be about the melting temperature of the annealing length of the second primer. In another embodiment, the annealing temperature for cycle 2 of PCR can be about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer. In another embodiment, the annealing temperature for the remaining cycles can be about the melting temperature of the entire sequence of the second primer.

[0049] In another embodiment, the recognition site on the second primer is for a restriction enzyme that cuts at a distance from its binding site and generates a 5′ overhang, which contains the locus of interest. In a preferred embodiment, the recognition site on the second primer is for a Type IIS restriction enzyme. The Type IIS restriction enzyme includes but is not limited to Alw I, Alw26 I, Bbs I, Bbv I, BceA I, Bmr I, Bsa I, Bst71 I, BsmA I, BsmB I, BsmF I, BspM I, Ear I, Fau I, Fok I, Hga I, Ple I, Sap I, SSfaN I, and Sthi32 I, and more preferably BceA I and BsmF I.

[0050] In one embodiment, the 3′ end of the second primer is adjacent to the locus of interest.

[0051] In another embodiment, the annealing length of the second primer is selected from the group consisting of 35-30, 30-25, 25-20, 20-15, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, and less than 4 bases.

[0052] In another embodiment, amplifying the loci of interest comprises using first and second primers that contain a portion of a restriction enzyme recognition site, wherein said recognition site contains at least one variable nucleotide, and after amplification the full restriction enzyme recognition site is generated, and the 3′ region of said primers can contain mismatches with the template DNA, and digestion with said restriction enzyme generates a 5′ overhang containing the locus of interest.

[0053] In a preferred embodiment, the recognition site for restriction enzymes including but not limited to BsaJ I (5′ C^↓CNNGG 3′), BssK I (5′^↓CCNGG 3′), Dde I (5′C^↓TNAG 3′), EcoN I (5′CCTNN^↓NNNAGG 3′) (SEQ ID NO: 7), Fnu4H I (5′GC^↓NGC 3′), Hinf I (5′G^↓ANTC 3′), PflF 1 (5′ GACN^↓NNGTC 3′), Sau96 I (5′ G^↓GNCC 3′), ScrF I (5′ CC^↓NGG 3′), Tthl 11 I (5′ GACN^↓NNGTC 3′), and more preferably Fnu4H I and EcoN I, is generated after amplification.

[0054] In another embodiment, the 5′ region of the first and/or second primer contains a recognition site for a restriction enzyme. In a preferred embodiment, the restriction enzyme recognition site is different from the restriction enzyme recognition site that generates a 5′ overhang containing the locus of interest.

[0055] In a further embodiment, the method of the invention further comprises digesting the DNA with a restriction enzyme that recognizes the recognition site at the 5′ region of the first and/or second primer.

[0056] The first and/or second primer can contain a tag at the 5′ terminus. Preferably, the first primer contains a tag at the 5′ terminus. The tag can be used to separate the amplified DNA from the template DNA. The tag can be used to separate the amplified DNA containing the labeled nucleotide from the amplified DNA that does not contain the labeled nucleotide. The tag can be any chemical moiety including but not limited to radioisotope, fluorescent reporter molecule, chemiluminescent reporter molecule, antibody, antibody fragment, hapten, biotin, derivative of biotin, photobiotin, iminobiotin, digoxigenin, avidin, enzyme, acridinium, sugar, enzyme, apoenzyme, homopolymeric oligonucleotide, hormone, ferromagnetic moiety, paramagnetic moiety, diamagnetic moiety, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, moiety having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity, or combinations thereof. Preferably, the tag is biotin. The biotin tag is used to separate amplified DNA from the template DNA using a streptavidin matrix. The streptavidin matrix is coated on wells of a microtiter plate.

[0057] The incorporation of a nucleotide in the method of the invention is by a DNA polymerase including but not limited to E. coli DNA polymerase, Klenow fragment of E. coli DNA polymerase I, T7 DNA polymerase, T4 DNA polymerase, T5 DNA polymerase, Klenow class polymerases, Taq polymerase, Pfu DNA polymerase, Vent polymerase, bacteriophage 29, REDTaq™ Genomic DNA polymerase, or sequenase. The incorporation of a nucleotide can further comprise using a mixture of labeled and unlabeled nucleotides. One nucleotide, two nucleotides, three nucleotides, four nucleotides, five nucleotides, or more than five nucleotides can be incorporated. A combination of labeled and unlabeled nucleotides can be incorporated. The labeled nucleotide is selected from the group consisting of a dideoxynucleotide triphosphate (also referred to as “dideoxy”) and deoxynucleotide triphosphate (also referred to as “deoxy”). The unlabeled nucleotide is selected from the group consisting of a dideoxynucleotide triphosphate and deoxynucleotide triphosphate. The labeled nucleotide is labeled with a molecule including but not limited to radioactive molecule, fluorescent molecule, antibody, antibody fragment, hapten, carbohydrate, biotin, and derivative of biotin, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, and moiety, having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity. Preferably, the labeled nucleotide is labeled with a fluorescent molecule. The incorporation of a fluorescent labeled nucleotide further comprises using a mixture of fluorescent and unlabeled nucleotides.

[0058] In one embodiment, the determination of the sequence of the locus of interest comprises detecting the incorporated nucleotide. In one embodiment, the detection is by a method selected from the group consisting of gel electrophoresis, capillary electrophoresis, microchannel electrophoresis, polyacrylamide gel electrophoresis, fluorescence detection, fluorescence polarization, DNA sequencing, Sanger dideoxy sequencing, ELISA, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry, fluorometry, infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry, DNA hybridization, DNA microarray, GeneChip arrays, HuSNP arrays, BeadArrays, MassExtend, SNP-IT, TaqMan assay, Invader assay, MassCleave, southern blot, slot blot, and dot blot.

[0059] In one embodiment, the sequence of alleles of one to tens to hundreds to thousands of loci of interest on a single chromosome on template DNA is determined. In a preferred embodiment, the sequence of alleles of one to tens to hundreds to thousands of loci of interest on multiple chromosomes is determined.

[0060] In a preferred embodiment, the locus of interest is suspected of containing a single nucleotide polymorphism or mutation. The method can be used for determining sequences of multiple loci of interest concurrently. The template DNA can comprise multiple loci from a single chromosome. The template DNA can comprise multiple loci from different chromosomes. The loci of interest on template DNA can be amplified in one reaction. Alternatively, each of the loci of interest on template DNA can be amplified in a separate reaction. The amplified DNA can be pooled together prior to digestion of the amplified DNA. Each of the labeled DNA containing a locus of interest can be separated prior to determining the sequence of the locus of interest. In one embodiment, at least one of the loci of interest is suspected of containing a single nucleotide polymorphism or a mutation.

[0061] In another embodiment, the ratio of alleles at a heterozygous locus of interest on a chromosome is compared to the ratio of alleles at a heterozygous locus of interest on a different chromosome. There is no limitation as to the chromosomes that can be compared. The ratio for the alleles at a heterozygous locus of interest on any chromosome can be compared to the ratio for the alleles at a heterozygous locus of interest on any other chromosome. In a preferred embodiment, the ratio of alleles at multiple heterozygous loci of interest on a chromosome are summed and compared to the ratio of alleles at multiple heterozygous loci of interest on a different chromosome.

[0062] In another embodiment, the ratio of alleles at a heterozygous locus of interest on a chromosome is compared to the ratio of alleles at a heterozygous locus of interest on two, three, four or more than four chromosomes. In another embodiment, the ratio of alleles at multiple loci of interest on a chromosome is compared to the ratio of alleles at multiple loci of interest on two, three, four, or more than four chromosomes.

[0063] In another embodiment, the ratio of the alleles at a locus of interest on a chromosome is compared to the ratio of the alleles at a locus of interest on a different chromosome, wherein a difference in the ratios indicates the presence or absence of a chromosomal abnormality. In another embodiment, the ratio of the alleles at multiple loci of interest on a chromosome is compared to the ratio of the alleles at multiple loci of interest on a different chromosome, wherein a difference in the ratios indicates the presence or absence of a chromosomal abnormality.

[0064] In another embodiment, the sequence of one to tens to hundreds to thousands of loci of interest on the template DNA obtained from a sample of a pregnant female is determined. In one embodiment, the loci of interest are on one chromosome. In another embodiment, the loci of interest are on multiple chromosomes.

[0065] In another embodiment, the present invention provides a method for isolating nucleic acid said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer, or cross-linker to the sample of (a); and (c) isolating nucleic acid. In a preferred embodiment, the method is used for isolating free nucleic acid. In a most preferred embodiment, the method is used for isolating free fetal nucleic acid.

[0066] In another embodiment, the present invention provides a method for detecting nucleic acid, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of the nucleic acid. In a preferred embodiment, the nucleic acid isolated is free nucleic acid.

[0067] In another embodiment, the present invention provides a method for detecting nucleic acid containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of nucleic acid containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid.

[0068] In another embodiment, the present invention provides a method for detecting nucleic acid containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a blood sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of a nucleic acid molecule containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid.

[0069] In another embodiment, the present invention provides a method for detecting a nucleic acid molecule containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a plasma sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to a blood sample prior to isolation of the plasma; and (b) detecting the presence or absence of a nucleic acid molecule containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid.

[0070] In another embodiment, the present invention provides a method for detecting a nucleic acid, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein an agent that impedes cell lysis was added to the sample; and (b) detecting the presence or absence of the nucleic acid.

[0071] In another embodiment, the present invention provides a method for isolating a nucleic acid, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein an agent that impedes cell lysis was added to the sample.

[0072] In another embodiment, the present invention provides a method for isolating nucleic acid said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer, or cross-linker to the sample of (a); and (c) isolating nucleic acid. In a preferred embodiment, the method is used for isolating free nucleic acid. In a most preferred embodiment, the method is used for isolating free fetal nucleic acid.

[0073] In another embodiment, the present invention provides a method for isolating free fetal nucleic acid said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer, or cross-linker to the sample of (a); (c) isolating the plasma from the blood sample, wherein the plasma is isolated by centrifuging the blood sample; and (d) removing the supernatant, which contains the plasma, using procedures to minimize disruption of the “buffy-coat.”

[0074] In another embodiment, the sample containing the nucleic acid is obtained from any nucleic acid containing source including but not limited to a cell, tissue, blood, serum, plasma, saliva, urine, tears, breast fluid, breast milk, vaginal secretion, sweat, umbilical cord blood, chorionic villi, amniotic fluid, embryonic tissue, embryo, a two-celled embryo, a four-celled embryo, an eight-celled embryo, a 16-celled embryo, a 32-celled embryo, a 64-celled embryo, a 128-celled embryo, a 256-celled embryo, a 512-celled embryo, a 1024-celled embryo, lymph fluid, cerebrospinal fluid, mucosa secretion, peritoneal fluid, ascitic fluid, fecal matter, or body exudate.

[0075] In one embodiment, the sample containing the nucleic acid is obtained from a pregnant female. In a preferred embodiment, the sample is obtained from a pregnant human female. In a preferred embodiment, the sample is blood obtained from a pregnant female.

[0076] In another embodiment, a cell lysis inhibitor, a cell membrane stabilizer or a cross-linker is added to the sample including but not limited to formaldehyde, and derivatives of formaldehyde, formalin, glutaraldehyde, and derivatives of glutaraldehyde, crosslinkers, primary amine reactive crosslinkers, sulfhydryl reactive crosslinkers, sulfhydryl addition or disulfide reduction, carbohydrate reactive crosslinkers, carboxyl reactive crosslinkers, photoreactive crosslinkers, cleavable crosslinkers, AEDP, APG, BASED, BM(PEO)₃, BM(PEO)₄, BMB, BMDB, BMH, BMOE, BS3, BSOCOES, DFDNB, DMA, DMP, DMS, DPDPB, DSG, DSP, DSS, DST, DTBP, DTME, DTSSP, EGS, HBVS, sulfo-BSOCOES, Sulfo-DST, Sulfo-EGS or compounds listed in Table XXIII.

[0077] An agent that stabilizes cell membranes may be added to the sample including but not limited to aldehydes, urea formaldehyde, phenol formaldehyde, DMAE (dimethylaminoethanol), cholesterol, cholesterol derivatives, high concentrations of magnesium, vitamin E, and vitamin E derivatives, calcium, calcium gluconate, taurine, niacin, hydroxylamine derivatives, bimoclomol, sucrose, astaxanthin, glucose, amitriptyline, isomer A hopane tetral phenylacetate, isomer B hopane tetral phenylacetate, citicoline, inositol, vitamin B, vitamin B complex, cholesterol hemisuccinate, sorbitol, calcium, coenzyme Q, ubiquinone, vitamin K, vitamin K complex, menaquinone, zonegran, zinc, ginkgo biloba extract, diphenylhydantoin, perftoran, polyvinylpyrrolidone, phosphatidylserine, tegretol, PABA, disodium cromglycate, nedocromil sodium, phenyloin, zinc citrate, mexitil, dilantin, sodium hyaluronate, or polaxamer 188.

[0078] In another embodiment, an agent that prevents DNA destruction is added to the sample including but not limited to DNase inhibitors, zinc chloride, ethylenediaminetetraacetic acid, guanidine-HCl, guanidine isothiocyanate, N-lauroylsarcosine, and Na-dodecylsulphate.

[0079] In a preferred embodiment, the nucleic acid is isolated from plasma obtained from blood of a pregnant female. In another embodiment, the nucleic acid is isolated from plasma, which is generated using procedures designed to minimize the amount of maternal cell lysis. In another embodiment, the nucleic acid is isolated from plasma by centrifuging blood from a pregnant female, and allowing the centrifuge to stop without applying a brake.

[0080] In a preferred embodiment, free nucleic acid is isolated from plasma obtained from blood from a pregnant female. In another embodiment, the free nucleic acid is isolated from plasma, which is generated by centrifuging blood obtained from a pregnant female, and allowing the centrifuge to stop without applying a brake (the centrifuge comes to a stop by natural deceleration). In another embodiment, the blood from a pregnant female is centrifuged at a speed including but not limited to 0-50 rpm, 50-100 rpm, 100-200 rpm, 200-300 rpm, 300-400 rpm, 400-500 rpm, 500-600 rpm, 600-700 rpm, 700-800 rpm, 800-900 rpm, 900-1000 rpm, 1000-2000 rpm, 2000-3000 rpm, 3000-4000 rpm, 4000-5000 rpm, 5000-6000 rpm, 6000-7000 rpm, 7000-8000 rpm, and greater than 8000 rpm. In a preferred embodiment, the blood from the pregnant female is centrifuged at a speed less than 4000 rpm. In another embodiment, the acceleration power of the centrifuge is not used.

[0132] The present invention provides a method for detecting genetic disorders, including but not limited to mutations, insertions, deletions, and chromosomal abnormalities, and is especially useful for the detection of genetic disorders of a fetus. The method is especially useful for detection of a translocation, addition, amplification, transversion, inversion, aneuploidy, polyploidy, monosomy, trisomy, trisomy 21, trisomy 13, trisomy 14, trisomy 15, trisomy 16, trisomy 18, trisomy 22, triploidy, tetraploidy, and sex chromosome abnormalities including but not limited to XO, XXY, XYY, and XXX. The method also provides a non-invasive technique for determining the sequence of fetal DNA and identifying mutations within the fetal DNA.

[0133] The invention is directed to a method for detecting chromosomal abnormalities, the method comprising: (a) determining the sequence of alleles of a locus of interest on a template DNA; and (b) quantitating a ratio for the alleles at a heterozygous locus of interest that was identified from the locus of interest of (a), wherein said ratio indicates the presence or absence of a chromosomal abnormality.

[0134] In another embodiment, the present invention provides a non-invasive method for determining the sequence of a locus of interest on fetal DNA, said method comprising: (a) obtaining a sample from a pregnant female; (b) adding a cell lysis inhibitor, cell membrane stabilizer or cross-linker to the sample of (a); (c) obtaining template DNA from the sample of (b), wherein said template DNA comprises fetal DNA and maternal DNA; and (d) determining the sequence of a locus of interest on template DNA.

[0135] In another embodiment, the present invention is directed to a method for isolating DNA, said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer or cross-linker to sample of (a); and (c) isolating the DNA. In another embodiment, the method is used for isolating free nucleic acid in a sample wherein the free nucleic acid is from a species different than the species from which the sample was taken. In another embodiment, the method is used for isolating free nucleic acid selected from the group consisting of bacteria, viruses, fungi, mycobacteria, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasites, animals, and archeabacteria. In another embodiment, the sample containing nucleic acid may contain more than one type of nucleic acid including but not limited to human and bacterial, human and viral, human and fungal, human, bacterial, and fungal, human, bacterial, fungal, and viral, human, bacterial and viral, and human, fungal and viral.

[0136] In another embodiment, the present invention provides a method for detecting nucleic acid, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of the nucleic acid. In a preferred embodiment, the nucleic acid isolated is free nucleic acid. In another embodiment, the method is used for isolating free nucleic acid in a sample, wherein the free nucleic acid is from a species different than the species from which the sample was taken. In another embodiment, the nucleic acid can be from any organism including but not limited to bacteria, viruses, fungi, mycobacteria, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasites, animals, and archeabacteria.

[0137] In another embodiment, the present invention provides a method for detecting nucleic acid containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a nucleic acid containing sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of nucleic acid containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid. In another embodiment, the method is used for isolating free nucleic acid in a sample, wherein the free nucleic acid is from a species different than the species from which the sample was taken. In another embodiment, the nucleic acid can be from any organism including but not limited to bacteria, viruses, fungi, mycobacteria, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasites, animals, and archeabacteria. In another embodiment, the method is used to detect or monitor a disease state including but not limited to diseases listed in Tables V and XV.

[0138] The nucleic acid containing sample can contain nucleic acid from multiple species. For example, to detect a bacterial infection in a human, a sample may contain the bacterial nucleic acid, and human nucleic acid. The nucleic acid can contain both normal and mutant forms of nucleic acid from the same species. For instance, for detection of a multi-drug resistant bacterial strain, a sample may contain nucleic acid from the multi-drug resistant bacteria, and nucleic acid from the drug-sensitive bacteria and human nucleic acid (see Example 24).

[0139] In a preferred embodiment, the method is used to detect, diagnose or monitor cancer including but not limited to carcinoma of the bladder, breast, bronchial, colon, kidney, liver, lung, esophagus, gall-bladder, ovary, pancreas, stomach, cervix, thyroid, prostate, and skin; small cell lung cancer, squamous cell carcinoma, hematopoietic tumors of lymphoid lineage, leukemia, acute lymphocytic leukemia, acute lymphoblastic leukemia, B-cell lymphoma, T-cell-lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, Burkett's lymphoma, hematopoietic tumors of myeloid lineage, acute and chronic myelogenous leukemias, myelodysplastic syndrome and promyelocytic leukemia, tumors of mesenchymal origin, fibrosarcoma and rhabdomyosarcoma, tumors of the central and peripheral nervous system, astrocytoma, neuroblastoma, glioma and schwannomas, melanoma, seminoma, teratocarcinoma, osteosarcoma, xenoderoma pigmentosum, keratoctanthoma, thyroid follicular cancer and Kaposi's sarcoma.

[0140] In another embodiment, the method is useful for monitoring a treatment including but not limited to a procedure e.g. surgery, radiation, lifestyle change, dietary protocol, supplementation or administration of a drug or drugs, or combinations of any of the above. When the treatment includes the administration of a drug, the drug may be any drug including but not limited to chemotherapeutic agents, anti-bacterial agents, anti-viral agents, anti-fungal agents, targeted-cancer drugs, cytoxoic agents, cytostatic agents, anti-proliferative agents, Avastin, altretamine, busulfan, chlorambucil, cyclophosphamide, Erbitux, Rituxan, ifosfamide, mechlorethamine, melphalan, thiotepa, cladribine, fluorouracil, floxuridine, gemcitabine, thioguanine, pentostatin, methotrexate, 6-mercaptopurine, cytarabine, carmustine, lomustine, streptozotocin, carboplatin, cisplatin, oxaliplatin, iproplatin, tetraplatin, lobaplatin, JM216, JM335, fludarabine, aminoglutethimide, flutamide, goserelin, leuprolide, megestrol acetate, cyproterone acetate, tamoxifen, anastrozole, bicalutamide, dexamethasone, diethylstilbestrol, prednisone, bleomycin, dactinomycin, daunorubicin, doxirubicin, idarubicin, mitoxantrone, losoxantrone, mitomycin-c, plicamycin, paclitaxel, docetaxel, CPT-11, epothilones, topotecan, irinotecan, 9-amino camptothecan, 9-nitro camptothecan, GS-211, etoposide, teniposide, vinblastine, vincristine, vinorelbine, procarbazine, asparaginase, pegaspargase, methotrexate, octreotide, estramustine, and hydroxyurea.

[0141] In another embodiment, the present invention provides a method for detecting nucleic acid containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a blood sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to the sample; and (b) detecting the presence or absence of a nucleic acid molecule containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid. In another embodiment, the method is used for isolating free nucleic acid in a sample, wherein the free nucleic acid is from a species different than the species from which the sample was taken. In another embodiment, the nucleic acid can be from any organism including but not limited to bacteria, viruses, fungi, mycobacteria, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasites, animals, and archeabacteria.

[0142] In another embodiment, the present invention provides a method for detecting a nucleic acid molecule containing at least one mutation, wherein said method comprises: (a) isolating nucleic acid from a plasma sample, wherein a cell lysis inhibitor, cell membrane stabilizer, or cross-linker was added to a blood sample prior to isolation of the plasma; and (b) detecting the presence or absence of a nucleic acid molecule containing the mutation. In a preferred embodiment, the nucleic acid isolated is free nucleic acid. In another embodiment, the method is used for isolating free nucleic acid in a sample, wherein the free nucleic acid is from a species different than the species from which the sample was taken. In another embodiment, the nucleic acid can be from any organism including but not limited to bacteria, viruses, fungi, mycobacteria, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasites, animals, and archeabacteria. In some embodiments, isolated nucleic acid is from a drug resistant strain of bacteria, virus or fungus.

[0143] In another embodiment, the nucleic acid can be isolated from any appropriate sample including but not limited to, nucleic acid-containing samples of tissue, bodily fluid (for example, blood, serum, plasma, saliva, urine, tears, peritoneal fluid, ascitic fluid, vaginal secretion, breast fluid, breast milk, lymph fluid, cerebrospinal fluid or mucosa secretion), umbilical cord blood, chorionic villi, amniotic fluid, an embryo, a two-celled embryo, a four-celled embryo, an eight-celled embryo, a 16-celled embryo, a 32-celled embryo, a 64-celled embryo, a 128-celled embryo, a 256-celled embryo, a 512-celled embryo, a 1024-celled embryo, embryonic tissues, lymph fluid, cerebrospinal fluid, mucosa secretion, or other body exudate, fecal matter, an individual cell or extract of the such sources that contain the nucleic acid of the same, and subcellular structures such as mitochondria, using protocols well established within the art. In some embodiments, isolated nucleic acid is from a drug resistant strain of bacteria, virus or fungus.

[0144] In another embodiment, the free nucleic acid is isolated using techniques and/or protocols that substantially reduce the lysis of cells present in the sample including but not limited to centrifuging the samples, with the braking power for the centrifuge set to zero (the brake on the centrifuge is not used), transferring the supernatant to a new tube with minimal or no disturbance of the “buffy-coat,” and transferring only a portion of the supernatant to a new tube. In a preferred embodiment, both acceleration power and braking power for the centrifuge are set to zero.

[0145] In a preferred embodiment, the nucleic acid is deoxyribonucleic acid. In another embodiment, the mutation can be any alteration that differs from the normal DNA sequence including but not limited to a single point mutation, multiple point mutations, an insertion, a frameshift, a truncation, a deletion, a duplication, or a transversion. In another embodiment, the mutation can be a mutation in any gene including but not limited to BRCA1, BRCA2, MSH6, MSH2, MLH1, RET, PTEN, ATM, H-RAS, p53, ELAC2, CDH1, APC, AR, PMS2, MLH3, CYP1A1, GSTP1, GSTM1, AXIN2, CYP19, MET, NAT1, CDKN2A, NQ01, trc8, RAD51, PMS1, TGFBR2, VHL, MC4R, POMC, NROB2, UCP2, PCSK1, PPARG, ADRB2, UCP3, glur1, cart, SORBS1, LEP, LEPR, SIM1, TNF, IL-6, IL-1, IL-2, IL-3, IL1A, TAP2, THPO, THRB, NBS1, RBM15, LIF, MPL, RUNX1, Her-2, glucocorticoid receptor, estrogen receptor, thyroid receptor, p21, p27, K-RAS, N-RAS, retinoblastoma protein, Wiskott-Aldrich (WAS) gene, Factor V Leiden, Factor II (prothrombin), methylene tetrahydrofolate reductase, cystic fibrosis, LDL receptor, HDL receptor, superoxide dismutase gene, SHOX gene, genes involved in nitric oxide regulation, genes involved in cell cycle regulation, tumor suppressor genes, oncogenes, genes associated with neurodegeneration, genes associated with obesity. In another embodiment, the mutation can be associated with any disease including but not limited to the diseases listed in Tables V, and Table XV.

[0146] In another embodiment, the free nucleic acid to be isolated is bacterial and can be any bacterial nucleic acid including but not limited to Cocci (round-shaped) bacteria, Bacilli (rod-shaped) bacteria, Spirilli (corkscrew-shaped) bacteria, pathogenic bacteria, non-pathogenic bacteria, normal flora bacteria, gram positive bacteria, gram-negative bacteria, drug-sensitive bacteria, drug-resistant bacteria, Acidaminococcus, Acinetobacter, Acinetobacter lwoffi, Aeromonas, Alcaligenes, Bacteroides, Bordetella, Branhamella, Brucella, Calymmatobacterium, Campylobacter, Cardiobacterium, Chromobacterium, Citrobacter, Citrobacter freundii, Coliform group, Edwardsiella, Enterobacter, Enterobacter sakazaki, Enterobacter aerogenes, Enterobacter cloacae, Enterobacter agglomerans, Enterococcus, Enterococcus faecalis, Enterococcus faecium, Escherichia, Escherichia coli, Escherichia coli-O157, Flavobacterium, Francisella, Fusobacterium, Haemophilus, Hafnia alvei, Klebsiella, Klebsiella oxytoca, Klebsiella pneumoniae, Legionella, Moraxella, Morganella, Morganella morganii, Neisseria, Pasturella, Plesiomonas, Proteus, Providencia, Proteus mirabilis, Pseudomonas, Pseudomonas aeruginosa, Salmonella, Salmonella typhimurium, Serratia, Serratia marcescens, Shigella, Shigella flexneri, Streptobacillus, Veillonella, Vibrio, Vibrio cholera, Yersinia, Yersinnia entercolitica, Xanthomanas maltophiia, Staphylococcus, Staphylococcus albus, Staphylococcus aureus, Streptococcus, Streptococcus dysgalacticae, Micrococcus, Peptococcus, Peptostreptococcus, Bacillus, Bacillus cereus, Clostridium, Lactobacillus, Listeria, Listeria monocytogenes, Erysipelothrix, Propionibacterium, Eubacterium, and Corynebacterium species.

[0147] In another embodiment, the nucleic acid to be isolated is fungal, and can be any fungal nucleic acid including but not limited to drug-sensitive fungus, drug-resistant fungus, Candida (including C. albicans, C. tropicalis, C. parapsilosis, C. stellatoidea, C. krusei, C. parakrusei, C. lusitanae, C. pseudotropicalis, C. guilliermondi and C. glabrata), Aspergillus (including A. fumigatus, A. flavus, A. niger, A. nidulans, A. terreus, A. sydowi, A. flavatus, and A. glaucus), Cryptococcus, Histoplasma, Coccidioides, Paracoccidioides, Blastomyces, Basidiobolus, Conidiobolus, Rhizopus, Rhizomucor, Mucor, Absidia, Mortierella, Cunninghamella, Saksenaea, Pseudallescheria, Sporotrichosis, Fusarium, Trichophyton, Trichosporon, Microsporum, Epidermophyton, Scytalidium, Malassezia, Actinomycetes, Sporothrix, Penicillium, Saccharomyces and Pneumocystis.

[0148] In another embodiment, the nucleic acid to be isolated can be any viral nucleic acid including but not limited to DNA virus, RNA virus, retrovirus, pathogenic virus, non-pathogenic virus, drug-resistant virus, drug-sensitive virus, adeno-associated virus, bird flu virus, cauliflower mosaic virus, Chlamydia caused by viral infection, cytomegalovirus (CMV), dengue virus, Epstein-Barr virus, feline leukemia virus, flavivirus, haemophilus influenza, hemorrhagic fever viruses, hepatitis virus including hepatitis A, B, C, and E, viruses, herpes simplex virus, human herpesvirus type A and B, human immunodeficiency virus (HIV), human papilloma virus, human T-cell lymphotrophic virus, HTLV Type I, HTLV Type II, influenza virus, Japanese encephalitis virus, moraxella catarrhalis, non-typeable haemophilus, reovirus, parainfluenza, parvovirus, papova virus, Respiratory syncytial virus, Rubella virus, rotavirus, SARS, tomato bushy stunt virus, varicella-zoster virus, and vaccinia virus.

[0149] In a preferred embodiment, free nucleic acid is isolated from plasma obtained from blood. In another embodiment, the free nucleic acid is isolated from plasma, which is generated by centrifuging blood, and allowing the centrifuge to stop without applying a brake (the centrifuge comes to a stop by natural deceleration). In another embodiment, the blood is centrifuged at a speed including but not limited to 0-50 rpm, 50-100 rpm, 100-200 rpm, 200-300 rpm, 300-400 rpm, 400-500 rpm, 500-600 rpm, 600-700 rpm, 700-800 rpm, 800-900 rpm, 900-1000 rpm, 1000-2000 rpm, 2000-3000 rpm, 3000-4000 rpm, 4000-5000 rpm, 5000-6000 rpm, 6000-7000 rpm, 7000-8000 rpm, and greater than 8000 rpm. In a preferred embodiment, the blood is centrifuged at a speed less than 4000 rpm. In another embodiment, the acceleration power of the centrifuge is not used.

[0150] In another embodiment, blood is collected by any method or process that results in a substantial increase in the ratio of mutant DNA/normal DNA in the resulting serum or plasma after appropriate processing. As used herein, a substantial increase in the ratio of mutant DNA/normal DNA is that which can be detected by the methods as described herein. Such methods or processes typically result in a substantial increase in the ratio of mutant DNA/normal DNA of about 5%, 10%, 15%, 20%, 30%, 50%, 70%, 80%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 1000% or more of the ratio of mutant DNA/normal DNA found in blood samples collected by standard procedures.

[0151] In other embodiments, blood is collected by any method or process that results in a substantial increase in the amount of free DNA compared to the amount of total DNA recovered or detected in the resulting serum or plasma after processing. Such methods or processes typically result in a substantial increase so the free DNA recovered or detected is about 1%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more of the total DNA recovered or detected in the processed plasma or serum sample.

[0152] In another embodiment, the sample is collected by any method or process that results in a substantial increase in the ratio of mutant DNA to normal DNA after appropriate processing. As used herein, a substantial increase in the ratio of mutant DNA to normal DNA is that which can be detected by the methods as described herein. Such methods or processes typically result in a substantial increase in the ratio of mutant DNA to normal DNA of about 5%, 10%, 15%, 20%, 30%, 50%, 70%, 80%, 100%, 150%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 1000% or more of the ratio of mutant DNA/normal DNA found in samples collected by standard procedures.

[0153] In another embodiment, the methods or processes of collecting blood samples may also include other steps that result in lessened or reduced cell lysis. For instance, blood collection devices may be modified to decrease cell lysis due to sheer forces in the collection needle, syringe or tubes used. For instance, needles of large gauge may be employed to reduce cell sheering or vacutainer tubes may be modified to reduce the velocity of blood flow. In another embodiment, the methods or processes of collecting blood samples may also include other steps that result in lessened or reduced destruction of free DNA.

[0154] In another embodiment, the methods or processes of collecting samples may also include other steps that result in lessened or reduced cell lysis. For example, urine samples can be collected and carefully handled and stored to reduce cell lysis. In another embodiment, the methods or processes of collecting samples may also include other steps that result in lessened or reduced destruction of free DNA.

[0155] In another embodiment, the present invention is directed to a composition comprising free mutant DNA and free normal DNA, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but is not limited to at least about 5% free mutant DNA, at least about 10% free mutant DNA, at least about 15% free mutant DNA, at least about 20% free mutant DNA, at least about 30% free mutant DNA, at least about 40% free mutant DNA, at least about 50% free mutant DNA, at least about 60% free mutant DNA, at least about 70% free mutant DNA, at least about 80% free mutant DNA, at least about 90% free mutant DNA, at least about 91% free mutant DNA, at least about 92% free mutant DNA, at least about 93% free mutant DNA, at least about 94% free mutant DNA, at least about 95% free mutant DNA, at least about 96% free mutant DNA, at least about 97% free mutant DNA, at least about 98% free mutant DNA, at least about 99% free mutant DNA, and at least about 99.5% free mutant DNA.

[0156] In another embodiment, the present invention is directed to a method of using a composition comprising free mutant DNA and free normal DNA for diagnostics, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but is not limited to at least about 5% free mutant DNA, at least about 10% free mutant DNA, at least about 15% free mutant DNA, at least about 20% free mutant DNA, at least about 30% free mutant DNA, at least about 40% free mutant DNA, at least about 50% free mutant DNA, at least about 60% free mutant DNA, at least about 70% free mutant DNA, at least about 80% free mutant DNA, at least about 90% free mutant DNA, at least about 91% free mutant DNA, at least about 92% free mutant DNA, at least about 93% free mutant DNA, at least about 94% free mutant DNA, at least about 95% free mutant DNA, at least about 96% free mutant DNA, at least about 97% free mutant DNA, at least about 98% free mutant DNA, at least about 99% free mutant DNA, and at least about 99.5% free mutant DNA.

[0157] In another embodiment, the present invention is directed to a composition comprising free mutant DNA and free normal DNA, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but not is limited to about 5-10% free mutant DNA, about 10-13% free mutant DNA, about 13-15% free mutant DNA, about 15-16% free mutant DNA, about 16-17% free mutant DNA, about 17-18% free mutant DNA, about 18-19% free mutant DNA, about 19-20% free mutant DNA, about 20-21% free mutant DNA, about 21-22% free mutant DNA, about 22-23% free mutant DNA, about 23-24% free mutant DNA, about 24-25% free mutant DNA, about 25-35% free mutant DNA, about 35-45% free mutant DNA, about 45-55% free mutant DNA, about 55-65% free mutant DNA, about 65-75% free mutant DNA, about 75-85% free mutant DNA, about 85-90% free mutant DNA, about 90-91% free mutant DNA, about 91-92% free mutant DNA, about 92-93% free mutant DNA, about 93-94% free mutant DNA, about 94-95% free mutant DNA, about 95-96% free mutant DNA, about 96-97% free mutant DNA, about 97-98% free mutant DNA, about 98-99% free mutant DNA, and about 99-99.7% free mutant DNA.

[0158] In another embodiment, the present invention is directed to a method of using a composition comprising free mutant DNA and free normal DNA for diagnostics, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but is not limited to about 5-10% free mutant DNA, about 10-13% free mutant DNA, about 13-15% free mutant DNA, about 15-16% free mutant DNA, about 16-17% free mutant DNA, about 17-18% free mutant DNA, about 18-19% free mutant DNA, about 19-20% free mutant DNA, about 20-21% free mutant DNA, about 21-22% free mutant DNA, about 22-23% free mutant DNA, about 23-24% free mutant DNA, about 24-25% free mutant DNA, about 25-35% free mutant DNA, about 35-45% free mutant DNA, about 45-55% free mutant DNA, about 55-65% free mutant DNA, about 65-75% free mutant DNA, about 75-85% free mutant DNA, about 85-90% free mutant DNA, about 90-91% free mutant DNA, about 91-92% free mutant DNA, about 92-93% free mutant DNA, about 93-94% free mutant DNA, about 94-95% free mutant DNA, about 95-96% free mutant DNA, about 96-97% free mutant DNA, about 97-98% free mutant DNA, about 98-99% free mutant DNA, or about 99-99.7% free mutant DNA.

[0159] In another embodiment, the present invention is directed to a composition comprising free mutant DNA and free normal DNA, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but is not limited to a maximum of about 5-10% free mutant DNA, a maximum of about 10-13% free mutant DNA, a maximum of about 13%-15% free mutant DNA, a maximum of about 15-18% free mutant DNA, a maximum of about 18-20% free mutant DNA; a maximum of about 20-40% free mutant DNA, a maximum of about 40-50% free mutant DNA, a maximum of about 50-60% free mutant DNA, a maximum of about 60-70% free mutant DNA, a maximum of about 70-80% free mutant DNA, a maximum of about 80-90% free mutant DNA, a maximum of about 90-92% free mutant DNA, a maximum of about 92-94% free mutant DNA, a maximum of about 94-95% free mutant DNA, a maximum of about 95-96% free mutant DNA, a maximum of about 96-97% free mutant DNA, a maximum of about 97-98% free mutant DNA, a maximum of about 98-99% free mutant DNA, a maximum of about 99-99.5% free mutant DNA, and a maximum of about 99.5-99.9% free mutant DNA.

[0160] In another embodiment, the present invention is directed to a method of using a composition comprising free mutant DNA and free normal DNA for diagnostics, wherein the relationship of free mutant DNA to free normal DNA in the composition includes but is not limited a maximum of about 5-10% free mutant DNA, a maximum of about 10-13% free mutant DNA, a maximum of about 13%-15% free mutant DNA, a maximum of about 15-18% free mutant DNA, a maximum of about 18-20% free mutant DNA, a maximum of about 20-40% free mutant DNA, a maximum of about 40-50% free mutant DNA, a maximum of about 50-60% free mutant DNA, a maximum of about 60-70% free mutant DNA, a maximum of about 70-80% free mutant DNA, a maximum of about 80-90% free mutant DNA, a maximum of about 90-92% free mutant DNA, a maximum of about 92-94% free mutant DNA, a maximum of about 94-95% free mutant DNA, a maximum of about 95-96% free mutant DNA, a maximum of about 96-97% free mutant DNA, a maximum of about 97-98% free mutant DNA, a maximum of about 98-99% free mutant DNA, a maximum of about 99-99.5% free mutant DNA, and a maximum of about 99.5-99.9% free mutant DNA.

[0161] In another embodiment, the present invention is directed to a method for isolating free DNA, said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer or cross-linker to sample of (a); and (c) isolating the DNA.

[0162] In another embodiment, the present invention is directed to a method for isolating free DNA from a sample containing nucleic acid to which a cell lysis inhibitor, cell membrane stabilizer or cross-linker has been added, said method comprising isolating the DNA.

[0163] In another embodiment, the present invention is directed to a method for isolating free fetal DNA, said method comprising (a) obtaining a sample containing nucleic acid; (b) adding a cell lysis inhibitor, cell membrane stabilizer or cross-linker to sample of (a); and (c) isolating the DNA. In another embodiment, the DNA is isolated using any technique suitable in the art including but not limited to cesium chloride gradients, gradients, sucrose gradients, glucose gradients, centrifugation protocols, boiling, Qiagen purification systems, QIA DNA blood purification kit, HiSpeed Plasmid Maxi Kit, QIAfilter plasmid kit, Promega DNA purification systems, MangeSil Paramagnetic Particle based systems, Wizard SV technology, Wizard Genomic DNA purification kit, Amersham purification systems, GFX Genomic Blood DNA purification kit, Invitrogen Life Technologies Purification Systems, CONCERT purification system, Mo Bio Laboratories purification systems, UltraClean BloodSpin Kits, and UltraClean Blood DNA Kit.

[0164] In another embodiment, the present invention is directed to a method for isolating free fetal DNA from a sample containing nucleic acid to which a cell lysis inhibitor, cell membrane stabilizer or cross-linker has been added, said method comprising isolating the DNA. In a preferred embodiment, the free fetal DNA is isolated from plasma or serum obtained from the blood of a pregnant female.

[0165] In another embodiment, the DNA is isolated using techniques and/or protocols that substantially reduce the amount of maternal DNA in the sample including but not limited to centrifuging the samples, with the braking power for the centrifuge set to zero (the brake on the centrifuge is not used), transferring the supernatant to a new tube with minimal or no disturbance of the “buffy-coat,” and transferring only a portion of the supernatant to a new tube. In a preferred embodiment, both acceleration power and braking power for the centrifuge are set to zero.

[0166] In another embodiment, the DNA is isolated using techniques and/or protocols that substantially reduce the amount of maternal DNA in the sample including but not limited to centrifuging the samples, with the acceleration power for the centrifuge set to zero, transferring the supernatant to a new tube with minimal or no disturbance of the “buffy-coat,” and transferring only a portion of the supernatant to a new tube.

[0167] In another embodiment, the “buffy-coat” is removed from the tube prior to removal of the supernatant using any applicable method including but not limited to using a syringe or needle to withdraw the “buffy-coat.”

[0168] In another embodiment, the braking power for the centrifuge is set at a percentage including but not limited to 1-5%, 5-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, 90-95%, 95-99% of maximum braking power.

[0169] In another embodiment, the acceleration power for the centrifuge is set at a percentage including but not limited to 1-5%, 5-10%, 10-20%, 20-30%, 30-40%, 40-50%, 50-60%, 60-70%, 70-80%, 80-90%, 90-95%, 95-99% of maximum acceleration power.

[0170] In another embodiment, the present invention is directed to a composition comprising free fetal DNA and free maternal DNA, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited to at least about 15% free fetal DNA, at least about 20% free fetal DNA, at least about 30% free fetal DNA, at least about 40% free fetal DNA, at least about 50% free fetal DNA, at least about 60% free fetal DNA, at least about 70% free fetal DNA, at least about 80% free fetal DNA, at least about 90% free fetal DNA, at least about 91% free fetal DNA, at least about 92% free fetal DNA, at least about 93% free fetal DNA, at least about 94% free fetal DNA, at least about 95% free fetal DNA, at least about 96% free fetal DNA, at least about 97% free fetal DNA, at least about 98% free fetal DNA, at least about 99% free fetal DNA, and at least about 99.5% free fetal DNA.

[0171] In another embodiment, the present invention is directed to a method of using a composition comprising free fetal DNA and free maternal DNA for prenatal diagnostics, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited to at least about 15% free fetal DNA, at least about 20% free fetal DNA, at least about 30% free fetal DNA, at least about 40% free fetal DNA, at least about 50% free fetal DNA, at least about 60% free fetal DNA, at least about 70% free fetal DNA, at least about 80% free fetal DNA, at least about 90% free fetal DNA, at least about 91% free fetal DNA, at least about 92% free fetal DNA, at least about 93% free fetal DNA, at least about 94% free fetal DNA, at least about 95% free fetal DNA, at least about 96% free fetal DNA, at least about 97% free fetal DNA, at least about 98% free fetal DNA, at least about 99% free fetal DNA, and at least about 99.5% free fetal DNA.

[0172] In another embodiment, the present invention is directed to a composition comprising free fetal DNA and free maternal DNA, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited to about 13-15% free fetal DNA, about 15-16% free fetal DNA, about 16-17% free fetal DNA, about 17-18% free fetal DNA, about 18-19% free fetal DNA, about 19-20% free fetal DNA, about 20-21% free fetal DNA, about 21-22% free fetal DNA, about 22-23% free fetal DNA, about 23-24% free fetal DNA, about 24-25% free fetal DNA, about 25-35% free fetal DNA, about 35-45% free fetal DNA, about 45-55% free fetal DNA, about 55-65% free fetal DNA, about 65-75% free fetal DNA, about 75-85% free fetal DNA, about 85-90% free fetal DNA, about 90-91% free fetal DNA, about 91-92% free fetal DNA, about 92-93% free fetal DNA, about 93-94% free fetal DNA, about 94-95% free fetal DNA, about 95-96% free fetal DNA, about 96-97% free fetal DNA, about 97-98% free fetal DNA, about 98-99% free fetal DNA, and about 99-99.7% free fetal DNA.

[0173] In another embodiment, the present invention is directed to a method of using a composition comprising free fetal DNA and free maternal DNA for prenatal diagnostics, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited to about 13-15% free fetal DNA, about 15-16% free fetal DNA, about 16-17% free fetal DNA, about 17-18% free fetal DNA, about 18-19% free fetal DNA, about 19-20% free fetal DNA, about 20-21% free fetal DNA, about 21-22% free fetal DNA, about 22-23% free fetal DNA, about 23-24% free fetal DNA, about 24-25% free fetal DNA, about 25-35% free fetal DNA, about 35-45% free fetal DNA, about 45-55% free fetal DNA, about 55-65% free fetal DNA, about 65-75% free fetal DNA, about 75-85% free fetal DNA, about 85-90% free fetal DNA, about 90-91% free fetal DNA, about 91-92% free fetal DNA, about 92-93% free fetal DNA, about 93-94% free fetal DNA, about 94-95% free fetal DNA, about 95-96% free fetal DNA, about 96-97% free fetal DNA, about 97-98% free fetal DNA, about 98-99% free fetal DNA, or about 99-99.7% free fetal DNA.

[0174] In another embodiment, the present invention is directed to a composition comprising free fetal DNA and free maternal DNA, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited a maximum of 13%-15% free fetal DNA, a maximum of 15-18% free fetal DNA, a maximum of 18-20% free fetal DNA, a maximum of 20-40% free fetal DNA, a maximum of 40-50% free fetal DNA, a maximum of 50-60% free fetal DNA, a maximum of 60-70% free fetal DNA, a maximum of 70-80% free fetal DNA, a maximum of 80-90% free fetal DNA, a maximum of 90-92% free fetal DNA, a maximum of 92-94% free fetal DNA, a maximum of 94-95% free fetal DNA, a maximum of 95-96% free fetal DNA, a maximum of 96-97% free fetal DNA, a maximum of 97-98% free fetal DNA, a maximum of 98-99% free fetal DNA, a maximum of 99-99.5% free fetal DNA, and a maximum of 99.5-99.9% free fetal DNA.

[0175] In another embodiment, the present invention is directed to a method of using a composition comprising free fetal DNA and free maternal DNA for prenatal diagnostics, wherein the composition comprises a relationship of free fetal DNA to free maternal DNA including but not limited a maximum of 13%-15% free fetal DNA, a maximum of 15-18% free fetal DNA, a maximum of 18-20% free fetal DNA, a maximum of 20-40% free fetal DNA, a maximum of 40-50% free fetal DNA, a maximum of 50-60% free fetal DNA, a maximum of 60-70% free fetal DNA, a maximum of 70-80% free fetal DNA, a maximum of 80-90% free fetal DNA, a maximum of 90-92% free fetal DNA, a maximum of 92-94% free fetal DNA, a maximum of 94-95% free fetal DNA, a maximum of 95-96% free fetal DNA, a maximum of 96-97% free fetal DNA, a maximum of 97-98% free fetal DNA, a maximum of 98-99% free fetal DNA, a maximum of 99-99.5% free fetal DNA, and a maximum of 99.5-99.9% free fetal DNA.

DNA Template

[0176] By a “locus of interest” is intended a selected region of nucleic acid that is within a larger region of nucleic acid. A locus of interest can include but is not limited to 1-100, 1-50, 1-20, or 1-10 nucleotides, preferably 1-6, 1-5, 1-4, 1-3, 1-2, or 1 nucleotide(s).

[0177] As used herein, an “allele” is one of several alternate forms of a gene or non-coding regions of DNA that occupy the same position on a chromosome. The term allele can be used to describe DNA from any organism including but not limited to bacteria, viruses, fungi, protozoa, molds, yeasts, plants, humans, non-humans, multi-cellular parasite, animals, and archeabacteria.

[0178] For example, bacteria typically have one large strand of DNA. The term allele with respect to bacterial DNA refers to the form of a gene found in one cell as compared to the form of the same gene in a different bacterial cell of the same species.

[0179] Alleles can have the identical sequence or can vary by a single nucleotide or more than one nucleotide. With regard to organisms that have two copies of each chromosome, if both chromosomes have the same allele, the condition is referred to as homozygous. If the alleles at the two chromosomes are different, the condition is referred to as heterozygous. For example, if the locus of interest is SNP X on chromosome 1, and the maternal chromosome contains an adenine at SNP X (A allele) and the paternal chromosome contains a guanine at SNP X (G allele), the individual is heterozygous at SNP X.

[0180] As used herein, sequence means the identity of one nucleotide or more than one contiguous nucleotides in a polynucleotide. In the case of a single nucleotide, e.g., a SNP, “sequence” and “identity” are used interchangeably herein.

[0181] The term “chromosomal abnormality” refers to a deviation between the structure of the subject chromosome and a normal homologous chromosome. The term “normal” refers to the predominate karyotype or banding pattern found in healthy individuals of a particular species. A chromosomal abnormality can be numerical or structural, and includes but is not limited to aneuploidy, polyploidy, inversion, a trisomy, a monosomy, duplication, deletion, deletion of a part of a chromosome, addition, addition of a part of chromosome, insertion, a fragment of a chromosome, a region of a chromosome, chromosomal rearrangement, and translocation. A chromosomal abnormality can be correlated with presence of a pathological condition or with a predisposition to develop a pathological condition. As defined herein, a single nucleotide polymorphism (“SNP”) is not a chromosomal abnormality.

[0182] As used herein, incorporation of a nucleotide by a polymerase is referred to as an elongation reaction or a fill-in reaction interchangeably.

[0183] As used herein with respect to individuals, “mutant alleles” refers to variant alleles that are associated with a disease state.

[0184] The term “template” refers to any nucleic acid molecule that can be used for amplification in the invention. RNA or DNA that is not naturally double stranded can be made into double stranded DNA so as to be used as template DNA. Any double stranded DNA or preparation containing multiple, different double stranded DNA molecules can be used as template DNA to amplify a locus or loci of interest contained in the template DNA.

[0185] The template DNA can be obtained from any source including but not limited to humans, non-humans, mammals, reptiles, cattle, cats, dogs, goats, swine, pigs, monkeys, apes, gorillas, bulls, cows, bears, horses, sheep, poultry, mice, rats, fish, dolphins, whales, and sharks.

[0186] The template DNA can be from any appropriate sample including but not limited to, nucleic acid-containing samples of tissue, bodily fluid (for example, blood, serum, plasma, saliva, urine, tears, peritoneal fluid, ascitic fluid, vaginal secretion, breast fluid, breast milk, lymph fluid, cerebrospinal fluid or mucosa secretion), umbilical cord blood, chorionic villi, amniotic fluid, an embryo, a two-celled embryo, a four-celled embryo, an eight-celled embryo, a 16-celled embryo, a 32-celled embryo, a 64-celled embryo, a 128-celled embryo, a 256-celled embryo, a 512-celled embryo, a 1024-celled embryo, embryonic tissues, lymph fluid, cerebrospinal fluid, mucosa secretion, or other body exudate, fecal matter, an individual cell or extract of the such sources that contain the nucleic acid of the same, and subcellular structures such as mitochondria, using protocols well established within the art.

[0187] In one embodiment, the template DNA can be obtained from a sample of a pregnant female.

[0188] In another embodiment, the template DNA can be obtained from an embryo. In a preferred embodiment, the template DNA can be obtained from a single-cell of an embryo.

[0189] In one embodiment, the template DNA is fetal DNA. Fetal DNA can be obtained from sources including but not limited to maternal blood, maternal serum, maternal plasma, fetal cells, umbilical cord blood, chorionic villi, amniotic fluid, urine, saliva, cells or tissues.

[0190] In another embodiment, a cell lysis inhibitor is added to the sample including but not limited to formaldehyde, formaldehyde derivatives, formalin, glutaraldehyde, glutaraldehyde derivatives, primary amine reactive crosslinkers, sulfhydryl reactive crosslinkers, sulfhydryl addition or disulfide reduction, carbohydrate reactive crosslinkers, carboxyl reactive crosslinkers, photoreactive crosslinkers, cleavable crosslinkers, AEDP, APG, BASED, BM(PEO)₃, BM(PEO)₄, BMB, BMDB, BMH, BMOE, BS3, BSOCOES, DFDNB, DMA, DMP, DMS, DPDPB, DSG, DSP, DSS, DST, DTBP, DTME, DTSSP, EGS, HBVS, sulfo-BSOCOES, Sulfo-DST, Sulfo-EGS or compounds listed in Table XXIII. In another embodiment, two, three, four, five or more than five cell lysis inhibitors can be added to the sample. In a preferred embodiment, formalin is present in the sample at a percentage including but not limited to 0.0001-0.03%, 0.03-0.05%, 0.05-0.08%, 0.08-0.1%, 0.1-0.3%, 0.3-0.5%, 0.5-0.7%, 0.7-0.9%, 0.9-1.2%, 1.2-1.5%, 1.5-2%, 2-3%, 3-5%, and greater than 5%. In another embodiment, any combination of cross-linker, cell membrane stabilizer, or cell lysis inhibitor can be added to the sample including but not limited to a cross-linker and a cell membrane stabilizer, a cross-linker and a cell lysis inhibitor, and a cell membrane stabilizer and a cell lysis inhibitor. More than one cross-linker can be used with more than one cell membrane stabilizer. More than one cross-linker can be used with more than one cell lysis inhibitor. More than one cell membrane stabilizer can be used with more than cell lysis inhibitor.

[0191] In another embodiment, the cell lysis inhibitor is added to the sample such that lysis is less than about 10% of the cells. In a preferred embodiment, the cell lysis inhibitor is added to the sample such that lysis is less than about 5% of the cells. In a most preferred embodiment, the cell lysis inhibitor is added to the sample such that lysis is less than about 1% of the cells.

[0192] In another embodiment, a cell membrane stabilizer is added to the sample such that lysis is less than about 10% of the cells. In a preferred embodiment, the cell membrane stabilizer is added to the sample such that lysis is less than about 5% of the cells. In a most preferred embodiment, the cell membrane stabilizer is added to the sample such that lysis is less than about 1% of the cells.

[0193] In another embodiment, a cross-linker is added to the sample such that lysis is less than about 10% of the cells. In a preferred embodiment, the cross-linker is added to the sample such that lysis is less than about 5% of the cells. In a most preferred embodiment, the cross-linker is added to the sample such that lysis is less than about 1% of the cells.

[0194] In another embodiment, the cell lysis inhibitor, cross-linker or cell membrane stabilizer is added to the sample in an applicable time period including but not limited to 1-10 seconds, 10-30 seconds, 30-60 seconds, 1-5 minutes, 5-10 minutes, 10-20 minutes, 20-30 minutes, 30-40 minutes, 40-50 minutes, 60-90 minutes, 90-180 minutes or greater than 180 minutes after collection of the sample. In another embodiment, the cell lysis inhibitor, cross-linker, or cell membrane stabilizer is present in the apparatus to which the sample is collected including but not limited to a glass tube, a plastic tube, a circular container, an eppendorf tube, an IV bag, or any other appropriate collection device. In another embodiment, after the addition of the cell lysis inhibitor, cell membrane stabilizer, or cross-linker, the sample is left at about room temperature for the period of time to allow the reagent to function, including but not limited to 1-5, 5-10, 10-20, 20-40, 40-60, 60-90, 90-120, 120-150, 150-180, 180-240, 240-300 or greater than 300 minutes.

[0195] In another embodiment, the template DNA contains both maternal DNA and fetal DNA. In a preferred embodiment, template DNA is obtained from blood of a pregnant female. Blood is collected using any standard technique for blood-drawing including but not limited to venipuncture. For example, blood can be drawn from a vein from the inside of the elbow or the back of the hand. Blood samples can be collected from a pregnant female at any time during fetal gestation. For example, blood samples can be collected from human females at 1-4, 4-8, 8-12, 12-16, 16-20, 20-24, 24-28, 28-32, 32-36, 36-40, or 40-44 weeks of fetal gestation, and preferably between 8-28 weeks of fetal gestation.

[0196] The blood sample is centrifuged to separate the plasma from the maternal cells. The plasma and maternal cell fractions are transferred to separate tubes and re-centrifuged. The plasma fraction contains cell-free fetal DNA and maternal DNA. Any standard DNA isolation technique can be used to isolate the fetal DNA and the maternal DNA including but not limited to QIAamp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183).

[0197] In a preferred embodiment, blood can be collected into an apparatus containing a magnesium chelator including but not limited to EDTA, and is stored at 4° C. Optionally, a calcium chelator, including but not limited to EGTA, can be added.

[0198] In another embodiment, a cell lysis inhibitor is added to the maternal blood including but not limited to formaldehyde, formaldehyde derivatives, formalin, glutaraldehyde, glutaraldehyde derivatives, a protein cross-linker, a nucleic acid cross-linker, a protein and nucleic acid cross-linker, primary amine reactive crosslinkers, sulfhydryl reactive crosslinkers, sulfhydryl addition or disulfide reduction, carbohydrate reactive crosslinkers, carboxyl reactive crosslinkers, photoreactive crosslinkers, cleavable crosslinkers, AEDP, APG, BASED, BM(PEO)₃, BM(PEO)₄, BMB, BMDB, BMH, BMOE, BS3, BSOCOES, DFDNB, DMA, DMP, DMS, DPDPB, DSG, DSP, DSS, DST, DTBP, DTME, DTSSP, EGS, HBVS, sulfo-BSOCOES, Sulfo-DST, Sulfo-EGS, or compounds listed in Table XXIII.

[0199] In another embodiment, an agent that stabilizes cell membranes may be added to the maternal blood samples to reduce maternal cell lysis including but not limited to aldehydes, urea formaldehyde, phenol formaldehyde, DMAE (dimethylaminoethanol), cholesterol, cholesterol derivatives, high concentrations of magnesium, vitamin E, and vitamin E derivatives, calcium, calcium gluconate, taurine, niacin, hydroxylamine derivatives, bimoclomol, sucrose, astaxanthin, glucose, amitriptyline, isomer A hopane tetral phenylacetate, isomer B hopane tetral phenylacetate, citicoline, inositol, vitamin B, vitamin B complex, cholesterol hemisuccinate, sorbitol, calcium, coenzyme Q, ubiquinone, vitamin K, vitamin K complex, menaquinone, zonegran, zinc, ginkgo biloba extract, diphenylhydantoin, perftoran, polyvinylpyrrolidone, phosphatidylserine, tegretol, PABA, disodium cromglycate, nedocromil sodium, phenyloin, zinc citrate, mexitil, dilantin, sodium hyaluronate, or polaxamer 188.

[0200] In another embodiment, the template DNA is obtained from the plasma or serum of the blood of the pregnant female. The percentage of fetal DNA in maternal plasma is between 0.39-11.9% (Pertl, and Bianchi, Obstetrics and Gynecology 98: 483-490 (2001)). The majority of the DNA in the plasma sample is maternal, which makes using the DNA for genotyping the fetus difficult. However, methods that increase the percentage of fetal DNA in the maternal plasma allow the sequence of the fetal DNA to be determined, and allow for the detection of genetic disorders including mutations, insertions, deletions, and chromosomal abnormalities. The addition of cell lysis inhibitors, cell membrane stabilizers or cross-linkers to the maternal blood sample can increase the relative percentage of fetal DNA. While lysis of both maternal and fetal cells is inhibited, the vast majority of cells are maternal, and thus by reducing the lysis of maternal cells, there is a relative increase in the percentage of free fetal DNA. See Example 4.

[0201] In another embodiment, any blood drawing technique, method, protocol, or equipment that reduce the amount of cell lysis can be used, including but not limited to a large boar needle, a shorter length needle, a needle coating that increases laminar flow, e.g., teflon, a modification of the bevel of the needle to increase laminar flow, or techniques that reduce the rate of blood flow. The fetal cells likely are destroyed in the maternal blood by the mother's immune system. However, it is likely that a large portion of the maternal cell lysis occurs as a result of the blood draw or processing of the blood sample. Thus, methods that prevent or reduce cell lysis will reduce the amount of maternal DNA in the sample, and increase the relative percentage of free fetal DNA.

[0202] In another embodiment, an agent that preserves or stabilizes the structural integrity of cells can be used to reduce the amount of cell lysis.

[0203] In another embodiment, any protocol that reduces the amount of free maternal DNA in the maternal blood can be used prior to obtaining the sample. In another embodiment, prior to obtaining the sample, the pregnant female rests without physical activity for a period of time including but not limited to 0-5, 5-10, 10-15, 15-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50, 50-55, 55-60, 60-120, 120-180, 180-240, 240-300, 300-360, 360-420, 420-480, 480-540, 540-600, 600-660, 660-720, 720-780, 780-840, 840-900, 900-1200, 1200-1500, 1500-1800, 1800-2100, 2100-2400, 2400-2700, 2700-3000, 3000-3300, 3300-3600, 3600-3900, 3900-4200, 4200-4500, and greater than 4500 minutes. In another embodiment, the sample is obtained from the pregnant female after her body has reached a relaxed state. The period of rest prior to obtaining the sample may reduce the amount of maternal nucleic acid in the sample. In another embodiment, the sample is obtained from the pregnant female in the a.m., including but not limited to 4-5 am, 5-6 am, 6-7 am, 7-8 am, 8-9 am, 9-10 am, 10-11 am, and 11-12 am.

[0204] In another embodiment, the sample is obtained from the pregnant female after she has slept for a period of time including but not limited to 0-1, 1-2, 2-3, 3-4, 4-5, 5-6, 6-7, 7-8, 8-9, 9-10, 10-11, 11-12, or greater than 12 hours.

[0205] In another embodiment, prior to obtaining the sample, the pregnant female exercises for a period of time followed by a period of rest. In another embodiment, the period of exercise includes but is not limited to 0-15, 15-30, 30-45, 45-60, 60-120, 120-240, or greater than 240 minutes.

[0206] In another embodiment, agents that prevent the destruction of DNA, including but not limited to a DNase inhibitor, zinc chloride, ethylenediaminetetraacetic acid, guanidine-HCl, guanidine isothiocyanate, N-lauroylsarcosine, and Na-dodecylsulphate, can be added to the blood sample.

[0207] In another embodiment, fetal DNA is obtained from a fetal cell, wherein said fetal cell can be isolated from sources including but not limited to maternal blood, umbilical cord blood, chorionic villi, amniotic fluid, embryonic tissues and mucous obtained from the cervix or vagina of the mother.

[0208] In a preferred embodiment, fetal cells are isolated from maternal peripheral blood. An antibody specific for fetal cells can be used to purify the fetal cells from the maternal serum (Mueller et al., Lancet 336: 197-200 (1990); Ganshirt-Ahlert et al., Am. J. Obstet. Gynecol. 166: 1350-1355 (1992)). Flow cytometry techniques can also be used to enrich fetal cells (Herzenberg et al., PNAS 76: 1453-1455 (1979); Bianchi et al., PNAS 87: 3279-3283 (1990); Bruch et al., Prenatal Diagnosis 11: 787-798 (1991)). U.S. Pat. No. 5,432,054 also describes a technique for separation of fetal nucleated red blood cells, using a tube having a wide top and a, narrow capillary bottom made of polyethylene. Centrifugation using a variable speed program results in a stacking of red blood cells in the capillary based on the density of the molecules. The density fraction containing low density red blood cells, including fetal red blood cells, is recovered and then differentially hemolyzed to preferentially destroy maternal red blood cells. A density gradient in a hypertonic medium is used to separate red blood cells, now enriched in the fetal red blood cells from lymphocytes and ruptured maternal cells. The use of a hypertonic solution shrinks the red blood cells, which increases their density, and facilitate purification from the more dense lymphocytes. After the fetal cells have been isolated, fetal DNA can be purified using standard techniques in the art.

[0209] The nucleic acid that is to be analyzed can be any nucleic acid, e.g., genomic, plasmid, cosmid, yeast artificial chromosomes, artificial or man-made DNA, including unique DNA sequences, and also DNA that has been reverse transcribed from an RNA sample, such as cDNA. The sequence of RNA can be determined according to the invention if it is capable of being made into a double stranded DNA form to be used as template DNA.

[0210] The terms “primer” and “oligonucleotide primer” are interchangeable when used to discuss an oligonucleotide that anneals to a template and can be used to prime the synthesis of a copy of that template.

[0211] “Amplified” DNA is DNA that has been “copied” once or multiple times, e.g. by polymerase chain reaction. When a large amount of DNA is available to assay, such that a sufficient number of copies of the locus of interest are already present in the sample to be assayed, it may not be necessary to “amplify” the DNA of the locus of interest into an even larger number of replicate copies. Rather, simply “copying” the template DNA once using a set of appropriate primers, which may contain hairpin structures that allow the restriction enzyme recognition sites to be double stranded, can suffice.

[0212] “Copy” as in “copied DNA” refers to DNA that has been copied once, or DNA that has been amplified into more than one copy.

[0213] In one embodiment, the nucleic acid is amplified directly in the original sample containing the source of nucleic acid. It is not essential that the nucleic acid be extracted, purified or isolated; it only needs to be provided in a form that is capable of being amplified. Hybridization of the nucleic acid template with primer, prior to amplification, is not required. For example, amplification can be performed in a cell or sample lysate using standard protocols well known in the art. DNA that is on a solid support, in a fixed biological preparation, or otherwise in a composition that contains non-DNA substances and that can be amplified without first being extracted from the solid support or fixed preparation or non-DNA substances in the composition can be used directly, without further purification, as long as the DNA can anneal with appropriate primers, and be copied, especially amplified, and the copied or amplified products can be recovered and utilized as described herein.

[0214] In a preferred embodiment, the nucleic acid is extracted, purified or isolated from non-nucleic acid materials that are in the original sample using methods known in the art prior to amplification.

[0215] In another embodiment, the nucleic acid is extracted, purified or isolated from the original sample containing the source of nucleic acid and prior to amplification, the nucleic acid is fragmented using any number of methods well known in the art including but not limited to enzymatic digestion, manual shearing, or sonication. For example, the DNA can be digested with one or more restriction enzymes that have a recognition site, and especially an eight base or six base pair recognition site, which is not present in the loci of interest. Typically, DNA can be fragmented to any desired length, including 50, 100, 250, 500, 1,000, 5,000, 10,000, 50,000 and 100,000 base pairs long. In another embodiment, the DNA is fragmented to an average length of about 1000 to 2000 base pairs. However, it is not necessary that the DNA be fragmented.

[0216] Fragments of DNA that contain the loci of interest can be purified from the fragmented DNA before amplification. Such fragments can be purified by using primers that will be used in the amplification (see “Primer Design” section below) as hooks to retrieve the loci of interest, based on the ability of such primers to anneal to the loci of interest. In a preferred embodiment, tag-modified primers are used, such as e.g. biotinylated primers.

[0217] By purifying the DNA fragments containing the loci of interest, the specificity of the amplification reaction can be improved. This will minimize amplification of nonspecific regions of the template DNA. Purification of the DNA fragments can also allow multiplex PCR (Polymerase Chain Reaction) or amplification of multiple loci of interest with improved specificity.

[0218] The loci of interest that are to be sequenced can be selected based upon sequence alone. In humans, over 1.42 million single nucleotide polymorphisms (SNPs) have been described (Nature 409:928-933 (2001); The SNP Consortium LTD). On the average, there is one SNP every 1.9 kb of human genome. However, the distance between loci of interest need not be considered when selecting the loci of interest to be sequenced according to the invention. If more than one locus of interest on genomic DNA is being analyzed, the selected loci of interest can be on the same chromosome or on different chromosomes.

[0219] In a preferred embodiment, the selected loci of interest can be clustered to a particular region on a chromosome. Multiple loci of interest can be located within a region of DNA such that even with any breakage or fragmentation of the DNA, the multiple loci of interest remain linked. For example, if the DNA is obtained and by natural forces is broken into fragments of 5 Kb, multiple loci of interest can be selected within the 5 Kb regions. This allows each fragment, as measured by the loci of interest within that fragment, to serve as an experimental unit, and will reduce any possible experimental noise of comparing loci of interest on multiple chromosomes.

[0220] The loci of interest on a chromosome can be any distance from each other including but not limited to 10-50, 50-100, 100-150, 150-200, 200-250, 250-500, 500-750, 750-1000, 1000-1500, 1500-2000, 2000-2500, 2500-3000, 3000-3500, 3500-4000, 4000-4500, 4500-5000, 5000-10,000 and greater than 10,000 base pairs.

[0221] In a preferred embodiment, the length of sequence that is amplified is preferably different for each locus of interest so that the loci of interest can be separated by size.

[0222] In fact, it is an advantage of the invention that primers that copy an entire gene sequence need not be utilized. Rather, the copied locus of interest is preferably only a small part of the total gene or a small part of a non-coding region of DNA. There is no advantage to sequencing the entire gene as this can increase cost and delay results. Sequencing only the desired bases or loci of interest maximizes the overall efficiency of the method because it allows for the sequence of the maximum number of loci of interest to be determined in the fastest amount of time and with minimal cost.

[0223] Because a large number of sequences can be analyzed together, the method of the invention is especially amenable to the large-scale screening of a number of loci of interest.

[0224] Any number of loci of interest can be analyzed and processed, especially at the same time, using the method of the invention. The sample(s) can be analyzed to determine the sequence at one locus of interest or at multiple loci of interest at the same time. The loci of interest can be present on a single chromosome or on multiple chromosomes.

[0225] Alternatively, 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-25, 25-30, 30-35, 35-40, 40-45, 45-50, 50-100, 100-250, 250-500, 500-1,000, 1,000-2,000, 2,000-3,000, 3,000-5,000, 5,000-10,000, 10,000-50,000 or more than 50,000 loci of interest can be analyzed at the same time when a global genetic screening is desired. Such a global genetic screening might be desired when using the method of the invention to provide a genetic fingerprint to identify an individual or for SNP genotyping.

[0226] The locus of interest to be copied can be within a coding sequence or outside of a coding sequence. Preferably, one or more loci of interest that are to be copied are within a gene. In a preferred embodiment, the template DNA that is copied is a locus or loci of interest that is within a genomic coding sequence, either intron or exon. In a highly preferred embodiment, exon DNA sequences are copied. The loci of interest can be sites where mutations are known to cause disease or predispose to a disease state. The loci of interest can be sites of single nucleotide polymorphisms. Alternatively, the loci of interest that are to be copied can be outside of the coding sequence, for example, in a transcriptional regulatory region, and especially a promoter, enhancer, or repressor sequence.

Method for Determining the Sequence of a Locus of Interest

[0227] Any method that provides information on the sequence of a nucleic acid can be used including but not limited to allele specific PCR, PCR, gel electrophoresis, ELISA, mass spectrometry, MALDI-TOF mass spectrometry hybridization, primer extension, fluorescence detection, fluorescence resonance energy transfer (FRET), fluorescence polarization, DNA sequencing, Sanger dideoxy sequencing, DNA sequencing gels, capillary electrophoresis on an automated DNA sequencing machine, microchannel electrophoresis, microarray, southern blot, slot blot, dot blot, single primer linear nucleic acid amplification, as described in U.S. Pat. No. 6,251,639, SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend, or MassCleave™ (hMC) method.

[0228] The preferred method of determining the sequence has previously been described in U.S. application Ser. No. 10/093,618, filed on Mar. 11, 2002, hereby incorporated by reference in its entirety.

I. Primer Design

[0229] Published sequences, including consensus sequences, can be used to design or select primers for use in amplification of template DNA. The selection of sequences to be used for the construction of primers that flank a locus of interest can be made by examination of the sequence of the loci of interest, or immediately thereto. The recently published sequence of the human genome provides a source of useful consensus sequence information from which to design primers to flank a desired human gene locus of interest.

[0230] By “flanking” a locus of interest is meant that the sequences of the primers are such that at least a portion of the 3′ region of one primer is complementary to the antisense strand of the template DNA and upstream from the locus of interest site (forward primer), and at least a portion of the 3′ region of the other primer is complementary to the sense strand of the template DNA and downstream of the locus of interest (reverse primer). A “primer pair” is intended a pair of forward and reverse primers. Both primers of a primer pair anneal in a manner that allows extension of the primers, such that the extension results in amplifying the template DNA in the region of the locus of interest.

[0231] Primers can be prepared by a variety of methods including but not limited to cloning of appropriate sequences and direct chemical synthesis using methods well known in the art (Narang et al., Methods Enzymol. 68:90 (1979); Brown et al., Methods Enzymol. 68:109 (1979)). Primers can also be obtained from commercial sources such as Operon Technologies, Amersham Pharmacia Biotech, Sigma, and Life Technologies. The primers can have an identical melting temperature. The lengths of the primers can be extended or shortened at the 5′ end or the 3′ end to produce primers with desired melting temperatures. In a preferred embodiment, one of the primers of the prime pair is longer than the other primer. In a preferred embodiment, the 3′ annealing lengths of the primers, within a primer pair, differ. Also, the annealing position of each primer pair can be designed such that the sequence and length of the primer pairs yield the desired melting temperature. The simplest equation for determining the melting temperature of primers smaller than 25 base pairs is the Wallace Rule (Td=2(A+T)+4(G+C)). Computer programs can also be used to design primers, including but not limited to Array Designer Software (Arrayit Inc.), Oligonucleotide Probe Sequence Design Software for Genetic Analysis (Olympus Optical Co.), NetPrimer, and DNAsis from Hitachi Software Engineering. The TM (melting or annealing temperature) of each primer is calculated using software programs such as Net Primer (free web based program at http://premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html; internet address as of Apr. 17, 2002).

[0232] In another embodiment, the annealing temperature of the primers can be recalculated and increased after any cycle of amplification, including but not limited to cycle 1, 2, 3, 4, 5, cycles 6-10, cycles 10-15, cycles 15-20, cycles 20-25, cycles 25-30, cycles 30-35, or cycles 35-40. After the initial cycles of amplification, the 5′ half of the primers is incorporated into the products from each loci of interest, thus the TM can be recalculated based on both the sequences of the 5′ half and the 3′ half of each primer.

[0233] For example, in FIG. 1B, the first cycle of amplification is performed at about the melting temperature of the 3′ region, which anneals to the template DNA, of the second primer (region “c”), which is 13 bases. After the first cycle, the annealing temperature can be raised to TM2, which is about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer, which is depicted as region “b.” The second primer cannot bind to the original template DNA because it only anneals to 13 bases in the original DNA template, and TM2 is about the melting temperature of approximately 20 bases, which is the 3′ annealing region of the first primer (FIG. 1C). However, the first primer can bind to the DNA that was copied in the first cycle of the reaction. In the third cycle, the annealing temperature is raised to TM3, which is about the melting temperature of the entire sequence of the second primer, which is depicted as regions “c” and “d.” The DNA template produced from the second cycle of PCR contains both regions c′ and d′, and therefore, the second primer can anneal and extend at TM3 (FIG. 1D). The remaining cycles are performed at TM3. The entire sequence of the first primer (a+b′) can anneal to the template from the third cycle of PCR, and extend (FIG. 1E). Increasing the annealing temperature will decrease non-specific binding and increase the specificity of the reaction, which is especially useful if amplifying a locus of interest from human genomic DNA, which is about 3×10⁹ base pairs long.

[0234] As used herein, the term “about” with regard to annealing temperatures is used to encompass temperatures within 10 degrees celsius of the stated temperatures.

[0235] In one embodiment, one primer pair is used for each locus of interest. However, multiple primer pairs can be used for each locus of interest.

[0236] In one embodiment, primers are designed such that one or both primers of the primer pair contain sequence in the 5′ region for one or more restriction endonucleases (restriction enzyme).

[0237] As used herein, with regard to the position at which restriction enzymes digest DNA, the “sense” strand is the strand reading 5′ to 3′ in the direction in which the restriction enzyme cuts. For example, BsmF I recognizes the following sequences:

[0238]

	5′ GGGAC(N)10 3′	(SEQ ID NO:1)
	3′ CCCTG(N)14 5′	(SEQ ID NO:2)
	5′ (N)14GTCCC 3′	(SEQ ID NO:2)
	3′ (N)10CAGGG 5′	(SEQ ID NO:1)

[0239] The sense strand is the strand containing the “GGGAC” sequence as it reads 5′ to 3′ in the direction that the restriction enzyme cuts.

[0240] As used herein, with regard to the position at which restriction enzymes digest DNA, the “antisense” strand is the strand reading 3′ to 5′ in the direction in which the restriction enzyme cuts.

[0241] In another embodiment, one of the primers in a primer pair is designed such that it contains a restriction enzyme recognition site for a restriction enzyme that cuts “n” nucleotides away from the recognition site, and produces a recessed 3′ end and a 5′ overhang that contains the locus of interest (herein referred to as a “second primer”). “N” is a distance from the recognition site to the site of the cut by the restriction enzyme. In other words, the second primer of a primer pair contains a recognition site for a restriction enzyme that does not cut DNA at the recognition site but cuts “n” nucleotides away from the recognition site. For example, if the recognition sequence is for the restriction enzyme BceA I, the enzyme will cut ten (10) nucleotides from the recognition site on the sense strand, and twelve (12) nucleotides away from the recognition site on the antisense strand.

[0242] The 3′ region and preferably, the 3′ half, of the primers is designed to anneal to a sequence that flanks the loci of interest (FIG. 1A). The second primer can anneal any distance from the locus of interest provided that digestion with the restriction enzyme that recognizes the restriction enzyme recognition site on this primer generates a 5′ overhang that contains the locus of interest. The 5′ overhangs can be of any size, including but not limited to 1, 2, 3, 4, 5, 6, 7, 8, and more than 8 bases.

[0243] In a preferred embodiment, the 3′ end of the primer that anneals closer to the locus of interest (second primer) can anneal 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more than 14 bases from the locus of interest or at the locus of interest.

[0244] In a preferred embodiment, the second primer is designed to anneal closer to the locus of interest than the other primer of a primer pair (the other primer is herein referred to as a “first primer”). The second primer can be a forward or reverse primer and the first primer can be a reverse or forward primer, respectively. Whether the first or second primer should be the forward or reverse primer can be determined by which design will provide better sequencing results.

[0245] For example, the primer that anneals closer to the locus of interest can contain a recognition site for the restriction enzyme BsmF I, which cuts ten (10) nucleotides from the recognition site on the sense strand, and fourteen (14) nucleotides from the recognition site on the antisense strand. In this case, the primer can be designed so that the restriction enzyme recognition site is 13 bases, 12 bases, 10 bases or 11 bases from the locus of interest. If the recognition site is 13 bases from the locus of interest, digestion with BsmF I will generate a 5′ overhang (RXXX), wherein the locus of interest (R) is the first nucleotide in the overhang (reading 3′ to 5′), and X is any nucleotide. If the recognition site is 12 bases from the locus of interest, digestion with BsmF I will generate a 5′ overhang (XRXX), wherein the locus of interest (R) is the second nucleotide in the overhang (reading 3′ to 5′). If the recognition site is 11 bases from the locus of interest, digestion with BsmF I will generate a 5′ overhang (XXRX), wherein the locus of interest (R) is the third nucleotide in the overhang (reading 3′ to 5′). The distance between the restriction enzyme recognition site and the locus of interest should be designed so that digestion with the restriction enzyme generates a 5′ overhang, which contains the locus of interest. The effective distance between the recognition site and the locus of interest will vary depending on the choice of restriction enzyme.

[0246] In another embodiment, the primer that anneals closer to the locus of interest site, relative to the other primer, can be designed so that the restriction enzyme that generates the 5′ overhang, which contains the locus of interest, will see the same sequence at the cut site, independent of the nucleotide at the locus of interest site. For example, if the primer that anneals closer to the locus of interest is designed so that the recognition site for the restriction enzyme BsmF I (5′ GGGAC 3′) is thirteen bases from the locus of interest, the restriction enzyme will cut the antisense strand one base from the locus of interest. The nucleotide at the locus of interest is adjacent to the cut site, and may vary from DNA molecule to DNA molecule. If it is desired that the nucleotides adjacent to the cut site be identical, the primer can be designed so that the restriction enzyme recognition site for BsmF I is twelve bases away from the locus of interest site. Digestion with BsmF I will generate a 5′ overhang, wherein the locus of interest site is in the second position of the overhang (reading 3′ to 5′) and is no longer adjacent to the cut site. Designing the primer so that the restriction enzyme recognition site is twelve (12) bases from the locus of interest site allows the nucleotides adjacent to the cut site to be the same, independent of the nucleotide at the locus of interest. Also, primers that have been designed so that the restriction enzyme recognition site, BsmF I, is eleven (11) or ten (10) bases from the locus of interest site will allow the nucleotides adjacent to the cut site to be the same, independent of the nucleotide at the locus of interest. Similar strategies of primer design can be employed with other restriction enzymes so that the nucleotides adjacent to the cut site will be the same, independent of the nucleotide at the loci of interest.

[0247] The 3′ end of the first primer (either the forward or the reverse) can be designed to anneal at a chosen distance from the locus of interest. Preferably, for example, this distance is between 1-10, 10-25, 25-50, 50-75, 75-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-550, 550-600, 600-650, 650-700, 700-750, 750-800, 800-850, 850-900, 900-950, 950-1000 and greater than 1000 bases away from the locus of interest. The annealing sites of the first primers are chosen such that each successive upstream primer is further and further away from its respective downstream primer.

[0248] For example, if at locus of interest 1 the 3′ ends of the first and second primers are Z bases apart, then at locus of interest 2, the 3′ ends of the upstream and downstream primers are Z+K bases apart, where K=1, 2, 3, 4, 5-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900-1000, or greater than 1000 bases (FIG. 2). The purpose of making the first primers further and further apart from their respective second primers is so that the PCR products of all the loci of interest differ in size and can be separated, e.g., on a sequencing gel. This allows for multiplexing by pooling the PCR products in later steps.

[0249] In one embodiment, the 5′ region of the first or second primer can have a recognition site for any type of restriction enzyme. In a preferred embodiment, the 5′ region of the first and/or second primer has at least one restriction enzyme recognition site that is different from the restriction enzyme recognition site that is used to generate the 5′ overhang, which contains the locus of interest.

[0250] In one embodiment, the 5′ region of the first primer can have a recognition site for any type of restriction enzyme. In a preferred embodiment, the first primer has at least one restriction enzyme recognition site that is different from the restriction enzyme recognition site in the second primer. In another preferred embodiment, the first primer anneals further away from the locus of interest than the second primer.

[0251] In a preferred embodiment, the second primer contains a restriction enzyme recognition sequence for a Type IIS restriction enzyme including but not limited to BceA I and BsmF I, which produce a two base 5′ overhang and a four base 5′ overhang, respectively. Restriction enzymes that are Type IIS are preferred because they recognize asymmetric base sequences (not palindromic like the orthodox Type II enzymes). Type IIS restriction enzymes cleave DNA at a specified position that is outside of the recognition site, typically up to 20 base pairs outside of the recognition site. These properties make Type IIS restriction enzymes, and the recognition sites thereof, especially useful in the method of the invention. Preferably, the Type IIS restriction enzymes used in this method leave a 5′ overhang and a recessed 3′.

[0252] A wide variety of Type IIS restriction enzymes are known and such enzymes have been isolated from bacteria, phage, archeabacteria and viruses of eukaryotic algae and are commercially available (Promega, Madison Wis.; New England Biolabs, Beverly, Mass.; Szybalski W. et al., Gene 100:13-26, 1991). Examples of Type IIS restriction enzymes that would be useful in the method of the invention include, but are not limited to enzymes such as those listed in Table I.

[0253]

	Recognition/
Enzyme-Source	Cleavage Site	Supplier
Alw I - Acinetobacter lwoffii	GGATC(4/5)	NE Biolabs
Alw26 I - Acinetobacter lwoffi	GTCTC(1/5)	Promega
Bbs I - Bacillus laterosporus	GAAGAC(2/6)	NE Biolabs
Bbv I - Bacillus brevis	GCAGC(8/12)	NE Biolabs
BceA I - Bacillus cereus 1315	IACGGC(12/14)	NE Biolabs
Bmr I - Bacillus megaterium	CTGGG(5/4)	NE Biolabs
Bsa I - Bacillus stearothermophilus	GGTCTC(1/5)	NE Biolabs
6-55
Bst71 I - Bacillus stearothermophilus	GCAGC(8/12)	Promega
71
BsmA I - Bacillus stearothermophilus	GTCTC(1/5)	NE Biolabs
A664
BsmB I - Bacillus stearothermophilus	CGTCTC(1/5)	NE Biolabs
B61
BsmF I - Bacillus stearothermophilus F	GGGAC(10/14)	NE Biolabs
BspM I - Bacillus species M	ACCTGC(4/8)	NE Biolabs
Ear I - Enterobacter aerogenes	CTCTTC(1/4)	NE Biolabs
Fau I - Flavobacterium aquatile	CCCGC(4/6)	NE Biolabs
Fok I - Flavobacterium okeonokoites	GGATG(9/13)	NE Biolabs
Hga I - Haemophilus gallinarum	GACGC(5/10)	NE Biolabs
Ple I - Pseudomonas lemoignei	GAGTC(4/5)	NE Biolabs
Sap I - Saccharopolyspora species	GCTCTTC(1/4)	NE Biolabs
SfaN I - Streptococcus faecalis ND547	GCATC(5/9)	NE Biolabs
Sth132 I - Streptococcus thermophilus	CCCG(4/8)	No
ST132		commercial
		supplier
		(Gene
		195:
		201-206
		(1997))

[0254] In one embodiment, a primer pair has sequence at the 5′ region of each of the primers that provides a restriction enzyme recognition site that is unique for one restriction enzyme.

[0255] In another embodiment, a primer pair has sequence at the 5′ region of each of the primers that provide a restriction site that is recognized by more than one restriction enzyme, and especially for more than one Type IIS restriction enzyme. For example, certain consensus sequences can be recognized by more than one enzyme. For example, BsgI, Eco571 and BpmI all recognize the consensus (G/C)TGnAG and cleave 16 by away on the antisense strand and 14 by away on the sense strand. A primer that provides such a consensus sequence would result in a product that has a site that can be recognized by any of the restriction enzymes BsgI, Eco571 and BpmI.

[0256] Other restriction enzymes that cut DNA at a distance from the recognition site, and produce a recessed 3′ end and a 5′ overhang include Type III restriction enzymes.

[0257] For example, the restriction enzyme EcoP15I recognizes the sequence 5′ CAGCAG 3′ and cleaves 25 bases downstream on the sense strand and 27 bases on the antisense strand. It will be further appreciated by a person of ordinary skill in the art that new restriction enzymes are continually being discovered and can readily be adopted for use in the subject invention.

[0258] In another embodiment, the second primer can contain a portion of the recognition sequence for a restriction enzyme, wherein the full recognition site for the restriction enzyme is generated upon amplification of the template DNA such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. For example, the recognition site for BsmF I is 5′ GGGACN₁₀^↓3′. The 3′ region, which anneals to the template DNA, of the second primer can end with the nucleotides “GGG,” which do not have to be complementary with the template DNA. If the 3′ annealing region is about 10-20 bases, even if the last three bases do not anneal, the primer will extend and, generate a BsmF I site.

[0259]

Second primer:
5′ GGAAATTCCATGATGCGTGGG→	(SEQ ID NO:3)
Template DNA
3′ CCTTTAAGGTACTACGCAN1N2N3TG 5′	(SEQ ID NO:27)
5′ GGAAATTCCATGATGCCTN1,N2,N3,AC 3′	(SEQ ID NO:4)

[0260] The second primer can be designed to anneal to the template DNA, wherein the next two bases of the template DNA are thymidine and guanine, such that an adenosine and cytosine are incorporated into the primer forming a recognition site for BsmF I, 5′ GGGACN₁₀^↓3′ (SEQ ID NO: 1). The second primer can be designed to anneal in such a manner that digestion with BsmF I generates a 5′ overhang containing the locus of interest.

[0261] In another embodiment, the second primer can contain an entire or full recognition site for a restriction enzyme or a portion of a recognition site, which generates a full recognition site upon primer-dependent replication of the template DNA such that digestion with a restriction enzyme that cuts at the recognition site and generates a 5′ overhang that contains the locus of interest. For example, the restriction enzyme BsaJ I binds the following recognition site: 5′ C^↓N₁N₂GG 3′. The second primer can be designed such that the 3′ region, which anneals to the template DNA of the primer ends with “CC”, the SNP of interest is represented by “N₁”, and the template sequence downstream of the SNP is “N₂GG.”

[0262]

Second primer:
5′ GGAAATTCCATGATGCGTACC→	(SEQ ID NO:5)
Template DNA
3′ CCTTTAAGGTACTACGCATGGN1N2CC 5′	(SEQ ID NO:28)
5′ GGAAATTCCATGATGCCTACCN1,N2,GG 3′	(SEQ ID NO:6)

[0263] After digestion with BsaJ I, a 5′ overhang of the following sequence would be generated:

[0264]

	5′ C         3′
	3′ GGN1N2CC 5′

[0265] If the nucleotide guanine is not reported at the locus of interest, the 3′ recessed end can be filled in with unlabeled cytosine, which is complementary to the first nucleotide in the overhang. After removing the excess cytosine, labeled ddNTPs can be used to fill in the next nucleotide, N₁, which represents the locus of interest. Other restriction enzymes can be used including but not limited to BssK I (5′ ^↓CCNGG 3′), Dde I (5′ C^↓TNAG 3′), EcoN I (5′ CCTNN^↓NNNAGG 3′ (SEQ ID NO: 7)), Fnu4H I (5′ GC^↓NGC 3′), Hinf I (5′ G^↓ANTC 3′) PflF I (5′ GACN^↓NNGTC 3′), Sau96 I (5′ G^↓GNCC 3′), ScrF I (5′ CC^↓NGG 3′), and Tthl 11 I (5′ GACN^↓NNGTC 3′).

[0266] It is not necessary that the 3′ region, which anneals to the template DNA, of the second primer be 100% complementary to the template DNA. For example, the last 1, 2, or 3 nucleotides of the 3′ end of the second primer can be mismatches with the template DNA. The region of the primer that anneals to the template DNA will target the primer, and allow the primer to extend. Even if the last two nucleotides are not complementary to the template DNA, the primer will extend and generate a restriction enzyme recognition site. For example, the last two nucleotides in the second primer are “CC.” The second primer anneals to the template DNA, and allows extension even if “CC” is not complementary to the nucleotides Na, and Nb, on the template DNA.

[0267]

	Second primer:
	5′ GGAAATTCCATGATGCGTACC→	(SEQ ID NO:5)
	Template DNA
	3′ CCTTTAAGGTACTACGCATNa,Nb,N1,N2,CC 5′	(SEQ ID NO:29)
	5′ GGAAATTCCATGATGCCTANaNbN1N2GG 3′	(SEQ ID NO:8)

[0268] After digestion with BsaJ I, a 5′ overhang of the following sequence would be generated:

[0269]

	5′ C          3′
	3′ GGN1N2CC 5′

[0270] If the nucleotide guanine is not reported at the locus of interest, the 5′ overhang can be filled in with unlabeled cytosine. The excess cytosine can be rinsed away, and filled in with labeled ddNTPs. The first nucleotide incorporated (N₁′) corresponds to the locus of interest. If guanine is reported at the locus of interest, the loci of interest can be filled in with unlabeled cytosine and a nucleotide downstream of the locus of interest can be detected. For example, assume N₂ is adenine. If the locus of interest is guanine, unlabeled cytosine can be used in the fill in reaction. After removing the cytosine, a fill in reaction with labeled thymidine can be used. The labeled thymidine will be incorporated only if the locus of interest was a guanine. Thus, the sequence of the locus of interest can be determined by detecting a nucleotide downstream of the locus of interest.

[0271] In another embodiment, the first and second primers contain a portion of a recognition sequence for a restriction enzyme, wherein the full recognition site for the restriction enzyme is generated upon amplification of the template DNA such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. The recognition site for any restriction enzyme that contains one or more than one variable nucleotide can be generated including but not limited to the restriction enzymes BssK I (5′^↓CCNGG 3′), Dde I (5′C^↓TNAG 3′), Econ I (5′CCTNN^↓NNNAGG 3′ (SEQ ID NO: 7)), Fnu4H I (5′GC^↓NGC 3′), Hinf I (5′G^↓ANTC 3′), PflF I (5′ GACN^↓NNGTC 3′), Sau96 I (5′ G^↓GNCC 3′), ScrF I (5′ CC^↓NGG 3′), and Tthl 11 I (5′ GACN^↓NNGTC 3′).

[0272] In a preferred embodiment, the 3′ regions of the first and second primers contain the partial sequence for a restriction enzyme, wherein the partial sequence contains 1, 2, 3, 4 or more than 4 mismatches with the template DNA; these mismatches create the restriction enzyme recognition site. The number of mismatches that can be tolerated at the 3′ end depends on the length of the primer. For example, if the locus of interest is represented by N₁, a first primer can be designed to be complementary to the template DNA, depicted below as region “a.” The 3′ region of the first primer ends with “CC,” which is not complementary to the template DNA. The second primer is designed to be complementary to the template DNA, which is depicted below as region “b′”. The 3′ region of the second primer ends with “CC,” which is not complementary to the template DNA.

[0273]

First primer	5′	a	CC→
Template DNA	3′	a′	AAN1,N2,TT		b′	5′
	5′	a	TTN1N2AA		b	3′
				←CC	b′	5′	Second primer

[0274] After one round of amplification the following products would be generated:

[0275]

	5′	a	CCN1N2AA	b	3′
and
	5′	b	CCN2,N1,AA	a′	3′.

[0276] In cycle two, the primers can anneal to the templates that were generated from the first cycle of PCR:

[0277]

5′	a	CCN1N2AA		b	3′
			←CC	b′	5′
			←CC	a	5′
5′	b′	CCN2N1AA		a′	3′

[0278] After cycle two of PCR, the following products would be generated:

[0279]

5′	a	CCN1N2GG	b	3′
3′	a′	GGN1N2CC	b′	5′

[0280] The restriction enzyme recognition site for BsaJ I is generated, and after digestion with BsaJ I, a 5′ overhang containing the locus of interest is created. The locus of interest can be detected as described in detail below.

[0281] In another embodiment, a primer pair has sequence at the 5′ region of each of the primers that provides two or more restriction sites that are recognized by two or more restriction enzymes.

[0282] In a most preferred embodiment, a primer pair has different restriction enzyme recognition sites at the 5′ regions, especially 5′ ends, such that a different restriction enzyme is required to cleave away any undesired sequences. For example, the first primer for locus of interest “A” can contain sequence recognized by a restriction enzyme, “X,” which can be any type of restriction enzyme, and the second primer for locus of interest “A,” which anneals closer to the locus of interest, can contain sequence for a restriction enzyme, “Y,” which is a Type IIS restriction enzyme that cuts “n” nucleotides away and leaves a 5′ overhang and a recessed 3′ end. The 5′ overhang contains the locus of interest. After binding the amplified DNA to streptavidin coated wells, one can digest with enzyme “Y,” rinse, then fill in with labeled nucleotides and rinse, and then digest with restriction enzyme “X,” which will release the DNA fragment containing the locus of interest from the solid matrix. The locus of interest can be analyzed by detecting the labeled nucleotide that was “filled in” at the locus of interest, e.g. SNP site.

[0283] In another embodiment, the second primers for the different loci of interest that are being amplified according to the invention contain recognition sequence in the 5′ regions for the same restriction enzyme and likewise all the first primers also contain the same restriction enzyme recognition site, which is a different enzyme from the enzyme that recognizes the second primers.

[0284] In another embodiment, the second primers for the multiple loci of interest that are being amplified according to the invention contain restriction enzyme recognition sequences in the 5′ regions for different restriction enzymes.

[0285] In another embodiment, the first primers for the multiple loci of interest that are being amplified according to the invention contain restriction enzyme recognition sequences in the 5′ regions for different restriction enzymes. Multiple restriction enzyme sequences provide an opportunity to influence the order in which pooled loci of interest are released from the solid support. For example, if 50 loci of interest are amplified, the first primers can have a tag at the extreme 5′ end to aid in purification and a restriction enzyme recognition site, and the second primers can contain a recognition site for a type IIS restriction enzyme. For example, several of the first primers can have a restriction enzyme recognition site for EcoR I, other first primers can have a recognition site for Pst I, and still other first primers can have a recognition site for BamH I. After amplification, the loci of interest can be bound to a solid support with the aid of the tag on the first primers. By performing the restriction digests one restriction enzyme at a time, one can serially release the amplified loci of interest. If the first digest is performed with EcoR I, the loci of interest amplified with the first primers containing the recognition site for EcoR I will be released, and collected while the other loci of interest remain bound to the solid support. The amplified loci of interest can be selectively released from the solid support by digesting with one restriction enzyme at a time. The use of different restriction enzyme recognition sites in the first primers allows a larger number of loci of interest to be amplified in a single reaction tube.

[0286] In a preferred embodiment, any region 5′ of the restriction enzyme digestion site of each primer can be modified with a functional group that provides for fragment manipulation, processing, identification, and/or purification. Examples of such functional groups, or tags, include but are not limited to biotin, derivatives of biotin, carbohydrates, haptens, dyes, radioactive molecules, antibodies, and fragments of antibodies, peptides, and immunogenic molecules.

[0287] In another embodiment, the template DNA can be replicated once, without being amplified beyond a single round of replication. This is useful when there is a large amount of the DNA available for analysis such that a large number of copies of the loci of interest are already present in the sample, and further copies are not needed. In this embodiment, the primers are preferably designed to contain a “hairpin” structure in the 5′ region, such that the sequence doubles back and anneals to a sequence internal to itself in a complementary manner. When the template DNA is replicated only once, the DNA sequence comprising the recognition site would be single-stranded if not for the “hairpin” structure. However, in the presence of the hairpin structure, that region is effectively double stranded, thus providing a double stranded substrate for activity by restriction enzymes.

[0288] To the extent that the reaction conditions are compatible, all the primer pairs to analyze a locus or loci of interest of DNA can be mixed together for use in the method of the invention. In a preferred embodiment, all primer pairs are mixed with the template DNA in a single reaction vessel. Such a reaction vessel can be, for example, a reaction tube, or a well of a microtiter plate.

[0289] Alternatively, to avoid competition for nucleotides and to minimize primer dimers and difficulties with annealing temperatures for primers, each locus of interest or small groups of loci of interest can be amplified in separate reaction tubes or wells, and the products later pooled if desired. For example, the separate reactions can be pooled into a single reaction vessel before digestion with the restriction enzyme that generates a 5′ overhang, which contains the locus of interest or SNP site, and a 3′ recessed end. Preferably, the primers of each primer pair are provided in equimolar amounts. Also, especially preferably, each of the different primer pairs is provided in equimolar amounts relative to the other pairs that are being used.

[0290] In another embodiment, combinations of primer pairs that allow efficient amplification of their respective loci of interest can be used (see e.g. FIG. 2). Such combinations can be determined prior to use in the method of the invention. Multi-well plates and PCR machines can be used to select primer pairs that work efficiently with one another. For example, gradient PCR machines, such as the Eppendorf Mastercycler® gradient PCR machine, can be used to select the optimal annealing temperature for each primer pair. Primer pairs that have similar properties can be used together in a single reaction tube.

[0291] In another embodiment, a multi-sample container including but not limited to a 96-well or more plate can be used to amplify a single locus of interest with the same primer pairs from multiple template DNA samples with optimal PCR conditions for that locus of interest. Alternatively, a separate multi-sample container can be used for amplification of each locus of interest and the products for each template DNA sample later pooled. For example, gene A from 96 different DNA samples can be amplified in microtiter plate 1, gene B from 96 different DNA samples can be amplified in microtiter plate 2, etc., and then the amplification products can be pooled.

[0292] The result of amplifying multiple loci of interest is a preparation that contains representative PCR products having the sequence of each locus of interest. For example, if DNA from only one individual is used as the template DNA and if hundreds of disease-related loci of interest were amplified from the template DNA, the amplified DNA would be a mixture of small, PCR products from each of the loci of interest. Such a preparation could be further analyzed at that time to determine the sequence at each locus of interest or at only some loci of interest. Additionally, the preparation could be stored in a manner that preserves the DNA and can be analyzed at a later time. Information contained in the amplified DNA can be revealed by any suitable method including but not limited to fluorescence detection, sequencing, gel electrophoresis, and mass spectrometry (see “Detection of Incorporated Nucleotide” section below).

II. Amplification of Loci of Interest

[0293] The template DNA can be amplified using any suitable method known in the art including but not limited to PCR (polymerase chain reaction), 3SR (self-sustained sequence reaction), LCR (ligase chain reaction), RACE-PCR (rapid amplification of cDNA ends), PLCR (a combination of polymerase chain reaction and ligase chain reaction), Q-beta phage amplification (Shah et al., J. Medical Micro. 33: 1435-41 (1995)), SDA (strand displacement amplification), SOE-PCR (splice overlap extension PCR), and the like. These methods can be used to design variations of the releasable primer mediated cyclic amplification reaction explicitly described in this application. In the most preferred embodiment, the template DNA is amplified using PCR (PCR: A Practical Approach, M. J. McPherson, et al., IRL Press (1991); PCR Protocols: A Guide to Methods and Applications, Innis, et al., Academic Press (1990); and PCR Technology: Principals and Applications of DNA Amplification, H. A. Erlich, Stockton Press (1989)). PCR is also described in numerous U.S. patents, including U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159; 4,965,188; 4,889,818; 5,075,216; 5,079,352; 5,104,792, 5,023,171; 5,091,310; and 5,066,584.

[0294] The components of a typical PCR reaction include but are not limited to a template DNA, primers, a reaction buffer (dependent on choice of polymerase), dNTPs (dATP, dTTP, dGTP, and dCTP) and a DNA polymerase. Suitable PCR primers can be designed and prepared as discussed above (see “Primer Design” section above). Briefly, the reaction is heated to 95° C. for 2 min. to separate the strands of the template DNA, the reaction is cooled to an appropriate temperature (determined by calculating the annealing temperature of designed primers) to allow primers to anneal to the template DNA, and heated to 72° C. for two minutes to allow extension.

[0295] In a preferred embodiment, the annealing temperature is increased in each of the first three cycles of amplification to reduce non-specific amplification. See also Example 1, below. The TM1 of the first cycle of PCR is about the melting temperature of the 3′ region of the second primer that anneals to the template DNA. The annealing temperature can be raised in cycles 2-10, preferably in cycle 2, to TM2, which is about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer. If the annealing temperature is raised in cycle 2, the annealing temperature remains about the same until the next increase in annealing temperature. Finally, in any cycle subsequent to the cycle in which the annealing temperature was increased to TM2, preferably cycle 3, the annealing temperature is raised to TM3, which is about the melting temperature of the entire second primer. After the third cycle, the annealing temperature for the remaining cycles can be at about TM3 or can be further increased. In this example, the annealing temperature is increased in cycles 2 and 3. However, the annealing temperature can be increased from a low annealing temperature in cycle 1 to a high annealing temperature in cycle 2 without any further increases in temperature or the annealing temperature can progressively change from a low annealing temperature to a high annealing temperature in any number of incremental steps. For example, the annealing temperature can be changed in cycles 2, 3, 4, 5, 6, etc.

[0296] After annealing, the temperature in each cycle is increased to an “extension” temperature to allow the primers to “extend” and then following extension the temperature in each cycle is increased to the denaturization temperature. For PCR products less than 500 base pairs in size, one can eliminate the extension step in each cycle and just have denaturization and annealing steps. A typical PCR reaction consists of 25-45 cycles of denaturation, annealing and extension as described above. However, as previously noted, one cycle of amplification (one copy) can be sufficient for practicing the invention.

[0297] In another embodiment, multiple sets of primers wherein a primer set comprises a forward primer and a reverser primer, can be used to amplify the template DNA for 1-5, 5-10, 10-15, 15-20 or more than 20 cycles, and then the amplified product is further amplified in a reaction with a single primer set or a subset of the multiple primer sets. In a preferred embodiment, a low concentration of each primer set is used to minimize primer-dimer formation. A low concentration of starting DNA can be amplified using multiple primer sets. Any number of primer sets can be used in the first amplification reaction including but not limiting to 1-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450, 450-500, 500-1000, and greater than 1000. In another embodiment, the amplified product is amplified in a second reaction with a single primer set. In another embodiment, the amplified product is further amplified with a subset of the multiple primer pairs including but not limited to 2-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, 150-200, 200-250, and more than 250.

[0298] The multiple primer sets will amplify the loci of interest, such that a minimal amount of template DNA is not limiting for the number of loci that can be detected. For example, if template DNA is isolated from a single cell or the template DNA is obtained from a pregnant female, which comprises both maternal template DNA and fetal template DNA, low concentrations of each primer set can be used in a first amplification reaction to amplify the loci of interest. The low concentration of primers reduces the formation of primer-dimer and increases the probability that the primers will anneal to the template DNA and allow the polymerase to extend. The optimal number of cycles performed with the multiple primer sets is determined by the concentration of the primers. Following the first amplification reaction, additional primers can be added to further amplify the loci of interest. Additional amounts of each primer set can be added and further amplified in a single reaction. Alternatively, the amplified product can be further amplified using a single primer set in each reaction or a subset of the multiple primers sets. For example, if 150 primer sets were used in the first amplification reaction, subsets of 10 primer sets can be used to further amplify the product from the first reaction.

[0299] Any DNA polymerase that catalyzes primer extension can be used including but not limited to E. coli DNA polymerase, Klenow fragment of E. coli DNA polymerase 1, T7 DNA polymerase, T4 DNA polymerase, Taq polymerase, Pfu DNA polymerase, Vent DNA polymerase, bacteriophage 29, REDTaq™ Genomic DNA polymerase, or sequenase. Preferably, a thermostable DNA polymerase is used. A “hot start” PCR can also be performed wherein the reaction is heated to 95° C. for two minutes prior to addition of the polymerase or the polymerase can be kept inactive until the first heating step in cycle 1. “Hot start” PCR can be used to minimize nonspecific amplification. Any number of PCR cycles can be used to amplify the DNA, including but not limited to 2, 5, 10, 15, 20, 25, 30, 35, 40, or 45 cycles. In a most preferred embodiment, the number of PCR cycles performed is such that equimolar amounts of each loci of interest are produced.

III. Purification of Amplified DNA

[0300] Purification of the amplified DNA is not necessary for practicing the invention. However, in one embodiment, if purification is preferred, the 5′ end of the primer (first or second primer) can be modified with a tag that facilitates purification of the PCR products. In a preferred embodiment, the first primer is modified with a tag that facilitates purification of the PCR products. The modification is preferably the same for all primers, although different modifications can be used if it is desired to separate the PCR products into different groups.

[0301] The tag can be any chemical moiety including but not limited to a radioisotope, fluorescent reporter molecule, chemiluminescent reporter molecule, antibody, antibody fragment, hapten, biotin, derivative of biotin, photobiotin, iminobiotin, digoxigenin, avidin, enzyme, acridinium, sugar, enzyme, apoenzyme, homopolymeric oligonucleotide, hormone, ferromagnetic moiety, paramagnetic moiety, diamagnetic moiety, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, moiety having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity, or combinations thereof.

[0302] As one example, the 5′ ends of the primers can be biotinylated (Kandpal et al., Nucleic Acids Res. 18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., Nucleic Acids Res. 18:6163-6164 (1990)). The biotin provides an affinity tag that can be used to purify the copied DNA from the genomic DNA or any other DNA molecules that are not of interest. Biotinylated molecules can be purified using a streptavidin coated matrix as shown in FIG. 1F, including but not limited to Streptawell, transparent, High-Bind plates from Roche Molecular Biochemicals (catalog number 1 645 692, as listed in Roche Molecular Biochemicals, 2001 Biochemicals Catalog).

[0303] The PCR product of each locus of interest is placed into separate wells of a Streptavidin coated plate. Alternatively, the PCR products of the loci of interest can be pooled and placed into a streptavidin coated matrix, including but not limited to the Streptawell, transparent, High-Bind plates from Roche Molecular Biochemicals (catalog number 1 645 692, as listed in Roche Molecular Biochemicals, 2001 Biochemicals Catalog).

[0304] The amplified DNA can also be separated from the template DNA using non-affinity methods known in the art, for example, by polyacrylamide gel electrophoresis using standard protocols.

IV. Digestion of Amplified DNA

[0305] The amplified DNA can be digested with a restriction enzyme that recognizes a sequence that had been provided on the first or second primer using standard protocols known within the art (FIGS. 6A-6D). Restriction enzyme digestions are performed using standard protocols well known within the art. The enzyme used depends on the restriction recognition site generated with the first or second primer. See “Primer Design” section, above, for details on restriction recognition sites generated on primers.

[0306] Type IIS restriction enzymes are extremely useful in that they cut approximately 10-20 base pairs outside of the recognition site. Preferably, the Type IIS restriction enzymes used are those that generate a 5′ overhang and a recessed 3′ end, including but not limited to BceA I and BsmF I (see e.g. Table 1). In a most preferred embodiment, the second primer (either forward or reverse) contains a restriction enzyme recognition sequence for BsmF I or BceA I. The Type IIS restriction enzyme BsmF I recognizes the nucleic acid sequence GGGAC, and cuts 14 nucleotides from the recognition site on the antisense strand and 10 nucleotides from the recognition site on the sense strand. Digestion with BsmF I generates a 5′ overhang of four (4) bases.

[0307] For example, if the second primer is designed so that after amplification the restriction enzyme recognition site is 13 bases from the locus of interest, then after digestion, the locus of interest is the first base in the 5′ overhang (reading 3′ to 5′), and the recessed 3′ end is one base from the locus of interest. The 3′ recessed end can be filled in with a nucleotide that is complementary to the locus of interest. One base of the overhang can be filled in using dideoxynucleotides. However, 1, 2, 3, or 4 bases of the overhang can be filled in using deoxynucleotides or a mixture of dideoxynucleotides and deoxynucleotides.

[0308] The restriction enzyme BsmF I cuts DNA ten (10) nucleotides from the recognition site on the sense strand and fourteen (14) nucleotides from the recognition site on the antisense strand. However, in a sequence dependent manner, the restriction enzyme BsmF I also cuts eleven (11) nucleotides from the recognition site on the sense strand and fifteen (15) nucleotides from the recognition site on the antisense strand. Thus, two populations of DNA molecules exist after digestion: DNA molecules cut at 10/14 and DNA molecules cut at 11/15. If the recognition site for BsmF I is 13 bases from the locus of interest in the amplified product, then DNA molecules cut at the 11/15 position will generate a 5′ overhang that contains the locus of interest in the second position of the overhang (reading 3′ to 5′). The 3′ recessed end of the DNA molecules can be filled in with labeled nucleotides. For example, if labeled dideoxynucleotides are used, the 3′ recessed end of the molecules cut at 11/15 would be filled in with one base, which corresponds to the base upstream from the locus of interest, and the 3′ recessed end of molecules cut at 10/14 would be filled in with one base, which corresponds to the locus of interest. The DNA molecules that have been cut at the 10/14 position and the DNA molecules that have been cut at the 11/15 position can be separated by size, and the incorporated nucleotides detected. This allows detection of both the nucleotide before the locus of interest, detection of the locus of interest, and potentially the three bases after the locus of interest.

[0309] Alternatively, if the base upstream from the locus of interest and the locus of interest are different nucleotides, then the 3′ recessed end of the molecules cut at 11/15 can be filled in with deoxynucleotide that is complementary to the upstream base. The remaining deoxynucleotide is washed away, and the locus of interest site can be filled in with either labeled deoxynucleotides, unlabeled deoxynucleotides, labeled dideoxynucleotides, or unlabeled dideoxynucleotides. After the fill in reaction, the nucleotide can be detected by any suitable method. Thus, after the first fill in reaction with dNTP, the 3′ recessed end of the molecules cut at 10/14 and 11/15 is upstream from the locus of interest. The 3′ recessed end can now be filled in one base, which corresponds to the locus of interest, two bases, three bases or four bases.

[0310] The restriction enzyme BceA I recognizes the nucleic acid sequence ACGGC and cuts 12 (twelve) nucleotides from the recognition site on the sense strand and 14 (fourteen) nucleotides from the recognition site on the antisense strand. If the distance from the recognition site for BceA I on the second primer is designed to be thirteen (13) bases from the locus of interest (see FIGS. 4A-4D), digestion with BceA I will generate a 5′ overhang of two bases, which contains the locus of interest, and a recessed 3′ end that is upstream from the locus of interest. The locus of interest is the first nucleotide in the 5′ overhang (reading 3′ to 5′).

[0311] Alternative cutting is also seen with the restriction enzyme BceA I, although at a much lower frequency than is seen with BsmF I. The restriction enzyme BceA I can cut thirteen (13) nucleotides from the recognition site on the sense strand and fifteen (15) nucleotides from the recognition site on the antisense strand. Thus, two populations of DNA molecules exist: DNA molecules cut at 12/14 and DNA molecules cut at 13/15. If the restriction enzyme recognition site is 13 bases from the locus of interest in the amplified product, DNA molecules cut at the 13/15 position yield a 5′ overhang, which contains the locus of interest in the second position of the overhang (reading 3′ to 5′). Labeled dideoxynucleotides can be used to fill in the 3′ recessed end of the DNA molecules. The DNA molecules cut at 13/15 will have the base upstream from the locus of interest filled in, and the DNA molecules cut at 12/14 will have the locus of interest site filled in. The DNA molecules cut at 13/15 and those cut at 12/14 can be separated by size, and the incorporated nucleotide detected. Thus, the alternative cutting can be used to obtain additional sequence information.

[0312] Alternatively, if the two bases in the 5′ overhang are different, the 3′ recessed end of the DNA molecules, which were cut at 13/15, can be filled in with the deoxynucleotide complementary to the first base in the overhang, and excess deoxynucleotide washed away. After filling in, the 3′ recessed end of the DNA molecules that were cut at 12/14 and the DNA molecules that were cut at 13/15 are upstream from the locus of interest. The 3′ recessed ends can be filled with either labeled dideoxynucleotides, unlabeled dideoxynucleotides, labeled deoxynucleotides, or unlabeled deoxynucleotides.

[0313] If the primers provide different restriction sites for certain of the loci of interest that were copied, all the necessary restriction enzymes can be added together to digest the copied DNA simultaneously. Alternatively, the different restriction digests can be made in sequence, for example, using one restriction enzyme at a time, so that only the product that is specific for that restriction enzyme is digested.

[0314] Optimal restriction enzyme digestion conditions, including but not limited to the concentration of enzyme, temperature, buffer conditions, and the time of digestion can be optimized for each restriction enzyme. For example, the alternative cutting seen with the type IIS restriction enzyme BsmF I can be reduced, if desired, by performing the restriction enzyme digestion at lower temperatures including but not limited to 25-16°, 16-12° C., 12-8° C., 8-4° C., or 4-0° C.

V. Incorporation of Labeled Nucleotides

[0315] Digestion with the restriction enzyme that recognizes the sequence on the second primer generates a recessed 3′ end and a 5′ overhang, which contains the locus of interest (FIG. 1G). The recessed 3′ end can be filled in using the 5′ overhang as a template in the presence of unlabeled or labeled nucleotides or a combination of both unlabeled and labeled nucleotides. The nucleotides can be labeled with any type of chemical group or moiety that allows for detection including but not limited to radioactive molecules, fluorescent molecules, antibodies, antibody fragments, haptens, carbohydrates, biotin, derivatives of biotin, phosphorescent moieties, luminescent moieties, electrochemiluminescent moieties, chromatic moieties, and moieties having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity. The nucleotides can be labeled with one or more than one type of chemical group or moiety. Each nucleotide can be labeled with the same chemical group or moiety. Alternatively, each different nucleotide can be labeled with a different chemical group or moiety. The labeled nucleotides can be dNTPs, ddNTPs, or a mixture of both dNTPs and ddNTPs. The unlabeled nucleotides can be dNTPs, ddNTPs or a mixture of both dNTPs and ddNTPs.

[0316] Any combination of nucleotides can be used to incorporate nucleotides including but not limited to unlabeled deoxynucleotides, labeled deoxynucleotides, unlabeled dideoxynucleotides, labeled dideoxynucleotides, a mixture of labeled and unlabeled deoxynucleotides, a mixture of labeled and unlabeled dideoxynucleotides, a mixture of labeled deoxynucleotides and labeled dideoxynucleotides, a mixture of labeled deoxynucleotides and unlabeled dideoxynucleotides, a mixture of unlabeled deoxynucleotides and unlabeled dideoxynucleotides, a mixture of unlabeled deoxynucleotides and labeled dideoxynucleotides, dideoxynucleotide analogues, deoxynucleotide analogues, a mixture of dideoxynucleotide analogues and deoxynucleotide analogues, phosphorylated nucleoside analogues, 2′-deoxynucleotide-5′-triphosphate, and modified 2′-deoxynucleotide-5′-triphosphate.

[0317] For example, as shown in FIG. 1H, in the presence of a polymerase, the 3′ recessed end can be filled in with fluorescent ddNTP using the 5′ overhang as a template. The incorporated ddNTP can be detected using any suitable method including but not limited to fluorescence detection.

[0318] All four nucleotides can be labeled with different fluorescent groups, which will allow one reaction to be performed in the presence of all four labeled nucleotides. Alternatively, four separate “fill in” reactions can be performed for each locus of interest; each of the four reactions will contain a different labeled nucleotide (e.g. ddATP*, ddTTP*, ddGTP*, or ddCTP*, where * indicates a labeled nucleotide). Each nucleotide can be labeled with different chemical groups or the same chemical groups. The labeled nucleotides can be dideoxynucleotides or deoxynucleotides.

[0319] In another embodiment, nucleotides can be labeled with fluorescent dyes including but not limited to fluorescein, pyrene, 7-methoxycoumarin, Cascade Blue™, Alexa Flur 350, Alexa Flur 430, Alexa Flur 488, Alexa Flur 532, Alexa Flur 546, Alexa Flur 568, Alexa Flur 594, Alexa Flur 633, Alexa Flur 647, Alexa Flur 660, Alexa Flur 680, AMCA-X, dialkylaminocoumarin, Pacific Blue, Marina Blue, BODIPY 493/503, BODIPY Fl-X, DTAF, Oregon Green 500, Dansyl-X, 6-FAM, Oregon Green 488, Oregon Green 514, Rhodamine Green-X, Rhodol Green, Calcein, Eosin, ethidium bromide, NBD, TET, 2′, 4′, 5′, 7′ tetrabromosulfonefluorescien, BODIPY-R6G, BODIPY-FI BR2, BODIPY 530/550, HEX, BODIPY 558/568, BODIPY-TMR-X, PyMPO, BODIPY 564/570, TAMRA, BODIPY 576/589, Cy3, Rhodamine Red-x, BODIPY 581/591, carboxyXrhodamine, Texas Red-X, BODIPY-TR-X, Cy5, Spectrum-Aqua, SpectrumGreen #1, SpectrumGreen #2, SpectrumOrange, SpectrumRed, or naphthofluorescein.

[0320] In another embodiment, the “fill in” reaction can be performed with fluorescently labeled dNTPs, wherein the nucleotides are labeled with different fluorescent groups. The incorporated nucleotides can be detected by any suitable method including but not limited to Fluorescence Resonance Energy Transfer (FRET).

[0321] In another embodiment, a mixture of both labeled ddNTPs and unlabeled dNTPs can be used for filling in the recessed 3′ end of the SNP or locus of interest. Preferably, the 5′ overhang consists of more than one base, including but not limited to 2, 3, 4, 5, 6 or more than 6 bases. For example, if the 5′ overhang consists of the sequence “XGAA,” wherein X is the locus of interest, e.g. SNP, then filling in with a mixture of labeled ddNTPs and unlabeled dNTPs will produce several different DNA fragments. If a labeled ddNTP is incorporated at position “X,” the reaction will terminate and a single labeled base will be incorporated. If however, an unlabeled dNTP is incorporated, the polymerase continues to incorporate other bases until a labeled ddNTP is incorporated. If the first two nucleotides incorporated are dNTPs, and the third is a ddNTP, the 3′ recessed end will be extend by three bases. This DNA fragment can be separated from the other DNA fragments that were extended by 1, 2, or 4 bases by size. A mixture of labeled ddNTPs and unlabeled dNTPs will allow all bases of the overhang to be filled in, and provides additional sequence information about the locus of interest, e.g. SNP (see FIGS. 7E and 9D).

[0322] After incorporation of the labeled nucleotide, the amplified DNA can be digested with a restriction enzyme that recognizes the sequence provided by the first primer. For example, in FIG. 1I, the amplified DNA is digested with a restriction enzyme that binds to region “a,” which releases the DNA fragment containing the incorporated nucleotide from the streptavidin matrix.

[0323] Alternatively, one primer of each primer pair for each locus of interest can be attached to a solid support matrix including but not limited to a well of a microtiter plate. For example, streptavidin-coated microtiter plates can be used for the amplification reaction with a primer pair, wherein one primer is biotinylated. First, biotinylated primers are bound to the streptavidin-coated microtiter plates. Then, the plates are used as the reaction vessel for PCR amplification of the loci of interest. After the amplification reaction is complete, the excess primers, salts, and template DNA can be removed by washing. The amplified DNA remains attached to the microtiter plate. The amplified DNA can be digested with a restriction enzyme that recognizes a sequence on the second primer and generates a 5′ overhang, which contains the locus of interest. The digested fragments can be removed by washing. After digestion, the SNP site or locus of interest is exposed in the 5′ overhang. The recessed 3′ end is filled in with a labeled nucleotide, including but not limited to, fluorescent ddNTP in the presence of a polymerase. The labeled DNA can be released into the supernatant in the microtiter plate by digesting with a restriction enzyme that recognizes a sequence in the 5′ region of the first primer.

[0324] In another embodiment, one nucleotide can be used to determine the sequence of multiple alleles of a gene. A nucleotide that terminates the elongation reaction can be used to determine the sequence of multiple alleles of a gene. At one allele, the terminating nucleotide is complementary to the locus of interest in the 5′ overhang of said allele. The nucleotide is incorporated and terminates the reaction. At a different allele, the terminating nucleotide is not complementary to the locus of interest, which allows a non-terminating nucleotide to be incorporated at the locus of interest of the different allele. However, the terminating nucleotide is complementary to a nucleotide downstream from the locus of interest in the 5′ overhang of said different allele. The sequence of the alleles can be determined by analyzing the patterns of incorporation of the terminating nucleotide. The terminating nucleotide can be labeled or unlabeled.

[0325] In a another embodiment, the terminating nucleotide is a nucleotide that terminates or hinders the elongation reaction including but not limited to a dideoxynucleotide, a dideoxynucleotide derivative, a dideoxynucleotide analog, a dideoxynucleotide homolog, a dideoxynucleotide with a sulfur chemical group, a deoxynucleotide, a deoxynucleotide derivative, a deoxynucleotide homolog, a deoxynucleotide analog, a deoxynucleotide with a sulfur chemical group, arabinoside triphosphate, a arabinoside triphosphate analog, a arabinoside triphosphate homolog, or an arabinoside derivative.

[0326] In another embodiment, a terminating nucleotide labeled with one signal generating moiety tag, including but not limited to a fluorescent dye, can be used to determine the sequence of the alleles of a locus of interest. The use of a single nucleotide labeled with one signal generating moiety tag eliminates any difficulties that can arise when using different fluorescent moieties. In addition, using one nucleotide labeled with one signal generating moiety tag to determine the sequence of alleles of a locus of interest reduces the number of reactions, and eliminates pipetting errors.

[0327] For example, if the second primer contains the restriction enzyme recognition site for BsmFI, digestion will generate a 5′ overhang of 4 bases. The second primer can be designed such that the locus of interest is located in the first position of the overhang. A representative overhang is depicted below, where R represents the locus of interest:

[0328]

	5′ CAC
	3′ GTG	R	T	G	G
Overhang position		1	2	3	4

[0329] One nucleotide with one signal generating moiety tag can be used to determine whether the variable site is homozygous or heterozygous. For example, if the variable site is adenine (A) or guanine (G), then either adenine or guanine can be used to determine the sequence of the alleles of the locus of interest, provided that there is an adenine or guanine in the overhang at position 2, 3, or 4.

[0330] For example, if the nucleotide in position 2 of the overhang is thymidine, which is complementary to adenine, then labeled ddATP, unlabeled dCTP, dGTP, and dTTP can be used to determine the sequence of the alleles of the locus of interest. The ddATP can be labeled with any signal generating moiety including but not limited to a fluorescent dye. If the template DNA is homozygous for adenine, then labeled ddATP* will be incorporated at position 1 complementary to the overhang at the alleles, and no nucleotide incorporation will be seen at position 2, 3 or 4 complementary to the overhang.

[0331]

Allele 1	5′ CCC	A*
	3′ GGG	T	T	G	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	A*
	3′ GGG	T	T	G	G
Overhang position		1	2	3	4

[0332] One signal will be seen corresponding to incorporation of labeled ddATP at position 1 complementary to the overhang, which indicates that the individual is homozygous for adenine at this position. This method of labeling eliminates any difficulties that may arise from using different dyes that have different quantum coefficients.

Homozygous Guanine:

[0333] If the template DNA is homozygous for guanine, then no ddATP will be incorporated at position 1 complementary to the overhang, but ddATP will be incorporated at the first available position, which in this case is position 2 complementary to the overhang. For example, if the second position in the overhang corresponds to a thymidine, then:

[0334]

Allele 1	5′ CCC	G	A*
	3′ GGG	C	T	G	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	A*
	3′ GGG	C	T	G	G
Overhang position		1	2	3	4

[0335] One signal will be seen corresponding to incorporation of ddATP at position 2 complementary to the overhang, which indicates that the individual is homozygous for guanine. The molecules that are filled in at position 2 complementary to the overhang will have a different molecular weight than the molecules filled in at position 1 complementary to the overhang.

[0336] Heterozygous Condition:

[0337]

Allele 1	5′ CCC	A*
	3′ GGG	T	T	G	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	A*
	3′ GGG	C	T	G	G
Overhang position		1	2	3	4

[0338] Two signals will be seen; the first signal corresponds to the ddATP filled in at position one complementary to the overhang and the second signal corresponds to the ddATP filled in at position 2 complementary to the overhang. The two signals can be separated based on molecular weight; allele 1 and allele 2 will be separated by a single base pair, which allows easy detection and quantitation of the signals. Molecules filled in at position one can be distinguished from molecules filled in at position two using any method that discriminates based on molecular weight including but not limited to gel electrophoresis, capillary gel electrophoresis, DNA sequencing, and mass spectrometry. It is not necessary that the nucleotide be labeled with a chemical moiety; the DNA molecules corresponding to the different alleles can be separated based on molecular weight.

[0339] If position 2 of the overhang is not complementary to adenine, it is possible that positions 3 or 4 may be complementary to adenine. For example, position 3 of the overhang may be complementary to the nucleotide adenine, in which case labeled ddATP may be used to determine the sequence of both alleles.

[0340] Homozygous for Adenine:

[0341]

Allele 1	5′ CCC	A*
	3′ GGG	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	A*
	3′ GGG	T	G	T	G
Overhang position		1	2	3	4

[0342] Homozygous for Guanine:

[0343]

Allele 1	5′ CCC	G	C	A*
	3′ GGG	C	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	C	A*
	3′ GGG	C	G	T	G
Overhang position		1	2	3	4

[0344] Heterozygous:

[0345]

Allele 1	5′ CCC	A*
	3′ GGG	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	C	A*
	3′ GGG	C	G	T	G
Overhang position		1	2	3	4

[0346] Two signals will be seen; the first signal corresponds to the ddATP filled in at position 1 complementary to the overhang and the second signal corresponds to the ddATP filled in at position 3 complementary to the overhang. The two signals can be separated based on molecular weight; allele 1 and allele 2 will be separated by two bases, which can be detected using any method that discriminates based on molecular weight.

[0347] Alternatively, if positions 2 and 3 are not complementary to adenine (i.e positions 2 and 3 of the overhang correspond to guanine, cytosine, or adenine) but position 4 is complementary to adenine, labeled ddATP can be used to determine the sequence of both alleles.

[0348] Homozygous for Adenine:

[0349]

Allele 1	5′ CCC	A*
	3′ GGG	T	G	G	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	A*
	3′ GGG	T	G	G	T
Overhang position		1	2	3	4

[0350] One signal will be seen that corresponds to the molecular weight of molecules filled in with ddATP at position one complementary to the overhang, which indicates that the individual is homozygous for adenine at the variable site.

[0351] Homozygous for Guanine:

[0352]

Allele 1	5′ CCC	G	C	C	A*
	3′ GGG	C	G	G	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	C	C	A*
	3′ GGG	C	G	G	T
Overhang position		1	2	3	4

[0353] One signal will be seen that corresponds to the molecular weight of molecules filled in at position 4 complementary to the overhang, which indicates that the individual is homozygous for guanine.

[0354] Heterozygous:

[0355]

Allele 1	5′ CCC	A*
	3′ GGG	T	G	G	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	G	C	C	A*
	3′ GGG	C	G	G	T
Overhang position		1	2	3	4

[0356] Two signals will be seen; the first signal corresponds to the ddATP filled in at position one complementary to the overhang and the second signal corresponds to the ddATP filled in at position 4 complementary to the overhang. The two signals can be separated based on molecular weight; allele 1 and allele 2 will be separated by three bases, which allows detection and quantitation of the signals. The molecules filled in at position 1 and those filled in at position 4 can be distinguished based on molecular weight.

[0357] As discussed above, if the variable site contains either adenine or guanine, either labeled adenine or labeled guanine can be used to determine the sequence of both alleles. If positions 2, 3, or 4 of the overhang are not complementary to adenine but one of the positions is complementary to a guanine, then labeled ddGTP can be used to determine whether the template DNA is homozygous or heterozygous for adenine or guanine. For example, if position 3 in the overhang corresponds to a cytosine then the following signals will be expected if the template DNA is homozygous for guanine, homozygous for adenine, or heterozygous:

[0358] Homozygous for Guanine:

[0359]

Allele 1	5′ CCC	G*
	3′ GGG	C	T	C	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	G*
	3′ GGG	C	T	C	T
Overhang position		1	2	3	4

[0360] One signal will be seen that corresponds to the molecular weight of molecules filled in with ddGTP at position one complementary to the overhang, which indicates that the individual is homozygous for guanine.

[0361] Homozygous for Adenine:

[0362]

Allele 1	5′ CCC	A	A	G*
	3′ GGG	T	T	C	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	A	A	G*
	3′ GGG	T	T	C	T
Overhang position		1	2	3	4

[0363] One signal will be seen that corresponds to the molecular weight of molecules filled in at position 3 complementary to the overhang, which indicates that the individual is homozygous for adenine at the variable site.

[0364] Heterozygous:

[0365]

Allele 1	5′ CCC	G*
	3′ GGG	C	T	C	T
Overhang position		1	2	3	4
Allele 2	5′ CCC	A	A	G*
	3′ GGG	T	T	C	T
Overhang position		1	2	3	4

[0366] Two signals will be seen; the first signal corresponds to the ddGTP filled in at position one complementary to the overhang and the second signal corresponds to the ddGTP filled in at position 3 complementary to the overhang. The two signals can be separated based on molecular weight; allele 1 and allele 2 will be separated by two bases, which allows easy detection and quantitation of the signals.

[0367] In another embodiment, the nucleotide labeled with a single chemical moiety, which is used to determine the sequence of alleles of interest, can be analyzed by a variety of methods including but not limited to fluorescence detection, DNA sequencing gel, capillary electrophoresis on an automated DNA sequencing machine, microchannel electrophoresis, and other methods of sequencing, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry or by DNA hybridization techniques including Southern Blots, Slot Blots, Dot Blots, and DNA microarrays, wherein DNA fragments would be useful as both “probes” and “targets,” ELISA, fluorimetry, Fluorescence Resonance Energy Transfer (FRET), SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend, or MassCleave™ (hMC) method.

[0368] Some type IIS restriction enzymes also display alternative cutting as discussed above. For example, BsmFI will cut at 10/14 and 11/15 from the recognition site. However, the cutting patterns are not mutually exclusive; if the 11/15 cutting pattern is seen at a particular sequence, 10/14 cutting is also seen. If the restriction enzyme BsmF I cuts at 10/14 from the recognition site, the 5′ overhang will be X₁X₂X₃X₄. If BsmF I cuts 11/15 from the recognition site, the 5′ overhang will be X₀X₁X₂X₃. If position X₀ of the overhang is complementary to the labeled nucleotide, the labeled nucleotide will be incorporated at position X₀ and provides an additional level of quality assurance. It provides additional sequence information.

[0369] For example, if the variable site is adenine or guanine, and position 3 in the overhang is complementary to adenine, labeled ddATP can be used to determine the genotype at the variable site. If position 0 of the 11/15 overhang contains the nucleotide complementary to adenine, ddATP will be filled in and an additional signal will be seen.

[0370] Heterozygous:

[0371]

10/14 Allele 1	5′ CCA	A*
	3′ GGT	T	G	T	G
Overhang position		1	2	3	4
10/14 Allele 2	5′ CCA	G	C	A*
	3′ GGT	C	G	T	G
Overhang position		1	2	3	4
11/15 Allele 1	5′ CC	A*
	3′ GG	T	T	G	T
Overhang position		0	1	2	3
11/15 Allele 2	5′ CC	A*
	3′ GG	T	C	G	T
Overhang position		0	1	2	3

[0372] Three signals are seen; one corresponding to the ddATP incorporated at position 0 complementary to the overhang, one corresponding to the ddATP incorporated at position 1 complementary to the overhang, and one corresponding to the ddATP incorporated at position 3 complementary to the overhang. The molecules filled in at position 0, 1, and 3 complementary to the overhang differ in molecular weight and can be separated using any technique that discriminates based on molecular weight including but not limited to gel electrophoresis, and mass spectrometry.

[0373] For quantitating the ratio of one allele to another allele or when determining the relative amount of a mutant DNA sequence in the presence of wild type DNA sequence, an accurate and highly sensitive method of detection must be used. The alternate cutting displayed by type IIS restriction enzymes may increase the difficulty of determining ratios of one allele to another allele because the restriction enzyme may not display the alternate cutting (11/15) pattern on the two alleles equally. For example, allele 1 may be cut at 10/14 80% of the time, and 11/15 20% of the time. However, because the two alleles may differ in sequence, allele 2 may be cut at 10/14 90% of the time, and 11/15 20% of the time.

[0374] For purposes of quantitation, the alternate cutting problem can be eliminated when the nucleotide at position 0 of the overhang is not complementary to the labeled nucleotide. For example, if the variable site corresponds to adenine or guanine, and position 3 of the overhang is complementary to adenine (i.e, a thymidine is located at position 3 of the overhang), labeled ddATP can be used to determine the genotype of the variable site. If position 0 of the overhang generated by the 11/15 cutting properties is not complementary to adenine, (i.e, position 0 of the overhang corresponds to guanine, cytosine, or adenine) no additional signal will be seen from the fragments that were cut 11/15 from the recognition site. Position 0 complementary to the overhang can be filled in with unlabeled nucleotide, eliminating any complexity seen from the alternate cutting pattern of restriction enzymes. This method provides a highly accurate method for quantitating the ratio of a variable site including but not limited to a mutation, or a single nucleotide polymorphism.

[0375] For instance, if SNP X can be adenine or guanine, this method of labeling allows quantitation of the alleles that correspond to adenine and the alleles that correspond to guanine, without determining if the restriction enzyme displays any differences between the alleles with regard to alternate cutting patterns.

[0376] Heterozygous:

[0377]

10/14 Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
10/14 Allele 2	5′ CCG	G	C	A*
	3′ GGC	C	G	T	G
Overhang position		1	2	3	4

[0378] The overhang generated by the alternate cutting properties of BsmF I is depicted below:

[0379]

11/15 Allele 1	5′ CC
	3′ GG	C	T	G	T
Overhang position		0	1	2	3
11/15 Allele 2	5′ CC
	3′ GG	C	C	G	T
Overhang position		0	1	2	3

[0380] After filling in with labeled ddATP and unlabeled dGTP, dCTP, dTTP, the following molecules would be generated:

[0381]

11/15 Allele 1	5′ CC	G	A*
	3′ GG	C	T	G	T
Overhang position		0	1	2	3
11/15 Allele 2	5′ CC	G	G	C	A*
	3′ GG	C	C	G	T
Overhang position		0	1	2	3

[0382] Two signals are seen; one corresponding to the molecules filled in with ddATP at position one complementary to the overhang and one corresponding to the molecules filled in with ddATP at position 3 complementary to the overhang. Position 0 of the 11/15 overhang is filled in with unlabeled nucleotide, which eliminates any difficulty in quantitating a ratio for the nucleotide at the variable site on allele 1 and the nucleotide at the variable site on allele 2.

[0383] Any nucleotide can be used including adenine, adenine derivatives, adenine homologues, guanine, guanine derivatives, guanine homologues, cytosine, cytosine derivatives, cytosine homologues, thymidine, thymidine derivatives, or thymidine homologues, or any combinations of adenine, adenine derivatives, adenine homologues, guanine, guanine derivatives, guanine homologues, cytosine, cytosine derivatives, cytosine homologues, thymidine, thymidine derivatives, or thymidine homologues.

[0384] The nucleotide can be labeled with any chemical group or moiety, including but not limited to radioactive molecules, fluorescent molecules, antibodies, antibody fragments, haptens, carbohydrates, biotin, derivatives of biotin, phosphorescent moieties, luminescent moieties, electrochemiluminescent moieties, chromatic moieties, and moieties having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity. The nucleotide can be labeled with one or more than one type of chemical group or moiety.

[0385] In another embodiment, labeled and unlabeled nucleotides can be used. Any combination of deoxynucleotides and dideoxynucleotides can be used including but not limited to labeled dideoxynucleotides and labeled deoxynucleotides; labeled dideoxynucleotides and unlabeled deoxynucleotides; unlabeled dideoxynucleotides and unlabeled deoxynucleotides; and unlabeled dideoxynucleotides and labeled deoxynucleotides.

[0386] In another embodiment, nucleotides labeled with a chemical moiety can be used in the PCR reaction. Unlabeled nucleotides then are used to fill-in the 5′ overhangs generated after digestion with the restriction enzyme. An unlabeled terminating nucleotide can be used to in the presence of unlabeled nucleotides to determine the sequence of the alleles of a locus of interest.

[0387] For example, if labeled dTTP was used in the PCR reaction, the following 5′ overhang would be generated after digestion with BsmF I:

[0388]

10/14 Allele 1	5′ CT*G	A
	3′ GA C	T	G	T	G
Overhang position		1	2	3	4
10/14 Allele 2	5′ CT*G	G	C	A
	3′ GA C	C	G	T	G
Overhang position		1	2	3	4

[0389] Unlabeled ddATP, unlabeled dCTP, unlabeled dGTP, and unlabeled dTTP can be used to fill-in the 5′ overhang. Two signals will be generated; one signal corresponds to the DNA molecules filled in with unlabeled ddATP at position 1 complementary to the overhang and the second signal corresponds to DNA molecules filled in with unlabeled ddATP at position 3 complementary to the overhang. The DNA molecules can be separated based on molecular weight and can be detected by the fluorescence of the dTTP, which was incorporated during the PCR reaction.

[0390] The labeled DNA loci of interest sites can be analyzed by a variety of methods including but not limited to fluorescence detection, DNA sequencing gel, capillary electrophoresis on an automated DNA sequencing machine, microchannel electrophoresis, and other methods of sequencing, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry or by DNA hybridization techniques including Southern Blots, Slot Blots, Dot Blots, and DNA microarrays, wherein DNA fragments would be useful as both “probes” and “targets,” ELISA, fluorimetry, Fluorescence Resonance Energy Transfer (FRET), SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend, or MassCleave™ (hMC) method.

[0391] This method of labeling is extremely sensitive and allows the detection of alleles of a locus of interest that are in various ratios including but not limited to 1:1, 1:2, 1:3, 1:4, 1:5, 1:6-1:10, 1:11-1:20, 1:21-1:30, 1:31-1:40, 1:41-1:50, 1:51-1:60, 1:61-1:70, 1:71-1:80, 1:81-1:90, 1:91:1:100, 1:101-1:200, 1:250, 1:251-1:300, 1:301-1:400, 1:401-1:500, 1:501-1:600, 1:601-1:700, 1:701-1:800, 1:801-1:900, 1:901-1:1000, 1:1001-1:2000, 1:2001-1:3000, 1:3001-1:4000, 1:4001-1:5000, 1:5001-1:6000, 1:6001-1:7000, 1:7001-1:8000, 1:8001-1:9000, 1:9001-1:10,000; 1:10,001-1:20,000, 1:20,001:1:30,000, 1:30,001-1:40,000, 1:40,001-1:50,000, and greater than 1:50,000.

[0392] For example, this method of labeling allows one nucleotide labeled with one signal generating moiety to be used to determine the sequence of alleles at a SNP locus, or detect a mutant allele amongst a population of normal alleles, or detect an allele encoding antibiotic resistance from a bacterial cell amongst alleles from antibiotic sensitive bacteria, or detect an allele from a drug resistant virus amongst alleles from drug-sensitive virus, or detect an allele from a non-pathogenic bacterial strain amongst alleles from a pathogenic bacterial strain.

[0393] As shown above, a single nucleotide can be used to determine the sequence of the alleles at a particular locus of interest. This method is especially useful for determining if an individual is homozygous or heterozygous for a particular mutation or to determine the sequence of the alleles at a particular SNP site. This method of labeling eliminates any errors caused by the quantum coefficients of various dyes. It also allows the reaction to proceed in a single reaction vessel including but not limited to a well of a microtiter plate, or a single eppendorf tube.

[0394] This method of labeling is especially useful for the detection of multiple genetic signals in the same sample. For example, this method is useful for the detection of fetal DNA in the blood, serum, or plasma of a pregnant female, which contains both maternal DNA and fetal DNA. The maternal DNA and fetal DNA may be present in the blood, serum or plasma at ratios such as 97:3; however, the above-described method can be used to detect the fetal DNA. This method of labeling can be used to detect two, three, four or more than four different genetic signals in the sample population

[0395] This method of labeling is especially useful for the detection of a mutant allele that is among a large population of wild type alleles. Furthermore, this method of labeling allows the detection of a single mutant cell in a large population of wild type cells. For example, this method of labeling can be used to detect a single cancerous cell among a large population of normal cells. Typically, cancerous cells have mutations in the DNA sequence. The mutant DNA sequence can be identified even if there is a large background of wild type DNA sequence. This method of labeling can be used to screen, detect, or diagnosis any type of cancer including but not limited to colon, renal, breast, bladder, liver, kidney, brain, lung, prostate, and cancers of the blood including leukemia.

[0396] This labeling method can also be used to detect pathogenic organisms, including but not limited to bacteria, fungi, viruses, protozoa, and mycobacteria. It can also be used to discriminate between pathogenic strains of microorganism and non-pathogenic strains of microorganisms including but not limited to bacteria, fungi, viruses, protozoa, and mycobacteria.

[0397] For example, there are several strains of Escherichia coli (E. coli), and most are non-pathogenic. However, several strains, such as E. coli O157 are pathogenic. There are genetic differences between non-pathogenic E. coli strains and pathogenic E. coli. The above described method of labeling can be used to detect pathogenic microorganisms in a large population of non-pathogenic organisms, which are sometimes associated with the normal flora of an individual.

VI. Analysis of the Locus of Interest

[0398] The loci of interest can be analyzed by a variety of methods including but not limited to fluorescence detection, DNA sequencing gel, capillary electrophoresis on an automated DNA sequencing machine, (e.g. the ABI Prism 3100 Genetic Analyzer or the ABI Prism 3700 Genetic Analyzer), microchannel electrophoresis, and other methods of sequencing, Sanger dideoxy sequencing, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry or by DNA hybridization techniques including Southern Blot, Slot Blot, Dot Blot, and DNA microarray, wherein DNA fragments would be useful as both “probes” and “targets,” ELISA, fluorimetry, fluorescence polarization, Fluorescence Resonance Energy Transfer (FRET), SNP-IT, GeneChips, HuSNP, BeadArray, TaqMan assay, Invader assay, MassExtend, or MassCleave™ (hMC) method.

[0399] The loci of interest can be analyzed using gel electrophoresis followed by fluorescence detection of the incorporated nucleotide. Another method to analyze or read the loci of interest is to use a fluorescent plate reader or fluorimeter directly on the 96-well streptavidin coated plates. The plate can be placed onto a fluorescent plate reader or scanner such as the Pharmacia 9200 Typhoon to read each locus of interest.

[0400] Alternatively, the PCR products of the loci of interest can be pooled and after “filling in” (FIG. 10), the products can be separated by size, using any method appropriate for the same, and then analyzed using a variety of techniques including but not limited to fluorescence detection, DNA sequencing gel, capillary electrophoresis on an automated DNA sequencing machine, microchannel electrophoresis, other methods of sequencing, Sanger dideoxy sequencing, DNA hybridization techniques including Southern Blot, Slot Blot, Dot Blot, and DNA microarray, mass spectrometry, time of flight mass spectrometry, quadrupole mass spectrometry, magnetic sector mass spectrometry, electric sector mass spectrometry infrared spectrometry, ultraviolet spectrometry, palentiostatic amperometry. For example, polyacrylamide gel electrophoresis can be used to separate DNA by size and the gel can be scanned to determine the color of fluorescence in each band (using e.g., ABI 377 DNA sequencing machine or a Pharmacia Typhoon 9200).

[0401] In another embodiment, the sequence of the locus of interest can be determined by detecting the incorporation of a nucleotide that is 3′ to the locus of interest, wherein said nucleotide is a different nucleotide from the possible nucleotides at the locus of interest. This embodiment is especially useful for the sequencing and detection of SNPs. The efficiency and rate at which DNA polymerases incorporate nucleotides varies for each nucleotide.

[0402] According to the data from the Human Genome Project, 99% of all SNPs are binary. The sequence of the human genome can be used to determine a nucleotide that is 3′ to the SNP of interest. When a nucleotide that is 3′ to the SNP site differs from the possible nucleotides at the SNP site, a nucleotide that is one or more than one base 3′ to the SNP can be used to determine the sequence of the SNP site.

[0403] For example, suppose the sequence of SNP X on chromosome 13 is to be determined. The sequence of the human genome indicates that SNP X can either be adenosine or guanine and that a nucleotide 3′ to the locus of interest is a thymidine. A primer that contains a restriction enzyme recognition site for BsmF I, which is designed to be 13 bases from the locus of interest after amplification, is used to amplify a DNA fragment containing SNP X. Digestion with the restriction enzyme BsmF I generates a 5′ overhang that contains the locus of interest, which can either be adenosine or guanine. The digestion products can be split into two “fill in” reactions: one contains dTTP, and the other reaction contains dCTP. If the locus of interest is homozygous for guanine, only the DNA molecules that were mixed with dCTP will be filled in. If the locus of interest is homozygous for adenosine, only the DNA molecules that were mixed with dTTP will be filled in. If the locus of interest is heterozygous, the DNA molecules that were mixed with dCTP will be filled in as well as the DNA molecules that were mixed with dTTP. After washing to remove the excess dNTP, the samples are filled in with labeled ddATP, which is complimentary to the nucleotide (thymidine) that is 3′ to the locus of interest. The DNA molecules that were filled in by the previous reaction will be filled in with labeled ddATP. If the individual is homozygous for adenosine, the DNA molecules that were mixed with dTTP subsequently will be filled in with the labeled ddATP. However, the DNA molecules that were mixed with dCTP, would not have incorporated that nucleotide, and therefore, could not incorporate the ddATP. Detection of labeled ddATP only in the molecules that were mixed with dTTP indicates that the nucleotide at SNP X on chromosome 13 is adenosine.

[0404] In another embodiment, large scale screening for the presence or absence of single nucleotide polymorphisms or mutations can be performed. One to tens to hundreds to thousands of loci of interest on a single chromosome or on multiple chromosomes can be amplified with primers as described above in the “Primer Design” section. The primers can be designed so that each amplified loci of interest is of a different size (FIG. 2). The multiple loci of interest can be of a DNA sample from one individual representing multiple loci of interest on a single chromosome, multiple chromosomes, multiple genes, a single gene, or any combination thereof.

[0405] When human data is being analyzed, the known sequence can be a specific sequence that has been determined from one individual (including e.g. the individual whose DNA is currently being analyzed), or it can be a consensus sequence such as that published as part of the human genome.

Ratio of Alleles at Heterozygous Locus of Interest

[0406] In one embodiment, the ratio of alleles at a heterozygous locus of interest can be calculated. The intensity of a nucleotide at the loci of interest can be quantified using any number of computer programs including but not limited to GeneScan and ImageQuant. For example, for a heterozygous SNP, there are two nucleotides, and each should be present in a 1:1 ratio. In a preferred embodiment, the ratio of multiple heterozygous SNPs can be calculated.

[0407] In one embodiment, the ratio for a variable nucleotide at alleles at a heterozygous locus of interest can be calculated. The intensity of each variable nucleotide present at the loci of interest can be quantified using any number of computer programs including but not limited to GeneScan and ImageQuant. For example, for a heterozygous SNP, there will be two nucleotides present, and each may be present in a 1:1 ratio. In a preferred embodiment, the ratio of multiple heterozygous SNPs can be calculated.

[0408] In another embodiment, the ratio of alleles at a heterozygous locus of interest on a chromosome is summed and compared to the ratio of alleles at a heterozygous locus of interest on a different chromosome. In a preferred embodiment, the ratio of alleles at multiple heterozygous loci of interest on a chromosome is summed and compared to the ratio of alleles at multiple heterozygous loci of interest on a different chromosome. The ratio obtained from SNP 1, SNP 2, SNP 3, SNP 4, etc on chromosome 1 can be summed. This ratio can then be compared to the ratio obtained from SNP A, SNP B, SNP C, SNP D, etc.

[0409] For example, 100 SNPs can be analyzed on chromosome 1. Of these 100 SNPs, assume 50 are heterozygous. The ratio of the alleles at heterozygous SNPs on chromosome 1 can be summed, and should give a ratio of approximately 50:50. Likewise, of 100 SNPs analyzed on chromosome 21, assume 50 are heterozygous. The ratio of alleles at heterozygous SNPs on chromosome 21 is summed. With a normal number of chromosomes, the ratio should be approximately 50:50, and thus there should be no difference between the ratio obtained from chromosome 1 and 21. However, if there is an additional copy of chromosome 21, an additional allele will be provided, and the ratio should be approximately 66:33. Thus, the ratio for nucleotides at heterozygous SNPs can be used to detect the presence or absence of chromosomal abnormalities. Any chromosomal abnormality can be detected including aneuploidy, polyploidy, inversion, a trisomy, a monosomy, duplication, deletion, deletion of a part of a chromosome, addition, addition of a part of chromosome, insertion, a fragment of a chromosome, a region of a chromosome, chromosomal rearrangement, and translocation. The method is especially useful for the detection of trisomy 13, trisomy 18, trisomy 21, XXY, and XYY.

[0410] The present invention provides a method to quantitate a ratio for the alleles at a heterozygous locus of interest. The loci of interest include but are not limited to single nucleotide polymorphisms, mutations. There is no need to amplify the entire sequence of a gene or to quantitate the amount of a particular gene product. The present invention does not rely on quantitative PCR.

Detection of Fetal Chromosomal Abnormalities

[0411] As discussed above in the section entitled “DNA template,” the template DNA can be obtained from a sample of a pregnant female, wherein the template DNA comprises maternal template DNA and fetal template DNA. In one embodiment, the template DNA is obtained from the blood of a pregnant female. In a preferred embodiment, the template DNA is obtained from the plasma or serum from the blood of a pregnant female.

[0412] In one embodiment, the template DNA from the sample from the pregnant female comprises both maternal template DNA and fetal template DNA. In another embodiment, maternal template DNA is obtained from any nucleic acid containing source including but not limited to cell, tissue, blood, serum, plasma, saliva, urine, tears, vaginal secretion, lymph fluid, cerebrospinal fluid, mucosa secretion, peritoneal fluid, ascitic fluid, fecal matter, or body exudates, and sequenced to identify homozygous or heterozygous loci of interest, which are the loci of interest analyzed on the template DNA obtained from the sample from the pregnant female.

[0413] In a preferred embodiment, the sequence of the alleles of multiple loci of interest on maternal template DNA is determined to identify homozygous loci of interest. In another embodiment, the sequence of the alleles of multiple loci of interest on maternal template DNA is determined to identify heterozygous loci of interest. The sequence of the alleles of multiple loci of interest on maternal template DNA can be determined in a single reaction or in multiple reactions.

[0414] For example, if 100 maternal loci of interest on chromosome 21 and 100 maternal loci of interest on chromosome 1 are analyzed, one would predict approximately 50 loci of interest on each chromosome to be homozygous and 50 to be heterozygous. The 50 homozygous loci of interest, or the 50 heterozygous loci of interest or the 50 homozygous and 50 heterozygous loci of interest, or any combination of the homozygous and heterozygous loci of interest on each chromosome can be analyzed using the template DNA from the sample from the pregnant female.

[0415] The locus of interest on the template DNA from the sample of the pregnant female is analyzed using the amplification, isolation, digestion, fill in, and detection methods described above. The same primers used to analyze the locus of interest on the maternal template DNA are used to screen the template DNA from the sample from the pregnant female. Any number of loci of interest can be analyzed on the template DNA from the sample from the pregnant female. For example, 1, 1-5, 5-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, 150-200, 200-250, 250-300, 300-500, 500-1000, 1000-2000, 2000-3000, 3000-4000 or more than 4000 homozygous maternal loci of interest can be analyzed in the template DNA from the sample from the pregnant female. In a preferred embodiment, multiple loci of interest on multiple chromosomes are analyzed.

[0416] From the population of homozygous maternal loci of interest, there will be both heterozygous and homozygous loci of interest from the template DNA from the sample from the pregnant female; the heterozygous loci of interest can be further analyzed. At heterozygous loci of interest, the ratio of alleles can be used to determine the number of chromosomes that are present.

[0417] The percentage of fetal DNA present in the sample from the pregnant female can be calculated by determining the ratio of alleles at a heterozygous locus of interest on a chromosome that is not typically associated with a chromosomal abnormality. In a preferred embodiment, the ratio of alleles at multiple heterozygous loci of interest on a chromosome can be used to determine the percentage of fetal DNA. For example, chromosome 1, which is the largest chromosome in the human genome, can be used to determine the percentage of fetal DNA.

[0418] For example, suppose SNP X is homozygous at the maternal template DNA (A/A). At SNP X, the template DNA from the sample from the pregnant female, which can contain both fetal DNA and maternal DNA, is heterozygous (A/G). The nucleotide guanine represents the fetal DNA because at SNP X the mother is homozygous, and thus the guanine is attributed to the fetal DNA. The guanine at SNP X can be used to calculate the percentage of fetal DNA in the sample.

[0419] Alternatively, multiple loci of interest on two or more chromosomes can be examined to determine the percentage of fetal DNA. For example, multiple loci of interest can be examined on chromosomes 13, and 18 to determine the percentage of fetal DNA because organisms with chromosomal abnormalities at chromosome 13 and 18 are not viable.

[0420] Alternatively, for a male fetus, a marker on the Y chromosome can be used to determine the amount of fetal DNA present in the sample. A panel of serial dilutions can be made using the template DNA isolated from the sample from the pregnant female, and quantitative PCR analysis performed. Two PCR reactions can be performed: one PCR reaction to amplify a marker on the Y chromosome, for example SRY, and the other reaction to amplify a region on any of the autosomal chromosomes. The amount of fetal DNA can be calculated using the following formula:
Percent Fetal DNA:(last dilution Y chromosome detected/last dilution autosomal chromosome detected)*2*100.

[0421] If at SNP A, the mother is homozygous A/A, and the fetus is heterozygous A/G, then the ratio of A:G can be used to detect chromosomal abnormalities. If the fetal DNA is fifty percent (50%) of the DNA in the maternal blood, then at SNP A where the maternal nucleotide is an adenine and the other nucleotide is a guanine, one would expect the ratio of adenine (two adenines from the maternal template DNA and one from the fetal template DNA) to guanine (from the fetal template DNA) to be 25:75 or 0.33. However, if the fetus has a trisomy of this particular chromosome, and the additional chromosome is contributed by the mother, and thus an additional adenine nucleotide is present, then one would expect the ratio of 0.25 (50 (G)/(2*50 maternal A+2*50 fetal A). Thus, there is a difference of 8% between the ratio obtained from a chromosome present in two copies, and a chromosome present in a trisomy condition. On the other hand, if the additional chromosome is contributed by the father, and thus, an additional guanine is present, then one would expect the ratio of 0.66 (2*50 for G fetal allele/(2*50 maternal A allele+50 for fetal A allele).

[0422] However, if the fetal DNA is 40% of the DNA in the maternal blood, the expected ratio without a trisomy is 0.25 (40 for fetal G allele/2*60 for maternal A allele+1*60 for fetal A allele). If the fetus has a trisomy, and the additional chromosome is provided by the mother, the expected ratio would be 0.20 (40 for fetal G allele/(2*60 for maternal A allele+2*40 for fetal A allele). A 5% difference between the ratios obtained from a chromosome present in two copies and a chromosome present in the Trisomy condition is detected.

[0423] In another embodiment, multiple loci of interest on multiple chromosomes can be examined. The ratios for the alleles at each heterozygous locus of interest on a chromosome can be summed and compared to the ratios for the alleles at each locus of interest on a different chromosome. The chromosomes that are compared can be of human origin, and include but are not limited to chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, and Y. The ratio obtained from multiple chromosomes can be compared to the ratio obtained for a single chromosome or from multiple chromosomes.

[0424] In one embodiment, one of the chromosomes used in the comparison can be chromosome 13, 15, 16; 18, 21, 22, X or Y. In a preferred embodiment, the ratios on chromosomes 13, 18, and 21 are compared.

[0425] For example, assuming 40% fetal DNA in the sample from the pregnant female, the ratio of the alleles at a heterozygous locus of interest on chromosome 1 will be 0.25 (40 for fetal G allele/(2*60 for maternal A allele+40 for fetal A allele). Likewise, the ratio of alleles at a heterozygous locus of interest on chromosome 21 will be present in a ratio of 0.25. However, in a fetus with trisomy 21 where the additional chromosome is contributed by the mother, the nucleotides at a heterozygous locus of interest on chromosome 21 will be present in a ratio of 0.20 (40 for fetal G allele/(60*2 for maternal A allele+40*2 for fetal A allele). By contrast, the ratio for chromosome I will remain at 0.25, and thus the 5% difference in ratios will signify an additional chromosome. One to tens to hundreds to thousands of loci of interest can be analyzed.

[0426] In another embodiment, the loci of interest on the template DNA from the sample from the pregnant female can be genotyped without prior identification of the homozygous maternal loci of interest. It is not necessary to genotype the maternal template DNA prior to analysis of the template DNA containing both maternal and fetal template DNA.

[0427] The ratio of the alleles at the loci of interest can be used to determine the presence or absence of a chromosomal abnormality. The template DNA from the sample from the pregnant female contains both maternal template DNA and fetal template DNA. There are 3 possibilities at each SNP for either the maternal template DNA or the fetal template DNA: heterozygous, homozygous for allele 1, or homozygous for allele 2. The possible nucleotide ratios for a SNP that is either an adenine or a guanine are shown in Table II. The ratios presented in Table II are calculated with the fetal DNA at 50% of the DNA in the sample from the pregnant female.

[0428]

TABLE II
Ratios for nucleotides for a heterozygous SNP.
	Fetal SNP
Maternal SNP	A/A	G/G	A/G
A/A	100% A	N/A	75% A, 25% G
G/G	N/A	100% G	25% A, 75% G
A/G	75% A, 25% G	25% A, 75% G	50% A, 50% G

[0429] There are three nucleotide ratios: 100% of a single nucleotide, 50:50, or 75:25. These ratios will vary depending on the amount of fetal DNA present in sample from the pregnant female. However, the percentage of fetal DNA should be constant regardless of the chromosome analyzed. Therefore, if chromosomes are present in two copies, the above calculated ratios will be seen.

[0430] On the other hand, these percentages will vary when an additional chromosome is present. For example, assume that SNP X can be adenine or guanine, and that the percentage of fetal DNA in the sample from the pregnant female is 50%. Analysis of the loci of interest on chromosome I will provide the ratios discussed above: 100:0, 50:50, and 75:25. The possible ratios for a SNP that is A/G with an additional chromosome are provided in Table III.

[0431]

TABLE III
Nucleotides ratios at a SNP when an additional
copy of a chromosome is present
Maternal	Fetal SNP
SNPX	A/A/A	G/G/G	A/G/G	A/A/G
A/A	100% A	N/A	60% A, 40% G	80% A, 20% G
G/G	N/A	100% G	20% A, 80% G	40% A, 60% G
A/G	80% A,	20% A, 80% G	40% A, 60% G	60% A, 40% G
	20% G

[0432] The possible ratios for the alleles at a heterozygous SNP with an additional copy of a chromosome are: 0:100, 40:60, and 20:80. Two of these ratios, 40:60, and 20:80 differ from the ratios of alleles at heterozygous SNPs obtained with two copies of a chromosome. As discussed above, the ratios for the nucleotides at a heterozygous SNP depend on the amount of fetal DNA present in the sample. However, the ratios, whatever they are, will remain constant across chromosomes unless there is a chromosomal abnormality.

[0433] The ratio of alleles at heterozygous loci of interest on a chromosome can be compared to the ratio for alleles at heterozygous loci of interest on a different chromosome. For example, the ratio for multiple loci of interest on chromosome 1 (the ratio at SNP 1, SNP 2, SNP 3, SNP 4, etc.) can be compared to the ratio for multiple loci of interest on chromosome 21 (the ratio at SNP A, SNP B, SNP C, SNP D, etc.). Any chromosome can be compared to any other chromosome. There is no limit to the number of chromosomes that can be compared.

[0434] Referring back to the data in Tables II and III, the ratios for nucleotides at a heterozygous SNP on chromosome 1, which was present in two copies, were 25:75, and 50:50. On the other, the ratio for nucleotides at a heterozygous SNP on chromosome 21, which was present in three copies, were 40:60, and 20:80. The difference between these two ratios indicates a chromosomal abnormality. The ratios can be pre-calculated for the full range of varying degrees of fetal DNA present in the maternal serum. Tables II and III demonstrate that both maternal homozygous and heterozygous loci of interest can be used to detect the presence of a fetal chromosomal abnormality.

[0435] The above example illustrates how the ratios for nucleotides at heterozygous SNPs can be used to detect the presence of an additional chromosome. The same type of analysis can be used to detect chromosomal rearrangements, translocations, mini-chromosomes, duplications of regions of chromosomes, monosomies, deletions of regions of chromosomes, and fragments of chromosomes. The method does not require genotyping of the mother or the father, however, it may be done to reduce the number of SNPs that need to be analyzed with the plasma sample.

[0436] The present invention does not quantitate the amount of a fetal gene product, nor is the utility of the present invention limited to the analysis of genes found on the Y chromosome. The present invention does not merely rely on the detection of a paternally inherited nucleic acid, rather, the present invention provides a method that allows the ratio of maternal to fetal alleles at loci of interest, including SNPs, to be calculated.

[0437] In another embodiment, a single allele at a locus of interest can be used to determine the presence or absence of a chromosomal abnormality and detect a genetic disorder in the fetus. In a preferred embodiment, the maternal allele at a locus of interest is used to determine the presence or absence of a chromosomal abnormality in the fetus. The biological mother can be genotyped to identify a homozygous locus of interest. Likewise, the biological father can be genotyped to identify a homozygous locus of interest. The locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA. Any number of loci of interest can be analyzed including but not limited to 1, 1-5, 5-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, 150-200, 200-250, 250-300, 300-500, 500-1000, 1000-2000, 2000-3000, 3000-4000, 4000-8000, 8000-16000, 16000-32000 or greater than 32000 loci of interest.

[0438] In a preferred embodiment, the signal from the maternal genome and the fetal allele, which was inherited from the mother, at the locus of interest is quantitated. For example, if the 5′ overhang, which is generated after digestion with the type IIS enzyme, is filled in with a nucleotide that is fluorescently labeled, the intensity of the incorporated dye can be quantitated

[0439] Maternal Template DNA—Homozygous for Adenine

[0440]

Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

[0441] Paternal Template DNA—Homozygous for Cytosine

[0442]

Allele 1	5′ CCG	C*
	3′ GGC	G	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	C*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

Template DNA in the plasma—both maternal template DNA and fetal template DNA

[0443] Maternal Template DNA—Homozygous for Adenine

[0444]

Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

[0445] Fetal Template DNA—Heterozygous

[0446]

Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	ddC
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

[0447] The template DNA obtained from the plasma of the pregnant female is filled in with labeled ddATP, and unlabeled ddCTP (depicted as ddC above), ddGTP, and ddTTP. The plasma DNA contains two maternal adenine alleles, and one fetal adenine allele. By filling in with labeled ddATP and unlabeled ddCTP, only the maternal allele and the fetal allele inherited from the mother are detected. The paternal allele is not detected in this manner. The fill-in reactions can be performed as described in the Examples below.

[0448] A single locus of interest can be analyzed or multiple loci of interest. The intensity of the maternal allele at multiple loci of interest can be quantitated. An average can be calculated for a chromosome and compared to the average obtained for a different chromosome. For example, the average intensity of the maternal allele and the fetal allele inherited from the mother at chromosome 1 can be compared to the average intensity of the maternal allele and the fetal allele inherited from the mother at chromosomes 13, 18, or 21. In a preferred embodiment, chromosomes 13, 15, 18, 21, 22, X and Y, when applicable, are compared.

[0449] The signal from a locus of interest may be stronger than another locus of interest. However, there is no reason why the signal from the locus of interest on one chromosome would be stronger than the signal from the locus of interest on another chromosome. While the signal from various loci of interest may be variable, the variation should be seen across the genome. The average signal of the loci of interest should be the same when any chromosomes are compared.

[0450] The conditions of the PCR reaction can be optimized so that an equivalent amount of PCR product is produced. For example, the concentration of the primers, the concentration of nucleotides, and the number of cycles for each loci of interest can be optimized. In addition, the fill-in reactions can be done under conditions such that any increase in a specific allele can be detected. The fill-in reaction conditions can be optimized to detect any increase in the allele of interest including but not limited to the concentration of reagents, the time of the fill-in reaction, and the temperature of the reaction.

[0451] With a normal genetic karyotype, the signal at each locus of interest comprise signal from the maternal genome, and signal from the fetal allele, which was inherited from the mother. The percent of fetal DNA in the sample remains constant, regardless of the chromosome that is analyzed. For example, if at SNP X, the maternal genome is A/A, and the paternal genome is G/G, then the fetal genome will be A/G, and the fetal adenine allele will comprise a specified percentage of the signal from the adenine allele. If the percentage of fetal DNA is 20% in the maternal plasma, then the fetal adenine allele will contribute 20% of the signal for the adenine allele. The contribution of the fetal allele, which was inherited from the mother, will be constant for any locus of interest that is analyzed.

[0452] When there is a chromosomal abnormality, the signal from the maternal genome and the fetal allele, which was inherited from the mother, at the loci of interest will differ from the signal observed for other chromosomes. For example, with a Trisomy, the signal at the locus of interest will comprise the maternal genome and two fetal alleles, which were inherited from the mother. The signal from the loci of interest for the chromosome that is present in three copies will have the contribution of an additional fetal allele, which will alter the signal of the alleles at these loci of interest.

[0453] In another embodiment, a ratio can be calculated using a single allele and a standard DNA of known quantity. In a preferred embodiment, a ratio is calculated using the alleles of the maternal genome, and the fetal allele, which was inherited from the mother, and a standard DNA. The biological mother can be genotyped to identify a homozygous locus of interest. Likewise, the biological father can be genotyped to identify a homozygous locus of interest. The locus of interest wherein the maternal template DNA is homozygous for one allele and the paternal template DNA is homozygous for the other allele is analyzed using the template DNA obtained from the plasma of the mother, which contains both maternal and fetal template DNA.

[0454] In a preferred embodiment, the signal from the maternal genome and the fetal allele, which was inherited from the mother, at the locus of interest is quantitated. For example, if the 5′ overhang, which is generated after digestion with the type IIS enzyme, is filled in with a nucleotide that is fluorescently labeled, the intensity of the incorporated dye can be quantitated.

[0455] Template DNA in the Plasma—Both Maternal Template DNA and Fetal Template DNA

[0456] Maternal Template DNA—Homozygous for Adenine

[0457]

Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

[0458] Fetal Template DNA—Heterozygous

[0459]

Allele 1	5′ CCG	A*
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4
Allele 2	5′ CCG	ddC
	3′ GGC	T	G	T	G
Overhang position		1	2	3	4

[0460] The template DNA obtained from the plasma of the pregnant female is filled in with labeled ddATP, and unlabeled ddCTP (depicted as ddC above), ddGTP, and ddTTP. The plasma DNA contains two maternal adenine alleles, and one fetal adenine allele. By filling in with labeled ddATP and unlabeled ddCTP, only the maternal allele and the fetal allele inherited from the mother are detected.

[0461] A single locus of interest or multiple loci of interest can be analyzed. For each locus of interest, a DNA molecule is designed to migrate at about the same position as the locus of interest. In a preferred embodiment, the DNA molecule is of known quantity. A ratio is calculated using the alleles of the maternal genome and the fetal allele, which was inherited from the mother, and the DNA molecule designed to migrate at about the same position as the locus of interest. For example, if the locus of interest is designed to migrate at 30 base pairs, the DNA molecule can be designed to migrate at about 30 base pairs including but not limited to 20-25, 25-30, 30-35, 35-45, and greater than 45. The alleles of the maternal genome and the fetal allele, which was inherited from the mother, and the standard DNA molecule can be analyzed in the same reaction or can be analyzed in a separate reaction. The alleles of the maternal genome and the fetal allele, which was inherited from the mother, and the standard DNA molecule can be analyzed in the same lane of a gel or can be analyzed in separate lanes of a gel. The use of standard DNA molecules of known quantity, which are designed to migrate at the same position as the loci of interest, will correct for various factors including but not limited to the intensity of the bands relative to the location on the gel.

[0462] The ratio of multiple loci of interest on a chromosome can be quantitated, and an average calculated. The average can be compared to the average obtained for another chromosome. The ratio is used to indicate the presence or absence of a chromosomal abnormality. Analysis of the alleles of the maternal genome and the fetal allele also allows detection of single gene or multi-gene genetic disorders.

[0463] Any chromosome of any organism can be analyzed using the methods of the invention. For example, in humans, chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X or Y can be analyzed using the methods of the invention. The ratio for the alleles at a heterozygous locus of interest on any chromosome can be compared to the ratio for the alleles at a heterozygous locus of interest on any other chromosome.

[0464] Thus, the present invention provides a non-invasive technique, which is independent of fetal cell isolation, for rapid, accurate and definitive detection of chromosome abnormalities in a fetus. The present invention also provides a non-invasive method for determining the sequence of DNA from a fetus. The present invention can be used to detect any alternation in gene sequence as compared to the wild type sequence including but not limited to point mutation, reading frame shift, transition, transversion, addition, insertion, deletion, addition-deletion, frame-shift, missense, reverse mutation, and microsatellite alteration.

Detection of Fetal Chromosomal Abnormalities Using Short Tandem Repeats

[0465] Short tandem repeats (STRs) are short sequences of DNA, normally of 2-5 base pairs in length, which are repeated numerous times in a head-tail manner. Tandemly repeated DNA sequences are widespread throughout the human genome, and show sufficient variability among the individuals in a population. Minisatellites have core repeats with 9-80 base pairs.

[0466] In another embodiment, short tandem repeats can be used to detect fetal chromosomal abnormalities. Template DNA can be obtained from a nucleic acid containing sample including but not limited to cell, tissue, blood, serum, plasma, saliva, urine, tears, vaginal secretion, lymph fluid, cerebrospinal fluid, mucosa secretion, peritoneal fluid, ascitic fluid, fecal matter, or body exudates. In another embodiment, a cell lysis inhibitor is added to the nucleic acid containing sample. In a preferred embodiment, the template DNA is obtained from the blood of a pregnant female. In another embodiment, the template DNA is obtained from the plasma or serum from the blood of a pregnant female.

[0467] The template DNA obtained from the blood of the pregnant female will contain both fetal DNA and maternal DNA. The fetal DNA comprises STRs from the mother and the father. The variation in the STRs between the mother and father can be used to detect chromosomal abnormalities.

[0468] Primers can be designed to amplify short tandem repeats. Any method of amplification can be used including but not limited to polymerase chain reaction, self-sustained sequence reaction, ligase chain reaction, rapid amplification of cDNA ends, polymerase chain reaction and ligase chain reaction, Q-beta phage amplification, strand displacement amplification, and splice overlap extension polymerase chain reaction. In a preferred embodiment, PCR is used.

[0469] Any number of short tandem repeats can be analyzed including but not limited to 1-5, 5-10, 10-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-1000, and greater than 1000. The short tandem repeats can be analyzed in a single PCR reaction or in multiple PCR reactions. In a preferred embodiment, STRs from multiple chromosomes are analyzed.

[0470] After amplification, the PCR products can be analyzed by any number of methods including but not restricted to gel electrophoresis, and mass spectrometry. The template DNA from the pregnant female comprises STRs of maternal and paternal origin. The STRs of paternal origin represent the fetal DNA. The paternal and maternal STRs may be identical in length or the maternal and the paternal STRs may differ.

[0471] Heterozygous STRs are those of which the maternal and paternal differ in length. The amount of each PCR product can be quantitated for each heterozygous STR. With a normal number of chromosomes, the amount of each PCR product should be approximately equal. However, with an extra chromosome, one of the STR PCR products will be present at a greater amount.

[0472] For example, multiple STRs on chromosome 1 can be analyzed on the template DNA obtained from the blood of the pregnant female. Each STR, whether of maternal or paternal origin, should be present at approximately the same amount. Likewise, with two chromosome 21s, each STR should be present at approximately the same amount. However, with a trisomy 21, one of the STR PCR products, when the maternal and paternal differ in length (a heterozygous STR) should be present at a higher amount. The ratio for each heterozygous STR on one chromosome can be compared to the ratio for each heterozygous STR on a different chromosome, wherein a difference indicates the presence or absence of a chromosomal abnormality.

Kits

[0473] The methods of the invention are most conveniently practiced by providing the reagents used in the methods in the form of kits. A kit preferably contains one or more of the following components: written instructions for the use of the kit, appropriate buffers, salts, DNA extraction detergents, primers, nucleotides, labeled nucleotides, 5′ end modification materials, and if desired, water of the appropriate purity, confined in separate containers or packages, such components allowing the user of the kit to extract the appropriate nucleic acid sample, and analyze the same according to the methods of the invention. The primers that are provided with the kit will vary, depending upon the purpose of the kit and the DNA that is desired to be tested using the kit.

[0474] A kit can also be designed to detect a desired or variety of single nucleotide polymorphisms, especially those associated with an undesired condition or disease. For example, one kit can comprise, among other components, a set or sets of primers to amplify one or more loci of interest associated with Huntington's disease. Another kit can comprise, among other components, a set or sets of primers for genes associated with a predisposition to develop type I or type II diabetes. Still, another kit can comprise, among other components, a set or sets of primers for genes associated with a predisposition to develop heart disease. Details of utilities for such kits are provided in the “Utilities” section below.

Utilities

[0475] The methods of the invention can be used whenever it is desired to know the genotype of an individual. The method of the invention is especially useful for the detection of genetic disorders. The method of the invention is especially useful as a non-invasive technique for the detection of genetic disorders in a fetus. In a preferred embodiment, the method of the invention provides a method for identification of single nucleotide polymorphisms.

[0476] In a preferred embodiment, the method is useful for detecting chromosomal abnormalities including but not limited to trisomies, monosomies, duplications, deletions, additions, chromosomal rearrangements, translocations, and other aneuploidies. The method is especially useful for the detection of chromosomal abnormalities in a fetus.

[0477] In a preferred embodiment, the method of the invention provides a method for identification of the presence of a disease in a fetus, especially a genetic disease that arises as a result of the presence of a genomic sequence, or other biological condition that it is desired to identify in an individual for which it is desired to know the same. The identification of such sequence in the fetus based on the presence of such genomic sequence can be used, for example, to determine if the fetus is a carrier or to assess if the fetus is predisposed to developing a certain genetic trait, condition or disease. The method of the invention is especially useful in prenatal genetic testing of parents and child.

[0478] Examples of diseases that can be diagnosed by this invention are listed in Table IV.

[0479]

	TABLE IV
	Achondroplasia
	Adrenoleukodystrophy, X-Linked
	Agammaglobulinemia, X-Linked
	Alagille Syndrome
	Alpha-Thalassemia X-Linked Mental Retardation Syndrome
	Alzheimer Disease
	Alzheimer Disease, Early-Onset Familial
	Amyotrophic Lateral Sclerosis Overview
	Androgen Insensitivity Syndrome
	Angelman Syndrome
	Ataxia Overview, Hereditary
	Ataxia-Telangiectasia
	Becker Muscular Dystrophy also The Dystrophinopathies)
	Beckwith-Wiedemann Syndrome
	Beta-Thalassemia
	Biotinidase Deficiency
	Branchiootorenal Syndrome
	BRCA1 and BRCA2 Hereditary Breast/Ovarian Cancer
	Breast Cancer
	CADASIL
	Canavan Disease
	Cancer
	Charcot-Marie-Tooth Hereditary Neuropathy
	Charcot-Marie-Tooth Neuropathy Type 1
	Charcot-Marie-Tooth Neuropathy Type 2
	Charcot-Marie-Tooth Neuropathy Type 4
	Charcot-Marie-Tooth Neuropathy Type X
	Cockayne Syndrome
	Colon Cancer
	Contractural Arachnodactyly, Congenital
	Craniosynostosis Syndromes (FGFR-Related)
	Cystic Fibrosis
	Cystinosis
	Deafness and Hereditary Hearing Loss
	DRPLA (Dentatorubral-Pallidoluysian Atrophy)
	DiGeorge Syndrome (also 22q11 Deletion Syndrome)
	Dilated Cardiomyopathy, X-Linked
	Down Syndrome (Trisomy 21)
	Duchenne Muscular Dystrophy (also The Dystrophinopathies)
	Dystonia, Early-Onset Primary (DYT1)
	Dystrophinopathies, The
	Ehlers-Danlos Syndrome, Kyphoscoliotic Form
	Ehlers-Danlos Syndrome, Vascular Type
	Epidermolysis Bullosa Simplex
	Exostoses, Hereditary Multiple
	Facioscapulohumeral Muscular Dystrophy
	Factor V Leiden Thrombophilia
	Familial Adenomatous Polyposis (FAP)
	Familial Mediterranean Fever
	Fragile X Syndrome
	Friedreich Ataxia
	Frontotemporal Dementia with Parkinsonism-17
	Galactosemia
	Gaucher Disease
	Hemochromatosis, Hereditary
	Hemophilia A
	Hemophilia B
	Hemorrhagic Telangiectasia, Hereditary
	Hearing Loss and Deafness, Nonsyndromic, DFNA (Connexin 26)
	Hearing Loss and Deafness, Nonsyndromic, DFNB 1 (Connexin 26)
	Hereditary Spastic Paraplegia
	Hermansky-Pudlak Syndrome
	Hexosaminidase A Deficiency (also Tay-Sachs)
	Huntington Disease
	Hypochondroplasia
	Ichthyosis, Congenital, Autosomal Recessive
	Incontinentia Pigmenti
	Kennedy Disease (also Spinal and Bulbar Muscular Atrophy)
	Krabbe Disease
	Leber Hereditary Optic Neuropathy
	Lesch-Nyhan Syndrome Leukemias
	Li-Fraumeni Syndrome
	Limb-Girdle Muscular Dystrophy
	Lipoprotein Lipase Deficiency, Familial
	Lissencephaly
	Marfan Syndrome
	MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, and
	Stroke-Like Episodes)
	Monosomies
	Multiple Endocrine Neoplasia Type 2
	Multiple Exostoses, Hereditary Muscular Dystrophy, Congenital
	Myotonic Dystrophy
	Nephrogenic Diabetes Insipidus
	Neurofibromatosis 1
	Neurofibromatosis 2
	Neuropathy with Liability to Pressure Palsies, Hereditary
	Niemann-Pick Disease Type C
	Nijmegen Breakage Syndrome Norrie Disease
	Oculocutaneous Albinism Type 1
	Oculopharyngeal Muscular Dystrophy
	Ovarian Cancer
	Pallister-Hall Syndrome
	Parkin Type of Juvenile Parkinson Disease
	Pelizaeus-Merzbacher Disease
	Pendred Syndrome
	Peutz-Jeghers Syndrome Phenylalanine Hydroxylase Deficiency
	Prader-Willi Syndrome
	PROP 1-Related Combined Pituitary Hormone Deficiency (CPHD)
	Prostate Cancer
	Retinitis Pigmentosa
	Retinoblastoma
	Rothmund-Thomson Syndrome
	Smith-Lemli-Opitz Syndrome
	Spastic Paraplegia, Hereditary
	Spinal and Bulbar Muscular Atrophy (also Kennedy Disease)
	Spinal Muscular Atrophy
	Spinocerebellar Ataxia Type 1
	Spinocerebellar Ataxia Type 2
	Spinocerebellar Ataxia Type 3
	Spinocerebellar Ataxia Type 6
	Spinocerebellar Ataxia Type 7
	Stickler Syndrome (Hereditary Arthroophthalmopathy)
	Tay-Sachs (also GM2 Gangliosidoses)
	Trisomies
	Tuberous Sclerosis Complex
	Usher Syndrome Type I
	Usher Syndrome Type II
	Velocardiofacial Syndrome (also 22q11 Deletion Syndrome)
	Von Hippel-Lindau Syndrome
	Williams Syndrome
	Wilson Disease
	X-Linked Adrenoleukodystrophy
	X-Linked Agammaglobulinemia
	X-Linked Dilated Cardiomyopathy (also The Dystrophinopathies)
	X-Linked Hypotonic Facies Mental Retardation Syndrome

[0480] The method of the invention is useful for screening an individual at multiple loci of interest, such as tens, hundreds, or even thousands of loci of interest associated with a genetic trait or genetic disease by sequencing the loci of interest that are associated with the trait or disease state, especially those most frequently associated with such trait or condition. The invention is useful for analyzing a particular set of diseases including but not limited to heart disease, cancer, endocrine disorders, immune disorders, neurological disorders, musculoskeletal disorders, ophthalmologic disorders, genetic abnormalities, trisomies, monosomies, transversions, translocations, skin disorders, and familial diseases.

[0481] The method of the invention can also be used to confirm or identify the relationship of a DNA of unknown sequence to a DNA of known origin or sequence, for example, for use in, maternity or paternity testing, and the like.

[0482] Having now generally described the invention, the same will become better understood by reference to certain specific examples which are included herein for purposes of illustration only and are not intended to be limiting unless other wise specified.

[0483] The following examples are illustrative only and are not intended to limit the scope of the invention as defined by the claims.

[0484] DNA sequences were amplified by PCR, wherein the annealing step in cycle 1 was performed at a specified temperature, and then increased in cycle 2, and further increased in cycle 3 for the purpose of reducing non-specific amplification. The TM1 of cycle 1 of PCR was determined by calculating the melting temperature of the 3′ region, which anneals to the template DNA, of the second primer. For example, in FIG. 1B, the TM1 can be about the melting temperature of region “c.” The annealing temperature was raised in cycle 2, to TM2, which was about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer. For example, in FIG. 1C, the annealing temperature (TM2) corresponds to the melting temperature of region “b.” In cycle 3, the annealing temperature was raised to TM3, which was about the melting temperature of the entire sequence of the second primer. For example, in FIG. 1D, the annealing temperature (TM3) corresponds to the melting temperature of region “c”+region “d”. The remaining cycles of amplification were performed at TM3.

Preparation of Template DNA

[0485] The template DNA was prepared from a 5 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. Blood was collected from 36 volunteers. Template DNA was isolated from each blood sample using QIAamp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183). Following isolation, the template DNA from each of the 36 volunteers was pooled for further analysis.

Primer Design

[0486] The following four single nucleotide polymorphisms were analyzed: SNP HC21S00340, identification number as assigned by Human Chromosome 21 cSNP Database, (FIG. 3, lane 1) located on chromosome 21; SNP TSC 0095512 (FIG. 3, lane 2) located on chromosome 1, SNP TSC 0214366 (FIG. 3, lane 3) located on chromosome 1; and SNP TSC 0087315 (FIG. 3, lane 4) located on chromosome 1. The SNP Consortium Ltd database can be accessed at http://snp.cshl.org/, website address effective as of Feb. 14, 2002.

[0487] SNP HC21S00340 was amplified using the following primers:

[0488]

First primer:
5′ TAGAATAGCACTGAATTCAGGAATACAATCATTGTCAC 3′	(SEQ ID NO: 9)
Second primer:
5′ ATCACGATAAACGGCCAAACTCAGGTTA 3′	(SEQ ID NO: 10)

[0489] SNP TSC0095512 was amplified using the following primers:

[0490]

First primer:
5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′	(SEQ ID NO: 11)
Second primer:
5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′	(SEQ ID NO: 12)

[0491] SNP TSC0214366 was amplified using the following primers:

[0492]

First primer:
5′ ATGACTAGCTATGAATTCGTTCAAGGTAGAAAATGGAA 3′	(SEQ ID NO: 13)
Second primer:
5′ GAGAATTAGAACGGCCCAAATCCCACTC 3′	(SEQ ID NO: 14)

[0493] SNP TSC 0087315 was amplified using the following primers:

[0494]

First primer:
5′ TTACAATGCATGAATTCATCTTGGTCTCTCAAAGTGC 3′	(SEQ ID NO: 15)
Second primer:
5′ TGGACCATAAACGGCCAAAAACTGTAAG 3′.	(SEQ ID NO: 16)

[0495] All primers were designed such that the 3′ region was complementary to either the upstream or downstream sequence flanking each locus of interest and the 5′ region contained a restriction enzyme recognition site. The first primer contained a biotin tag at the 5′ end and a recognition site for the restriction enzyme EcoRI. The second primer contained the recognition site for the restriction enzyme BceA I.

PCR Reaction

[0496] All four loci of interest were amplified from the template genomic DNA using PCR (U.S. Pat. Nos. 4,683,195 and 4,683,202). The components of the PCR reaction were as follows: 40 ng of template DNA, 5 μM first primer, 5 μM second primer, 1× HotStarTaq Master Mix as obtained from Qiagen (Catalog No. 203443). The HotStarTaq Master Mix contained DNA polymerase, PCR buffer, 200 μM of each dNTP, and 1.5 mM MgCl₂.

[0497] Amplification of each template DNA that contained the SNP of interest was performed using three different series of annealing temperatures, herein referred to as low stringency annealing temperature, medium stringency annealing temperature, and high stringency annealing temperature. Regardless of the annealing temperature protocol, each PCR reaction consisted of 40 cycles of amplification. PCR reactions were performed using the HotStarTaq Master Mix Kit supplied by QIAGEN. As instructed by the manufacturer, the reactions were incubated at 95° C. for 15 min. prior to the first cycle of PCR. The denaturation step after each extension step was performed at 95° C. for 30 sec. The annealing reaction was performed at a temperature that permitted efficient extension without any increase in temperature.

[0498] The low stringency annealing reaction comprised three different annealing temperatures in each of the first three cycles. The annealing temperature for the first cycle was 37° C. for 30 sec.; the annealing temperature for the second cycle was 57° C. for 30 sec.; the annealing temperature for the third cycle was 64° C. for 30 sec. Annealing was performed at 64° C. for subsequent cycles until completion.

[0499] As shown in the photograph of the gel (FIG. 3A), multiple bands were observed after amplification of SNP TSC 0087315 (lane 4). Amplification of SNP HC21S00340 (lane 1), SNP TSC0095512 (lane 2), and SNP TSC0214366 (lane 3) generated a single band of high intensity and one band of faint intensity, which was of higher molecular weight. When the low annealing temperature conditions were used, the correct size product was generated and this was the predominant product in each reaction.

[0500] The medium stringency annealing reaction comprised three different annealing temperatures in each of the first three cycles. The annealing temperature for the first cycle was 40° C. for 30 seconds; the annealing temperature for the second cycle was 60° C. for 30 seconds; and the annealing temperature for the third cycle was 67° C. for 30 seconds. Annealing was performed at 67° C. for subsequent cycles until completion. Similar to what was observed under low stringency annealing conditions, amplification of SNP TSC0087315 (FIG. 3B, lane 4) generated multiple bands under conditions of medium stringency. Amplification of the other three SNPs (lanes 1-3) produced a single band. These results demonstrate that variable annealing temperatures can be used to cleanly amplify loci of interest from genomic DNA with a primer that has an annealing length of 13 bases.

[0501] The high stringency annealing reaction was comprised of three different annealing temperatures in each of the first three cycles. The annealing temperature of the first cycle was 46° C. for 30 seconds; the annealing temperature of the second cycle was 65° C. for 30 seconds; and the annealing temperature for the third cycle was 72° C. for 30 seconds. Annealing was performed at 72° C. for subsequent cycles until completion. As shown in the photograph of the gel (FIG. 3C), amplification of SNP TSC0087315 (lane 4) using the high stringency annealing temperatures generated a single band of the correct molecular weight. By raising the annealing temperatures for each of the first three cycles, non-specific amplification was eliminated. Amplification of SNP TSC0095512 (lane 2) generated a single band. SNPs HC21S00340 (lane 1), and TSC0214366 (lane 3) failed to amplify at the high stringency annealing temperatures, however, at the medium stringency annealing temperatures, these SNPs amplified as a single band. These results demonstrate that variable annealing temperatures can be used to reduce non-specific PCR products, as demonstrated for SNP TSC0087315 (FIG. 3, lane 4).

[0502] SNPs on chromosomes 1 (TSC0095512), 13 (TSC0264580), and 21 (HC21S00027) were analyzed. SNP TSC0095512 was analyzed using two different sets of primers, and SNP HC21S00027 was analyzed using two types of reactions for the incorporation of nucleotides.

Preparation of Template DNA

[0503] The template DNA was prepared from a 5 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. Template DNA was isolated using the QIAmp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183). The template DNA was isolated as per instructions included in the kit. Following isolation, template DNA from thirty-six human volunteers were pooled together and cut with the restriction enzyme EcoRI. The restriction enzyme digestion was performed as per manufacturer's instructions.

Primer Design

[0504] SNP HC21S00027 was amplified by PCR using the following primer set:

[0505]

First primer:
5′ ATAACCGTATGCGAATTCTATAATTTTCCTGATAAAGG 3′	(SEQ ID NO: 17)
Second primer:
5′ CTTAAATCAGGGGACTAGGTAAACTTCA 3′.	(SEQ ID NO: 18)

[0506] The first primer contained a biotin tag at the extreme 5′ end, and the nucleotide sequence for the restriction enzyme EcoRI. The second primer contained the nucleotide sequence for the restriction enzyme BsmF I (FIG. 4A).

[0507] Also, SNP HC21S00027 was amplified by PCR using the same first primer but a different second primer with the following sequence:

[0508]

Second primer:
5′ CTTAAATCAGACGGCTAGGTAAACTTCA 3′	(SEQ ID NO: 19)

[0509] This second primer contained the recognition site for the restriction enzyme BceA I (FIG. 4B).

[0510] SNP TSC0095512 was amplified by PCR using the following primers:

[0511]

First primer:
5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′	(SEQ ID NO: 11)
Second primer:
5′ TCTCCAACTAGGGACTCATCGAGTAAAG 3′.	(SEQ ID NO: 20)

[0512] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The second primer contained a restriction enzyme recognition site for BsmF I (FIG. 4C).

[0513] Also, SNP TSC0095512 was amplified using the same first primer and a different second primer with the following sequence:

[0514]

Second primer:
5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′	(SEQ ID NO: 12)

[0515] This second primer contained the recognition site for the restriction enzyme BceA I (FIG. 4D).

[0516] SNP TSC0264580, which is located on chromosome 13, was amplified with the following primers:

[0517]

First primer:
5′ AACGCCGGGCGAGAATTCAGTTTTTCAACTTGCAAGG 3′	(SEQ ID NO: 21)
Second primer:
5′ CTACACATATCTGGGACGTTGGCCATCC 3′.	(SEQ ID NO: 22)

[0518] The first primer contained a biotin tag at the extreme 5′ end and had a restriction enzyme recognition site for EcoRI. The second primer contained a restriction enzyme recognition site for BsmF I.

PCR Reaction

[0519] All loci of interest were amplified from the template genomic DNA using the polymerase chain reaction (PCR, U.S. Pat. Nos. 4,683,195 and 4,683,202, incorporated herein by reference). In this example, the loci of interest were amplified in separate reaction tubes but they could also be amplified together in a single PCR reaction. For increased specificity, a “hot-start” PCR was used. PCR reactions were performed using the HotStarTaq Master Mix Kit supplied by QIAGEN (catalog number 203443). The amount of template DNA and primer per reaction can be optimized for each locus of interest but in this example, 40 ng of template human genomic DNA and 5 μM of each primer were used. Forty cycles of PCR were performed. The following PCR conditions were used:

[0520] (1) 95° C. for 15 minutes and 15 seconds;

[0521] (2) 37° C. for 30 seconds;

[0522] (3) 95° C. for 30 seconds;

[0523] (4) 57° C. for 30 seconds;

[0524] (5) 95° C. for 30 seconds;

[0525] (6) 64° C. for 30 seconds;

[0526] (7) 95° C. for 30 seconds;

[0527] (8) Repeat steps 6 and 7 thirty nine (39) times;

[0528] (9) 72° C. for 5 minutes.

[0529] In the first cycle of PCR, the annealing temperature was about the melting temperature of the 3′ annealing region of the second primers, which was 37° C. The annealing temperature in the second cycle of PCR was about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer, which was 57° C. The annealing temperature in the third cycle of PCR was about the melting temperature of the entire sequence of the second primer, which was 64° C. The annealing temperature for the remaining cycles was 64° C. Escalating the annealing temperature from TM1 to TM2 to TM3 in the first three cycles of PCR greatly improves specificity. These annealing temperatures are representative, and the skilled artisan will understand the annealing temperatures for each cycle are dependent on the specific primers used.

[0530] The temperatures and times for denaturing, annealing, and extension, can be optimized by trying various settings and using the parameters that yield the best results. The PCR products for SNP HC21S00027 and SNP TSC095512 are shown in FIGS. 5A-5D.

Purification of Fragment of Interest

[0531] The PCR products were separated from the genomic template DNA. Each PCR product was divided into four separate reaction wells of a Streptawell, transparent, High-Bind plate from Roche Diagnostics GmbH (catalog number 1 645 692, as listed in Roche Molecular Biochemicals, 2001 Biochemicals Catalog). The first primers contained a 5′ biotin tag so the PCR products bound to the Streptavidin coated wells while the genomic template DNA did not. The streptavidin binding reaction was performed using a Thermomixer (Eppendorf) at 1000 rpm for 20 min. at 37° C. Each well was aspirated to remove unbound material, and washed three times with 1×PBS, with gentle mixing (Kandpal et al., Nucl. Acids Res. 18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., Nucl. Acids Res. 18:6163-6164 (1990)).

Restriction Enzyme Digestion of Isolated Fragments

[0532] The purified PCR products were digested with the restriction enzyme that bound the recognition site incorporated into the PCR products from the second primer. SNP HC21S00027 (FIGS. 6A and 6B) and SNP TSC0095512 (FIGS. 6C and 6D) were amplified in separate reactions using two different second primers. FIG. 6A (SNP HC21S00027) and FIG. 6C(SNP TSC0095512) depict the PCR products after digestion with the restriction enzyme BsmF I (New England Biolabs catalog number R0572S). FIG. 6B (SNP HC21S00027) and FIG. 6D (SNP TSC0095512) depict the PCR products after digestion with the restriction enzyme BceA I (New England Biolabs, catalog number R0623 S). The digests were performed in the Streptawells following the instructions supplied with the restriction enzyme. SNP TSC0264580 was digested with BsmF I. After digestion with the appropriate restriction enzyme, the wells were washed three times with PBS to remove the cleaved fragments.

Incorporation of Labeled Nucleotide

[0533] The restriction enzyme digest described above yielded a DNA fragment with a 5′ overhang, which contained the SNP site or locus of interest and a 3′ recessed end. The 5′ overhang functioned as a template allowing incorporation of a nucleotide or nucleotides in the presence of a DNA polymerase.

[0534] For each SNP, four separate fill in reactions were performed; each of the four reactions contained a different fluorescently labeled dideoxynucleotide (ddATP, ddCTP, ddGTP, or ddTTP). The following components were added to each fill in reaction: 1 μl of a fluorescently labeled dideoxynucleotide, 0.5 μl of unlabeled ddNTPs (40 μM), which contained all nucleotides except the nucleotide that was fluorescently labeled, 2 μl of 10× sequenase buffer, 0.25 μl of Sequenase, and water as needed for a 20 μl reaction. All of the fill in reactions were performed at 40° C. for 10 min. Non-fluorescently labeled nucleotides was purchased from Fermentas Inc. (Hanover, Md.). All other labeling reagents were obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565). In the presence of fluorescently labeled ddNTPs, the 3′ recessed end was extended by one base, which corresponds to the SNP or locus of interest (FIG. 7A-7D).

[0535] A mixture of labeled ddNTPs and unlabeled dNTPs also was used for the “fill in” reaction for SNP HC21S00027. The “fill in” conditions were as described above except that a mixture containing 40 μM unlabeled dNTPs, 1 μl fluorescently labeled ddATP, 1 μl fluorescently labeled ddCTP, 1 μl fluorescently labeled ddGTP, and 1 μl ddTTP was used. The fluorescent ddNTPs were obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565; Amersham did not publish the concentrations of the fluorescent nucleotides). SNP HC21S00027 was digested with the restriction enzyme BsmF I, which generated a 5′ overhang of four bases. As shown in FIG. 7E, if the first nucleotide incorporated is a labeled dideoxynucleotide, the 3′ recessed end is filled in by one base, allowing detection of the SNP or locus of interest. However, if the first nucleotide incorporated is a dNTP, the polymerase continues to incorporate nucleotides until a ddNTP is filled in. For example, the first two nucleotides can be filled in with dNTPs, and the third nucleotide with a ddNTP, allowing detection of the third nucleotide in the overhang. Thus, the sequence of the entire 5′ overhang can be determined, which increases the information obtained from each SNP or locus of interest.

[0536] After labeling, each Streptawell was rinsed with 1×PBS (100 μl) three times. The “filled in” DNA fragments were then released from the Streptawells by digestion with the restriction enzyme EcoRI, according to the manufacturer's instructions that were supplied with the enzyme (FIGS. 8A-8D). Digestion was performed for 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

[0537] After release from the streptavidin matrix, 2-3 μl of the 10 μl sample was loaded in a 48 well membrane tray (The Gel Company, catalog number TAM48-01). The sample in the tray was absorbed with a 48 Flow Membrane Comb (The Gel Company, catalog number AM48), and inserted into a 36 cm 5% acrylamide (urea) gel (BioWhittaker Molecular Applications, Long Ranger Run Gel Packs, catalog number 50691).

[0538] The sample was electrophoresed into the gel at 3000 volts for 3 min. The membrane comb was removed, and the gel was run for 3 hours on an ABI 377 Automated Sequencing Machine. The incorporated labeled nucleotide was detected by fluorescence.

[0539] As shown in FIG. 9A, from a sample of thirty six (36) individuals, one of two nucleotides, either adenosine or guanine, was detected at SNP HC21S00027. These are the two nucleotides reported to exist at SNP HC21S00027 (http://snp.cshl.org/snpsearch.shtml).

[0540] One of two nucleotides, either guanine or cytosine, was detected at SNP TS00095512 (FIG. 9B). The same results were obtained whether the locus of interest was amplified with a second primer that contained a recognition site for BceA I or the second primer contained a recognition site for BsmF I.

[0541] As shown in FIG. 9C, one of two nucleotides was detected at SNP TSC0264580, which was either adenosine or cytosine. These are the two nucleotides reported for this SNP site (http://snp.cshl.org/snpsearch.shtml). In addition, a thymidine was detected one base from the locus of interest. In a sequence dependent manner, BsmF I cuts some DNA molecules at the 10/14 position and other DNA molecules, which have the same sequence, at the 11/15 position. When the restriction enzyme BsmF I cuts 11 nucleotides away on the sense strand and 15 nucleotides away on the antisense strand, the 3′ recessed end is one base from the SNP site. The sequence of SNP TSC0264580 indicated that the base immediately preceding the SNP site was a thymidine. The incorporation of a labeled ddNTP into this position generated a fragment one base smaller than the fragment that was cut at the 10/14 position. Thus, the DNA molecules cut at the 11/15 position provided sequence information about the base immediately preceding the SNP site, and the DNA molecules cut at the 10/14 position provided sequence information about the SNP site.

[0542] SNP HC21S00027 was amplified using a second primer that contained the recognition site for BsmF I. A mixture of labeled ddNTPs and unlabeled dNTPs was used to fill in the 5′ overhang generated by digestion with BsmF I. If a dNTP was incorporated, the polymerase continued to incorporate nucleotides until a ddNTP was incorporated. A population of DNA fragments, each differing by one base, was generated, which allowed the full sequence of the overhang to be determined.

[0543] As seen in FIG. 9D, an adenosine was detected, which was complementary to the nucleotide (a thymidine) immediately preceding the SNP or locus of interest. This nucleotide was detected because of the 11/15 cutting property of BsmF I, which is described in detail above. A guanine and an adenosine were detected at the SNP site, which are the two nucleotides reported for this SNP site (FIG. 9A). The two nucleotides were detected at the SNP site because the molecular weights of the dyes differ, which allowed separation of the two nucleotides. The next nucleotide detected was a thymidine, which is complementary to the nucleotide immediately downstream of the SNP site. The next nucleotide detected was a guanine, which was complementary to the nucleotide two bases downstream of the SNP site. Finally, an adenosine was detected, which was complementary to the third nucleotide downstream of the SNP site. Sequence information was obtained not only for the SNP site but for the nucleotide immediately preceding the SNP site and the next three nucleotides.

[0544] None of the loci of interest contained a mutation. However, if one of the loci of interest harbored a mutation including but not limited to a point mutation, insertion, deletion, translocation or any combination of said mutations, it could be identified by comparison to the consensus or published sequence. Comparison of the sequences attributed to each of the loci of interest to the native, non-disease related sequence of the gene at each locus of interest determines the presence or absence of a mutation in that sequence. The finding of a mutation in the sequence is then interpreted as the presence of the indicated disease, or a predisposition to develop the same, as appropriate, in that individual. The relative amounts of the mutated vs. normal or non-mutated sequence can be assessed to determine if the subject has one or two alleles of the mutated sequence, and thus whether the subject is a carrier, or whether the indicated mutation results in a dominant or recessive condition.

[0545] Four loci of interest from chromosome 1 and two loci of interest from chromosome 21 were amplified in separate PCR reactions, pooled together, and analyzed. The primers were designed so that each amplified locus of interest was a different size, which allowed detection of the loci of interest.

Preparation of Template DNA

[0546] The template DNA was prepared from a 5 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. Template DNA was isolated using the QIAmp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183). The template DNA was isolated as per instructions included in the kit. Template DNA was isolated from thirty-six human volunteers, and then pooled into a single sample for further analysis.

Primer Design

[0547] SNP TSC 0087315 was amplified using the following primers:

[0548]

First primer:
5′ TTACAATGCATGAATTCATCTTGGTCTCTCAAAGTGC 3′	(SEQ ID NO: 15)
Second primer:
5′ TGGACCATAAACGGCCAAAAACTGTAAG 3′.	(SEQ ID NO: 16)

[0549] SNP TSC0214366 was amplified using the following primers:

[0550]

First primer:
5′ ATGACTAGCTATGAATTCGTTCAAGGTAGAAAATGGAA 3′	(SEQ ID NO: 13)
Second primer:
5′ GAGAATTAGAACGGCCCAAATCCCACTC 3′	(SEQ ID NO: 14)

[0551] SNP TSC 0413944 was amplified with the following primers:

[0552]

First primer:
5′ TACCTTTTGATCGAATTCAAGGCCAAAAATATTAAGTT 3′	(SEQ ID NO: 23)
Second primer:
5′ TCGAACTTTAACGGCCTTAGAGTAGAGA 3′	(SEQ ID NO: 24)

[0553] SNP TSC0095512 was amplified using the following primers:

[0554]

First primer:
5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′	(SEQ ID NO: 11)
Second primer:
5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′	(SEQ ID NO: 12)

[0555] SNP HC21S00131 was amplified with the following primers:

[0556]

First primer:
5′ CGATTTCGATAAGAATTCAAAAGCAGTTCTTAGTTCAG 3′	(SEQ ID NO: 25)
Second primer:
5′ TGCGAATCTTACGGCTGCATCACATTCA 3′	(SEQ ID NO: 26)

[0557] SNP HC21S00027 was amplified with the following primers:

[0558]

First primer:
5′ ATAACCGTATGCGAATTCTATAATTTTCCTGATAAAGG 3′	(SEQ ID NO: 17)
Second primer:
5′ CTTAAATCAGACGGCTAGGTAAACTTCA 3′	(SEQ ID NO: 19)

[0559] For each SNP, the first primer contained a recognition site for the restriction enzyme EcoRI and had a biotin tag at the extreme 5′ end. The second primer used to amplify each SNP contained a recognition site for the restriction enzyme BceA I.

PCR Reaction

[0560] The PCR reactions were performed as described in Example 2 except that the following annealing temperatures were used: the annealing temperature for the first cycle of PCR was 37° C. for 30 seconds, the annealing temperature for the second cycle of PCR was 57° C. for 30 seconds, and the annealing temperature for the third cycle of PCR was 64° C. for 30 seconds. All subsequent cycles had an annealing temperature of 64° C. for 30 seconds. Thirty seven (37) cycles of PCR were performed. After PCR, ¼ of the volume was removed from each reaction, and combined into a single tube.

Purification of Fragment of Interest

[0561] The PCR products (now combined into one sample, and referred to as “the sample”) were separated from the genomic template DNA as described in Example 2 except that the sample was bound to a single well of a Streptawell microtiter plate.

Restriction Enzyme Digestion of Isolated Fragments

[0562] The sample was digested with the restriction enzyme BceA I, which bound the recognition site in the second primer. The restriction enzyme digestions were performed following the instructions supplied with the enzyme. After the restriction enzyme digest, the wells were washed three times with 1×PBS.

Incorporation of Nucleotides

[0563] The restriction enzyme digest described above yielded DNA molecules with a 5′ overhang, which contained the SNP site or locus of interest and a 3′ recessed end. The 5′ overhang functioned as a template allowing incorporation of a nucleotide in the presence of a DNA polymerase.

[0564] The following components were used for the fill in reaction: 1 μl of fluorescently labeled ddATP; 1 μl of fluorescently labeled ddTTP; 1 μl of fluorescently labeled ddGTP; 1 μl of fluorescently labeled ddCTP; 2 μl of 10× sequenase buffer, 0.25 μl of Sequenase, and water as needed for a 20 μl reaction. The fill in reaction was performed at 40° C. for 10 min. All labeling reagents were obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit (US 79565); the concentration of the ddNTPS provided in the kit is proprietary and not published by Amersham). In the presence of fluorescently labeled ddNTPs, the 3′ recessed end was filled in by one base, which corresponds to the SNP or locus of interest.

[0565] After the incorporation of nucleotide, the Streptawell was rinsed with 1×PBS (100 μl) three times. The “filled in” DNA fragments were then released from the Streptawell by digestion with the restriction enzyme EcoRI following the manufacturer's instructions. Digestion was performed for 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

[0566] After release from the streptavidin matrix, 2-3 μl of the 10 μl sample was loaded in a 48 well membrane tray (The Gel Company, catalog number TAM48-01). The sample in the tray was absorbed with a 48 Flow Membrane Comb (The Gel Company, catalog number AM48), and inserted into a 36 cm 5% acrylamide (urea) gel (BioWhittaker Molecular Applications, Long Ranger Run Gel Packs, catalog number 50691).

[0567] The sample was electrophoresed into the gel at 3000 volts for 3 min. The membrane comb was removed, and the gel was run for 3 hours on an ABI 377 Automated Sequencing Machine. The incorporated nucleotide was detected by fluorescence.

[0568] The primers were designed so that each amplified locus of interest differed in size. As shown in FIG. 10, each amplified loci of interest differed by about 5-10 nucleotides, which allowed the loci of interest to be separated from one another by gel electrophoresis. Two nucleotides were detected for SNP TSC0087315, which were guanine and cytosine. These are the two nucleotides reported to exist at SNP TSC0087315 (http://snp.cshl.org/snpsearch.shtml). The sample comprised template DNA from 36 individuals and because the DNA molecules that incorporated a guanine differed in molecular weight from those that incorporated a cytosine, distinct bands were seen for each nucleotide.

[0569] Two nucleotides were detected at SNP HC21S00027, which were guanine and adenosine (FIG. 10). The two nucleotides reported for this SNP site are guanine and adenosine (http://snp.cshl.org/snpsearch.shtml). As discussed above, the sample contained template DNA from thirty-six individuals, and one would expect both nucleotides to be represented in the sample. The molecular weight of the DNA fragments that incorporated a guanine was distinct from the DNA fragments that incorporated an adenosine, which allowed both nucleotides to be detected.

[0570] The nucleotide cytosine was detected at SNP TSC0214366 (FIG. 10). The two nucleotides reported to exist at this SNP position are thymidine and cytosine.

[0571] The nucleotide guanine was detected at SNP TSC0413944 (FIG. 10). The two nucleotides reported for this SNP are guanine and cytosine (http://spp.cshl.org/snpsearch.shtml).

[0572] The nucleotide cytosine was detected at SNP TS00095512 (FIG. 10). The two nucleotides reported for this SNP site are guanine and cytosine (http://snp.cshl.org/snpsearch.shtml).

[0573] The nucleotide detected at SNP HC21S00131 was guanine. The two nucleotides reported for this SNP site are guanine and adenosine (http://snp.cshl.org/snpsearch.shtml).

[0574] As discussed above, the sample was comprised of DNA templates from thirty-six individuals and one would expect both nucleotides at the SNP sites to be represented. For SNP TSC0413944, TSC0095512, TSC0214366 and HC21S00131, one of the two nucleotides was detected. It is likely that both nucleotides reported for these SNP sites are present in the sample but that one fluorescent dye overwhelms the other. The molecular weight of the DNA molecules that incorporated one nucleotide did not allow efficient separation of the DNA molecules that incorporated the other nucleotide. However, the SNPs were readily separated from one another, and for each SNP, a proper nucleotide was incorporated. The sequences of multiple loci of interest from multiple chromosomes, which were treated as a single sample after PCR, were determined.

[0575] A single reaction containing fluorescently labeled ddNTPs was performed with the sample that contained multiple loci of interest. Alternatively, four separate fill in reactions can be performed where each reaction contains one fluorescently labeled nucleotide (ddATP, ddTTP, ddGTP, or ddCTP) and unlabeled ddNTPs (see Example 2, FIGS. 7A-7D and FIGS. 9A-C). Four separate “fill in” reactions will allow detection of any nucleotide that is present at the loci of interest. For example, if analyzing a sample that contains multiple loci of interest from a single individual, and said individual is heterozygous at one or more than one loci of interest, four separate “fill in” reactions can be used to determine the nucleotides at the heterozygous loci of interest.

[0576] Also, when analyzing a sample that contains templates from multiple individuals, four separate “fill in” reactions will allow detection of nucleotides present in the sample, independent of how frequent the nucleotide is found at the locus of interest. For example, if a sample contains DNA templates from 50 individuals, and 49 of the individuals have a thymidine at the locus of interest, and one individual has a guanine, the performance of four separate “fill in” reactions, wherein each “fill in” reaction is run in a separate lane of a gel, such as in FIGS. 9A-9C, will allow detection of the guanine. When analyzing a sample comprised of multiple DNA templates, multiple “fill in” reactions will alleviate the need to distinguish multiple nucleotides at a single site of interest by differences in mass.

[0577] In this example, multiple single nucleotide polymorphisms were analyzed. It is also possible to determine the presence or absence of mutations, including but not limited to point mutations, transitions, transversions, translocations, insertions, and deletions from multiple loci of interest. The multiple loci of interest can be from a single chromosome or from multiple chromosomes. The multiple loci of interest can be from a single gene or from multiple genes.

[0578] The sequence of multiple loci of interest that cause or predispose to a disease phenotype can be determined. For example, one could amplify one to tens to hundreds to thousands of genes implicated in cancer or any other disease. The primers can be designed so that each amplified loci of interest differs in size. After PCR, the amplified loci of interest can be combined and treated as a single sample. Alternatively, the multiple loci of interest can be amplified in one PCR reaction or the total number of loci of interest, for example 100, can be divided into samples, for example 10 loci of interest per PCR reaction, and then later pooled. As demonstrated herein, the sequence of multiple loci of interest can be determined. Thus, in one reaction, the sequence of one to ten to hundreds to thousands of genes that predispose or cause a disease phenotype can be determined.

[0579] The ability to determine the sequence or detect chromosomal abnormalities of a fetus using free fetal DNA in a sample from a pregnant female has been hindered by the low percentage of free fetal DNA. Increasing the percentage of free fetal DNA would enhance the detection of mutation, insertion, deletion, translocation, transversion, monosomy, trisomy, trisomy 21, trisomy 18, trisomy 13, XXY, XXX, other aneuoplodies, deletion, addition, amplification, translocation and rearrangement. The percent of fetal DNA in plasma obtained from a pregnant female was determined both in the absence and presence of inhibitors of cell lysis. A genetic marker on the Y chromosome was used to calculate the percent of fetal DNA.

Preparation of Template DNA

[0580] The DNA template was prepared from a 5 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. The blood was aliquoted into two tubes (Fischer Scientific, 9 ml EDTA Vacuette tubes, catalog number NC9897284). Formaldehyde (25 μl/ml of blood) was added to one of the tubes. The sample in the other tube remained untreated, except for the presence of the EDTA. The tubes were spun at 1000 rpm for ten minutes. Two milliliters of the supernatant (the plasma) of each sample was transferred to a new tube and spun at 3000 rpm for ten minutes. 800 μl of each sample was used for DNA purification. DNA was isolated using the Qiagen Midi Kit for purification of DNA from blood cells (QIAmp DNA Blood Midi Kit, Catalog number 51183). DNA was eluted in 100 μl of distilled water. Two DNA templates were obtained: one from the blood sample treated with EDTA, and one from the blood sample treated with EDTA and formaldehyde.

Primer Design

[0581] Two different sets of primers were used: one primer set was specific for the Y chromosome, and thus specific for fetal DNA, and the other primer set was designed to amplify the cystic fibrosis gene, which is present on both maternal template DNA and fetal template DNA.

[0582] In this example, the first and second primers were designed so that the entire 5′ and 3′ sequence of each primer annealed to the template DNA. In this example, the fetus had an XY genotype, and the Y chromosome was used as a marker for the presence of fetal DNA. The following primers were designed to amplify the SRY gene on the Y chromosome.

[0583]

First primer:
5′ TGGCGATTAAGTCAAATTCGC 3′	(SEQ ID NO: 263)
Second primer:
5 CCCCCTAGTACCCTGACAATGTATT 3′	(SEQ ID NO: 264)

[0584] Primers designed to amplify any gene, or region of a region, or any part of any chromosome could be used to detect maternal and fetal DNA. In this example, the following primers were designed to amplify the cystic fibrosis gene:

[0585]

First primer:
5′ CTGTTCTGTGATATTATGTGTGGT 3′	(SEQ ID NO: 265)
Second primer:
5′ AATTGTTGGCATTCCAGCATTG 3′	(SEQ ID NO: 266)

PCR Reaction

[0586] The SRY gene and the cystic fibrosis gene were amplified from the template genomic DNA using PCR (U.S. Pat. Nos. 4,683,195 and 4,683,202). For increased specificity, a “hot-start” PCR was used. PCR reactions were performed using the HotStarTaq Master Mix Kit supplied by Qiagen (Catalog No. 203443). For amplification of the SRY gene, the DNA eluted from the Qiagen purification column was diluted serially 1:2. For amplification of the cystic fibrosis gene, the DNA from the Qiagen purification column was diluted 1:4, and then serially diluted 1:2. The following components were used for each PCR reaction: 8 μl of template DNA (diluted or undiluted), 1 μl of each primer (5 μM), 10 μl of HotStar Taq mix. The following PCR conditions were used:

[0587] (1) 950 C for 15′

[0588] (2) 94° C. for 1′

[0589] (3) 54° C. for 15″

[0590] (4) 72° C. for 30″

[0591] (5) Repeat steps 2-4 for 45 cycles.

[0592] (6) 10′ at 72° C.

Quantification of Fetal DNA

[0593] The DNA templates that were eluted from the Qiagen columns were serially diluted to the following concentrations: 1:2, 1:4, 1:8, 1:16, 1:32, 1:64, 1:128, 1:256, 1:512, 1:1024, 1:2048, and 1:4096. Amplification of the SRY gene was performed using the templates that were undiluted, 1:2, 1:4, 1:8, 1:16, 1:32, 1:64, 1:128, 1:256, 1:512. Amplification of the cystic fibrosis gene was performed using the DNA templates that were diluted 1:4, 1:8, 1:16, 1:32, 1:64, 1:128, 1:256, 1:512, 1:1024, 1:2048, and 1:4096. The same dilution series was performed with the DNA templates that were purified from the plasma sample treated with EDTA alone and the plasma sample treated with EDTA and formaldehyde.

[0594] The results of the PCR reactions using the DNA template that was isolated from the plasma sample treated with EDTA are shown in FIG. 11A. The SRY gene was amplified from the undiluted DNA template, and also in the sample that was diluted 1:2 (FIG. 11A). The SRY gene was not amplified in the next seven serial dilutions. On the other hand, the cystic fibrosis gene was detected in the serial dilutions up to 1:256. A greater presence of the cystic fibrosis gene was expected because of the higher percentage of maternal DNA present in the plasma. The last dilution sample that provided for amplification of the gene product was assumed to have one copy of the cystic fibrosis gene or the SRY gene.

[0595] The results of the PCR reactions using the DNA template that was isolated from the plasma sample treated with formaldehyde and EDTA are shown in FIG. 11B. The SRY gene was amplified from the undiluted DNA template, and also in the sample that was diluted 1:2 (FIG. 11B). The SRY gene was not amplified in the next six dilutions. However, in the 1:256 dilution, the SRY gene was detected. It is unlikely that the amplification in the 1:256 sample represents a real signal because the prior six dilution series were all negative for amplification of SRY. Amplification of the SRY gene in this sample was likely an experimental artifact resulting from the high number of PCR cycles used. Thus, the 1:256 sample was not used in calculating the amount of fetal DNA present in the sample.

[0596] Amplification of the cystic fibrosis gene was detected in the sample that was diluted 1:16 (FIG. 11B). The presence of the formalin prevents maternal cell lysis, and thus, there is a lower percentage of maternal DNA in the sample. This is in strong contrast to the sample that was treated with only EDTA, which supported amplification up to a dilution of 1:256.

[0597] The percent of fetal DNA present in the maternal plasma was calculated using the following formula:
% fetal DNA=(amount of SRY gene/amount of cystic fibrosis gene)*2*100.

[0598] The amount of SRY gene was represented by the highest dilution value in which the gene was amplified. Likewise, the amount of cystic fibrosis gene was represented by the highest dilution value in which it was amplified. The formula contains a multiplication factor of two (2), which is used to normalize for the fact that there is only one copy of the SRY gene (located on the Y chromosome), while there are two copies of the cystic fibrosis gene.

[0599] For the above example, the percentage of fetal DNA present in the sample that was treated with only EDTA was 1.56% (2/256*2*100). The reported percentage of fetal DNA present in the plasma is between 0.39-11.9% (Pertl and Bianchi, Obstetrics and Gynecology, Vol. 98, No. 3, 483-490 (2001). The percentage of fetal DNA present in the sample treated with formalin and EDTA was 25% (2/16*2*100). The experiment was repeated numerous times, and each time the presence of formalin increased the overall percentage of fetal DNA.

[0600] The percent fetal DNA from eighteen blood samples with and without formalin was calculated as described above with the exception that serial dilutions of 1:5 were performed. As 1:5 dilutions were performed, the last serial dilution that allowed detection of either the SRY gene or the cystic fibrosis gene may have had one copy of the gene or it may have had 4 copies of the gene. The results from the eighteen samples with and without formalin are summarized in Table V. The low range assumes that the last dilution sample had one copy of the genes and the high range assumes that the last dilution had four copies of the genes.

[0601]

TABLE V
Mean Percentage Fetal DNA with and without formalin.
	Sample	Lower Range	Upper Range
	Formalin	19.47	43.69
	Without Formalin	7.71	22.1

[0602] An overall increase in fetal DNA was achieved by reducing the maternal cell lysis, and thus, reducing the amount of maternal DNA present in the sample. In this example, formaldehyde was used to prevent lysis of the cells, however any agent that prevents the lysis of cells or increases the structural integrity of the cells can be used. Two or more than two cell lysis inhibitors can be used. The increase in fetal DNA in the maternal plasma allows the sequence of the fetal DNA to be determined, and provides for the rapid detection of abnormal DNA sequences or chromosomal abnormalities including but not limited to point mutation, reading frame shift, transition, transversion, addition, insertion, deletion, addition-deletion, frame-shift, missense, reverse mutation, and microsatellite alteration, trisomy, monosomy, other aneuploidies, amplification, rearrangement, translocation, transversion, deletion, addition, amplification, fragment, translocation, and rearrangement.

[0603] A DNA template from an individual with a genotype of trisomy 21 was analyzed. Three loci of interest were analyzed on chromosome 13 and two loci of interest were analyzed on chromosome 21.

Preparation of Template DNA

[0604] The template DNA was prepared from a 5 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. The human volunteer had previously been genotyped to have an additional chromosome 21 (trisomy 21). Template DNA was isolated using QIAamp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183).

Primer Design

[0605] The following five single nucleotide polymorphisms were analyzed: SNP TSC 0115603 located on chromosome 21; SNP TSC 03209610 located on chromosome 21; SNP TSC 0198557 located on chromosome 13; and SNP TSC 0200347 located on chromosome 13. The DNA template from another individual was used as an internal control. The SNP TSC 0200347, which was previously identified as being homozygous for guanine, was used as the internal control. The SNP Consortium Ltd database can be accessed at http://snp.cshl.org/, website address effective as of Apr. 1, 2002.

[0606] SNP TSC 0115603 was amplified using the following primers:

[0607]

First Primer:
5′ GTGCACTTACGTGAATTCAGATGAACGTGATGTAGTAG 3′	(SEQ ID NO: 267)
Second Primer:
5′ TCCTCGTACTCAACGGCTTTCTCTGAAT 3′	(SEQ ID NO: 268)

[0608] The first primer was biotinylated at the 5′ end, and contained the restriction enzyme recognition site for EcoR I. The second primer contained the restriction enzyme recognition site for the restriction enzyme BceA I.

[0609] SNP TSC 0309610 was amplified using the following primers:

[0610]

First primer:
5′ TCCGGAACACTAGAATTCTTATTTACATACACACTTGT 3′	(SEQ ID NO: 269)
Second primer:
5′ CGAATAAGGTAGACGGCAACAATGAGAA 3′	(SEQ ID NO: 270)

[0611] The first primer contained a biotin group at the 5′ end, and a restriction enzyme recognition site for the restriction enzyme EcoR I. The second primer contained the restriction enzyme recognition site for BceA I.

[0612] Submitted SNP (ss) 813773 (accession number assigned by the NCBI Submitted SNP (ss) Database) was amplified with the following primers:

[0613]

First primer:
5′ CGGTAAATCGGAGAATTCAGAGGATTTAGAGGAGCTAA 3′	(SEQ ID NO: 271)
Second primer:
5′ CTCACGTTCGTTACGGCCATTGTGATAGC 3′	(SEQ ID NO: 272)

[0614] The first primer contains a biotin group at the 5′ end, and a recognition site for the restriction enzyme EcoR I. The second primer contained the restriction enzyme recognition site for BceA I.

[0615] SNP TSC 0198557 was amplified with the following primers:

[0616]

First primer:
5′ GGGGAAACAGTAGAATTCCATATGGACAGAGCTGTACT 3′	(SEQ ID NO: 273)
Second primer:
5′ TGAAGCTGTCGGACGGCCTTTGCCCTCTC 3′	(SEQ ID NO: 274)

[0617] The first primer contains a biotin group at the 5′ end, and a recognition site for the restriction enzyme EcoR I. The second primer contained the restriction enzyme recognition site for BceA I.

[0618] SNP TSC 0197279 was amplified with the following primers:

[0619]

First primer:
5′ ATGGGCAGTTATGAATTCACTACTCCCTGTAGCTTGTT 3′	(SEQ ID NO: 275)
Second primer:
5′ TGATTGGCGCGAACGGCACTCAGAGAAGA 3′	(SEQ ID NO: 276)

[0620] The first primer contained a biotin group at the 5′ end, and a recognition site for the restriction enzyme for EcoR I. The second primer contained the recognition site for the restriction enzyme BceA I.

[0621] SNP TSC 0200347 was amplified with the following primers:

[0622]

First primer:
5′ CTCAAGGGGACCGAATTCGCTGGGGTCTTCTGTGGGTC 3′	(SEQ ID NO: 277)
Second primer:
5′ TAGGGCGGCGTGACGGCCAGCCAGTGGT 3′	(SEQ ID NO: 278)

[0623] The first primer contained a biotin group at the 5′ end, and the recognition site for the restriction enzyme EcoR I. The second primer contained the restriction enzyme recognition site for BceA I.

PCR Reaction

[0624] All five loci of interest were amplified from the template genomic DNA using PCR (U.S. Pat. Nos. 4,683,195 and 4,683,202). For increased specificity, a “hot-start” PCR was used. PCR reactions were performed using the HotStarTaq Master Mix Kit supplied by QIAGEN (catalog number 203443). The amount of template DNA and primer per reaction can be optimized for each locus of interest; in this example, 40 ng of template human genomic DNA and 5 μM of each primer were used. Thirty-eight cycles of PCR were performed. The following PCR conditions were used for SNP TSC 0115603, SNP TSC 0309610, and SNP TSC 02003437:

[0625] (1) 95° C. for 15 minutes and 15 seconds;

[0626] (2) 42° C. for 30 seconds;

[0627] (3) 95° C. for 30 seconds;

[0628] (4) 60° C. for 30 seconds;

[0629] (5) 95° C. for 30 seconds;

[0630] (6) 69° C. for 30 seconds;

[0631] (7) 95° C. for 30 seconds;

[0632] (8) Repeat steps 6 and 7 thirty nine (37) times;

[0633] (9) 72° C. for 5 minutes.

[0634] The following PCR conditions were used for SNP ss813773, SNP TSC 0198557, and SNP TSC 0197279:

[0635] (1) 95° C. for 15 minutes and 15 seconds;

[0636] (2) 37° C. for 30 seconds;

[0637] (3) 95° C. for 30 seconds;

[0638] (4) 57° C. for 30 seconds;

[0639] (5) 95° C. for 30 seconds;

[0640] (6) 64° C. for 30 seconds;

[0641] (7) 95° C. for 30 seconds;

[0642] (8) Repeat steps 6 and 7 thirty nine (37) times; and

[0643] (9) 72° C. for 5 minutes.

[0644] In the first cycle of each PCR, the annealing temperature was about the melting temperature of the 3′ annealing region of the second primer. The annealing temperature in the second cycle of PCR was about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer. The annealing temperature in the third cycle of PCR was about the melting temperature of the entire sequence of the second primer. Escalating the annealing temperature from TM1 to TM2 to TM3 in the first three cycles of PCR greatly improves specificity. These annealing temperatures are representative, and the skilled artisan will understand the annealing temperatures for each cycle are dependent on the specific primers used. The temperatures and times for denaturing, annealing, and extension, can be optimized by trying various settings and using the parameters that yield the best results.

Purification of Fragment of Interest

[0645] PCR products were separated from the components of the PCR reaction using Qiagen's MinElute PCR Purification Kit following manufacturer's instructions (Catalog number 28006). The PCR products were eluted in 20 μl of distilled water. For each amplified SNP, one microliter of PCR product, 1 μl of amplified internal control DNA (SNP TSC 0200347), and 8 μl of distilled water were mixed. Five microliters of each sample was placed into two separate reaction wells of a Pierce StreptaWell Microtiter plate (catalog number 15501). The first primers contained a 5′ biotin tag so the PCR products bound to the Streptavidin coated wells while the genomic template DNA did not. The streptavidin binding reaction was performed using a Thermomixer (Eppendorf) at 150 rpm for 1 hour at 45° C. Each well was aspirated to remove unbound material, and washed three times with 1×PBS, with gentle mixing (Kandpal et al., Nucl. Acids Res. 18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., Nucl. Acids Res. 18:6163-6164 (1990)).

Restriction Enzyme Digestion of Isolated Fragments

[0646] The purified PCR products were digested with the restriction enzyme that bound the recognition site that was incorporated into the PCR products from the second primer. The purified PCR products were digested with the restriction enzyme BceA I (New England Biolabs, catalog number R0623S). The digests were performed in the wells of the microtiter plate following the instructions supplied with the restriction enzyme. After digestion with the appropriate restriction enzyme, the wells were washed three times with PBS to remove the cleaved fragments.

Incorporation of Labeled Nucleotide

[0647] The restriction enzyme digest described above yielded a DNA fragment with a 5′ overhang, which contained the SNP and a 3′ recessed end. The 5′ overhang functioned as a template allowing incorporation of a nucleotide or nucleotides in the presence of a DNA polymerase.

[0648] For each SNP, two fill in reactions were performed; each reaction contained a different fluorescently labeled dideoxynucleotide (ddATP, ddCTP, ddGTP, or ddTTP, depending on the reported nucleotides to exist at a particular SNP). For example, the nucleotides adenine and thymidine have been reported at SNP TSC 0115603. Therefore, the digested PCR product for SNP TSC 0115603 was mixed with either fluorescently labeled ddATP or fluorescently labeled ddTTP. Each reaction contained fluorescently labeled ddGTP for the internal control. The following components were added to each fill in reaction: 2 μl of a ROX-conjugated dideoxynucleotide (depending on the nucleotides reported for each SNP), 2 μl of ROX-conjugated ddGTP (internal control), 2.5 μl of 10× sequenase buffer, 2 μl of Sequenase, and water as needed for a 25 μl reaction. All of the fill in reactions were performed at 45° C. for 45 min. However, shorter time periods of incorporation can be used. Non-fluorescently labeled ddNTPs were purchased from Fermentas Inc. (Hanover, Md.). The ROX-conjugated ddNTPs were obtained from Perkin Elmer. In the presence of fluorescently labeled ddNTPs, the 3′ recessed end was extended by one base, which corresponds to the SNP or locus of interest.

[0649] After labeling, each Streptawell was rinsed with 1×PBS (100 μl) three times. The “filled in” DNA fragments were then released from the Streptawells by digestion with the restriction enzyme EcoR I following manufacturer's recommendations. Digestion was performed for 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

[0650] After release from the streptavidin matrix, 3 μl of the 10 μl sample was loaded in a 48 well membrane tray (The Gel Company, catalog number TAM48-01). The sample in the tray was absorbed with a 48 Flow Membrane Comb (The Gel Company, catalog number AM48), and inserted into a 36 cm 5% acrylamide (urea) gel (BioWhittaker Molecular Applications, Long Ranger Run Gel Packs, catalog number 50691).

[0651] The sample was electrophoresed into the gel at 3000 volts for 3 min. The membrane comb was removed, and the gel was run for 3 hours on an ABI 377 Automated Sequencing Machine. The incorporated labeled nucleotide was detected by fluorescence.

[0652] As seen in FIG. 12, SNP TSC 0115603 was “filled in” with labeled ddTTP (lane 1) and in a separate reaction with labeled ddATP (lane 3). The calculated ratio between the nucleotides, using the raw data, was 66:34, which is consistent with the theoretical ratio of 66:33 for a SNP on chromosome 21 in an individual with trisomy 21. Both the ddTTP and ddATP were labeled with the same fluorescent dye to minimize variability in incorporation efficiencies of the dyes. However, nucleotides with different fluorescent labels or any detectable label can be used. It is preferable to calculate the coefficients of incorporation when different labels are used.

[0653] Each fill in reaction was performed in a separate well so it was possible that there could be variability in DNA binding between the wells of the microtiter plate. To account for the potential variability of DNA binding to the streptavidin-coated plates, an internal control was used. The internal control (SNP TSC 0200347), which is homozygous for guanine, was added to the sample prior to splitting the sample into two separate wells, and thus, an equal amount of the internal control should be present in each well. The amount of incorporated ddGTP can be fixed between the two reactions. If the amount of DNA in each well is equal, the amount of incorporated ddGTP should be equal because the reaction is performed under saturating conditions, with saturating conditions being defined as conditions that support incorporation of a nucleotide at each template molecule. Using the internal control, the ratio of incorporated ddATP to ddTTP was 63.4:36.6. This ratio was very similar to the ratio obtained with the raw data, indicating that there are minor differences in the two fill in reactions for a particular SNP.

[0654]

TABLE VI
Allele Frequencies at Multiple SNPs on DNA Template from Individual with Trisomy 21
		Peak	Allele	Internal		Allele
SNP	Allele	Area	Ratio	Control	Normalized Peak Area	Ratio (%)
TSC	A	5599	66	723	5599	63.4
0115603	T	2951	34	661	3227 ((723/661) * 2951)	36.6
TSC	T	4126	64	1424	4126	66.8
0309610	C	2342	36	1631	2045 ((1424/1631) * 2342)	33.2
ss813773	A	4199	46	808	4199	41
	C	4870	54	647	6082 ((808/647) * 4870)	59
TSC	T	3385	55	719	3385	49
0198557	C	2741	45	559	3525 719/559 * 2741)	51
TSC	T	8085	53	2752	8085	50.7
0197279	C	7202	47	2520	7865 (2752/2520 * 7202	49.3

[0655] SNP TSC 0309610 was filled in with ddTTP (lane 3) or ddCTP (lane 4) (FIG. 12). The calculated ratio for the nucleotides, using the raw data, was 64:36. Both ddTTP and ddCTP were labeled with the same fluorescent dye. After normalization to the internal control, as discussed above, the calculated allele ratio of ddTTP to ddCTP was 66.8:33.2 (Table VI). Again, both the calculated ratio from the raw data and the calculated ratio using the internal control are very similar to the theoretical ratio of 66.6:33.4 for a SNP on chromosome 21 in an individual with trisomy.

[0656] To demonstrate that the 66:33 ratios for nucleotides at heterozygous SNPS represented loci on chromosomes present in three copies, SNPs on chromosome 13 were analyzed. The individual from whom the blood sample was obtained had previously been genotyped with one maternal chromosome 13, and one paternal chromosome 13.

[0657] Submitted SNP (ss) 813773 was filled in with ddATP (lane 5) or ddCTP (lane 6) (FIG. 12). The calculated ratio for the nucleotides at this heterozygous SNP, using the raw data, was 46:54. This ratio is within 10% of the expected ratio of 50:50. Importantly, the ratio does not approach the 66:33 ratio expected when there is an additional copy of a chromosome.

[0658] After normalization to the internal control, the calculated ratio was 41:59. Contrary to the expected result, normalization to the internal control increased the discrepancy between the calculated ratio and the theoretical ratio. This result may represent experimental error that occurred in aliquoting the DNA samples.

[0659] Also, it is possible that the restriction enzyme used to generate the overhang, which was used as a template for the “fill-in” reaction, preferentially cut one DNA template over the other DNA template. The two templates differ, with respect to the nucleotide at the SNP site, and this may influence the cutting. The primers can be designed such that the nucleotides adjacent to the cut site are the same, independent of the nucleotide at the SNP site (discussed further in the section entitled “Primer Design”).

[0660] SNP TSC 0198557, which is on chromosome 13, was filled in with ddTTP (lane 7) in one reaction and ddCTP (lane 8) in another (FIG. 12). The calculated ratio for the nucleotides at this SNP, using the raw data, was 55:45. After normalization to the internal control, the calculated allele ratio of T:C was 49:51. The normalized ratio was closer to the theoretical ratio of 50:50 for an individual with two copies of chromosome 13.

[0661] SNP TSC 0197279, which is on chromosome 13, was filled in with ddTTP (lane 9) in one reaction and ddCTP (lane 10) in another (FIG. 12). The calculated ratio for the nucleotides at this SNP, using the raw data, was 53:47. After normalization to the internal control, the calculated allele ratio of T:C was 50.7:49.3. This is consistent with the theoretical ratio of 50:50 for an individual with only two copies of chromosome 13.

[0662] The ratio for the nucleotides at two of the analyzed SNPs on chromosome 13 was approximately 50:50. One SNP, ss813773, showed a ratio of 46:54, and when normalized to the internal control, the ratio was 41:59. These ratios deviate from the expected 50:50, but at the same time, the ratios are not indicative of an extra chromosome, which is indicated with a ratio of 66:33. While the data from this particular SNP is inconclusive, it does not represent a false positive. No conclusion could be drawn on the data from this SNP. However, the other two SNPs provided data that indicated a normal number of chromosomes. It is preferable to analyze multiple SNPs on a chromosome including but not limited to 1-5, 5-10, 10-50, 50-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700, 700-800, 800-900, 900-1000, 1000-2000, 2000-3000, and greater than 3000. Preferably, the average of the ratios for a particular chromosome will be used to determine the presence or absence of a chromosomal abnormality. However, it is still possible to analyze one locus of interest. In the event that inconclusive data is obtained, another locus of interest can be analyzed.

[0663] The individual from whom the DNA template was obtained had previously been genotyped with trisomy 21, and the allele frequencies at SNPs on chromosome 21 indicate the presence of an additional chromosome 21. The additional chromosome contributes an additional nucleotide for each SNP, and thus alters the traditional 50:50 ratio at a heterozygous SNP. These results are consistent for multiple SNPs, and are specific for those found on chromosome 21. The allele frequencies for SNPs on chromosome 13 gave the expected ratios of approximately 50:50. These results demonstrate that this method of SNP detection can be used to detect chromosomal abnormalities including but not limited to translocations, transversions, monosomies, trisomy 21, trisomy 18, trisomy 13, other aneuplodies, deletions, additions, amplifications, translocations and rearrangements.

[0664] Genomic DNA was obtained from four individuals after informed consent was obtained. Six SNPs on chromosome 13 (TSC0837969, TSC0034767, TSC1130902, TSC0597888, TSC0195492, TSC0607185) were analyzed using the template DNA. Information regarding these SNPs can be found at the following website www.snp.chsl.org/snpsearch.shtml; website active as of Feb. 11, 2003).

[0665] A single nucleotide labeled with one fluorescent dye was used to genotype the individuals at the six selected SNP sites. The primers were designed to allow the six SNPs to be analyzed in a single reaction.

Preparation of Template DNA

[0666] The template DNA was prepared from a 9 ml sample of blood obtained by venipuncture from a human volunteer with informed consent. Template DNA was isolated using the QIAmp DNA Blood Midi Kit supplied by QIAGEN (Catalog number 51183). The template DNA was isolated as per instructions included in the kit.

Design of Primers

[0667] SNP TSC0837969 was amplified using the following primer set:

[0668]

First primer:
5′ GGGCTAGTCTCCGAATTCCACCTATCCTACCAAATGTC 3′	(SEQ ID NO: 30)
Second primer:
5′ TAGCTGTAGTTAGGGACTGTTCTGAGCAC 3′	(SEQ ID NO: 31)

[0669] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 44 bases from the locus of interest. The second primer contained a restriction enzyme recognition site for BsmF I.

[0670] SNP TSC0034767 was amplified using the following primer set:

[0671]

First primer:
5′ CGAATGCAAGGCGAATTCGTTAGTAATAACACAGTGCA 3′	(SEQ ID NO: 32)
Second primer:
5′ AAGACTGGATCCGGGACCATGTAGAATAC 3′	(SEQ ID NO: 33)

[0672] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 50 bases from the locus of interest. The second primer contained a restriction enzyme recognition site for BsmF I.

[0673] SNP TSC1130902 was amplified using the following primer set:

[0674]

First primer:
5′ TCTAACCATTGCGAATTCAGGGCAAGGGGGGTGAGATC 3′	(SEQ ID NO: 34)
Second primer:
5′ TGACTTGGATCCGGGACAACGACTCATCC 3′	(SEQ ID NO: 35)

[0675] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 60 bases from the locus of interest. The second primer contained a restriction enzyme recognition site for BsmF I.

[0676] SNP TSC0597888 was amplified using the following primer set:

[0677]

First primer:
5′ ACCCAGGCGCCAGAATTCTTTAGATAAAGCTGAAGGGA 3′	(SEQ ID NO: 36)
Second primer:
5′ GTTACGGGATCCGGGACTCCATATTGATC 3′	(SEQ ID NO: 37)

[0678] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 70 bases from the locus of interest. The second primer contained a restriction enzyme recognition site for BsmF I.

[0679] SNP TSC0195492 was amplified using the following primer set:

[0680]

First primer:
5′ CGTTGGCTTGAGGAATTCGACCAAAAGAGCCAAGAGAA 3′	(SEQ ID NO: 38)
Second primer:
5′ AAAAAGGGATCCGGGACCTTGACTAGGAC 3′	(SEQ ID NO: 39)

[0681] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 80 bases from the locus of interest. The second primer contained a restriction enzyme recognition site for BsmF I.

[0682] SNP TSC0607185 was amplified using the following primer set:

[0683]

First primer:
5′ ACTTGATTCCGTGAATTCGTTATCAATAAATCTTACAT 3′	(SEQ ID NO: 40)
Second primer:
5′ CAAGTTGGATCCGGGACCCAGGGCTAACC 3′	(SEQ ID NO: 41)

[0684] The first primer had a biotin tag at the 5′ end and contained a restriction enzyme recognition site for EcoRI. The first primer was designed to anneal 90 bases from the locus of interest. The second primer contained a restriction, enzyme recognition site for BsmF I.

[0685] All loci of interest were amplified from the template genomic DNA using the polymerase chain reaction (PCR, U.S. Pat. Nos. 4,683,195 and 4,683,202, incorporated herein by reference). In this example, the loci of interest were amplified in separate reaction tubes but they could also be amplified together in a single PCR reaction. For increased specificity, a “hot-start” PCR was used. PCR reactions were performed using the HotStarTaq Master Mix Kit supplied by QIAGEN (catalog number 203443). The amount of template DNA and primer per reaction can be optimized for each locus of interest but in this example, 40 ng of template human genomic DNA and 5 μM of each primer were used. Forty cycles of PCR were performed. The following PCR conditions were used:

[0686] (1) 95° C. for 15 minutes and 15 seconds;

[0687] (2) 37° C. for 30 seconds;

[0688] (3) 95° C. for 30 seconds;

[0689] (4) 57° C. for 30 seconds;

[0690] (5) 95° C. for 30 seconds;

[0691] (6) 64° C. for 30 seconds;

[0692] (7) 95° C. for 30 seconds;

[0693] (8) Repeat steps 6 and 7 thirty nine (39) times;

[0694] (9) 72° C. for 5 minutes.

[0695] In the first cycle of PCR, the annealing temperature was about the melting temperature of the 3′ annealing region of the second primers, which was 37° C. The annealing temperature in the second cycle of PCR was about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer, which was 57° C. The annealing temperature in the third cycle of PCR was about the melting temperature of the entire sequence of the second primer, which was 64° C. The annealing temperature for the remaining cycles was 64° C. Escalating the annealing temperature from TM1 to TM2 to TM3 in the first three cycles of PCR greatly improves specificity. These annealing temperatures are representative, and the skilled artisan will understand the annealing temperatures for each cycle are dependent on the specific primers used.

[0696] The temperatures and times for denaturing, annealing, and extension, can be optimized by trying various settings and using the parameters that yield the best results. In this example, the first primer was designed to anneal at various distances from the locus of interest. The skilled artisan understands that the annealing location of the first primer can be 5-10, 11-15, 16-20, 21-25, 26-30, 31-35, 36-40, 41-45, 46-50, 51-55, 56-60, 61-65, 66-70, 71-75, 76-80, 81-85, 86-90, 91-95, 96-100, 101-105, 106-110, 111-115, 116-120, 121-125, 126-130, 131-140, 1410-160, 1610-180, 1810-200, 2010-220, 2210-240, 2410-260, 2610-280, 2810-300, 3010-350, 3510-400, 4010-450, 450-500, or greater than 500 bases from the locus of interest.

Purification of Fragment of Interest

[0697] The PCR products were separated from the genomic template DNA. After the PCR reaction, ¼ of the volume of each PCR reaction from one individual was mixed together in a well of a Streptawell, transparent, High-Bind plate from Roche Diagnostics GmbH (catalog number 1 645 692, as listed in Roche Molecular Biochemicals, 2001 Biochemicals Catalog). The first primers contained a 5′ biotin tag so the PCR products bound to the Streptavidin coated wells while the genomic template DNA did not. The streptavidin binding reaction was performed using a Thermomixer (Eppendorf) at 1000 rpm for 20 min. at 37° C. Each well was aspirated to remove unbound material, and washed three times with 1×PBS, with gentle mixing (Kandpal et al., Nucl. Acids Res. 18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., Nucl. Acids Res. 18:6163-6164 (1990)).

Restriction Enzyme Digestion of Isolated Fragments

[0698] The purified PCR products were digested with the restriction enzyme BsmF I, which binds to the recognition site incorporated into the PCR products from the second primer. The digests were performed in the Streptawells following the instructions supplied with the restriction enzyme. After digestion, the wells were washed three times with PBS to remove the cleaved fragments.

Incorporation of Labeled Nucleotide

[0699] The restriction enzyme digest with BsmF I yielded a DNA fragment with a 5′ overhang, which contained the SNP site or locus of interest and a 3′ recessed end. The 5′ overhang functioned as a template allowing incorporation of a nucleotide or nucleotides in the presence of a DNA polymerase.

[0700] Below, a schematic of the 5′ overhang for SNP TSC0837969 is shown. The entire DNA sequence is not reproduced, only the portion to demonstrate the overhang (where R indicates the variable site).

[0701]

	5′ TTAA
	3′ AATT	R	A	C	A
Overhang position		1	2	3	4

[0702] The observed nucleotides for TSC0837969 on the 5′ sense strand (here depicted as the top strand) are adenine and guanine. The third position in the overhang on the antisense strand corresponds to cytosine, which is complementary to guanine. As this variable site can be adenine or guanine, fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP was used to determine the sequence of both alleles. The fill-in reactions for an individual homozygous for guanine, homozygous for adenine or heterozygous are diagrammed below.

[0703] Homozygous for guanine at TSC 0837969:

[0704]

Allele 1	5′ TTAA	G*
	3′ AATT	C	A	C	A
Overhang position		1	2	3	4
Allele 2	5′ TTAA	G*
	3′ AATT	C	A	C	A
Overhang position		1	2	3	4

[0705] Labeled ddGTP is incorporated into the first position of the overhang. Only one signal is seen, which corresponds to the molecules filled in with labeled ddGTP at the first position of the overhang.

[0706] Homozygous for adenine at TSC 0837969:

[0707]

Allele 1	5′ TTAA	A	T	G*
	3′ AATT	T	A	C	A
Overhang position		1	2	3	4
Allele 2	5′ TTAA	A	T	G*
	3′ AATT	T	A	C	A
Overhang position		1	2	3	4

[0708] Unlabeled dATP is incorporated at position one of the overhang, and unlabeled dTTP is incorporated at position two of the overhang. Labeled ddGTP was incorporated at position three of the overhang. Only one signal will be seen; the molecules filled in with ddGTP at position 3 will have a different molecular weight from molecules filled in at position one, which allows easy identification of individuals homozygous for adenine or guanine.

[0709] Heterozygous at TSC0837969:

[0710]

Allele 1	5′ TTAA	G*
	3′ AATT	C	A	C	A
Overhang position		1	2	3	4
Allele 2	5′ TTAA	A	T	G*
	3′ AATT	T	A	C	A
Overhang position		1	2	3	4

[0711] Two signals will be seen; one signal corresponds to the DNA molecules filled in with ddGTP at position 1, and a second signal corresponding to molecules filled in at position 3 of the overhang. The two signals can be separated using any technique that separates based on molecular weight including but not limited to gel electrophoresis.

[0712] Below, a schematic of the 5′ overhang for SNP TSC0034767 is shown. The entire DNA sequence is not reproduced, only the portion to demonstrate the overhang (where R indicates the variable site).

[0713]

A	C	A	R	GTGT 3′
				CACA 5′
4	3	2	1		Overhang Position

[0714] The observed nucleotides for TSC0034767 on the 5′ sense strand (here depicted as the top strand) are cytosine and guanine. The second position in the overhang corresponds to adenine, which is complementary to thymidine. The third position in the overhang corresponds to cytosine, which is complementary to guanine. Fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP is used to determine the sequence of both alleles.

[0715] In this case, the second primer anneals upstream of the locus of interest, and thus the fill-in reaction occurs on the anti-sense strand (here depicted as the bottom strand). Either the sense strand or the antisense strand can be filled in depending on whether the second primer, which contains the type IIS restriction enzyme recognition site, anneals upstream or downstream of the locus of interest.

[0716] Below, a schematic of the 5′ overhang for SNP TSC1130902 is shown. The entire DNA sequence is not reproduced, only a portion to demonstrate the overhang (where R indicates the variable site).

[0717]

	5′ TTCAT
	3′ AAGTA	R	T	C	C
Overhang position		1	2	3	4

[0718] The observed nucleotides for TSC1130902 on the 5′ sense strand (here depicted as the top strand) are adenine and guanine. The second position in the overhang corresponds to a thymidine, and the third position in the overhang corresponds to cytosine, which is complementary to guanine.

[0719] Fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP is used to determine the sequence of both alleles.

[0720] Below, a schematic of the 5′ overhang for SNP TSC0597888 is shown. The entire DNA sequence is not reproduced, only the portion to demonstrate the overhang (where R indicates the variable site).

[0721]

T	C	T	R	ATTC 3′
				TAAG 5′
4	3	2	1		Overhang position

[0722] The observed nucleotides for TSC0597888 on the 5′ sense strand (here depicted as the top strand) are cytosine and guanine. The third position in the overhang corresponds to cytosine, which is complementary to guanine. Fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP is used to determine the sequence of both alleles.

[0723] Below, a schematic of the 5′ overhang for SNP TSC0607185 is shown. The entire DNA sequence is not reproduced, only the portion to demonstrate the overhang (where R indicates the variable site).

[0724]

C	C	T	R	TGTC 3′
				ACAG 5′
4	3	2	1		Overhang position

[0725] The observed nucleotides for TSC0607185 on the 5′ sense strand (here depicted as the top strand) are cytosine and thymidine. In this case, the second primer anneals from the locus of interest, which allows the anti-sense strand to be filled in. The anti-sense strand (here depicted as the bottom strand) will be filled in with guanine or adenine.

[0726] The second position in the 5′ overhang is thymidine, which is complementary to adenine, and the third position in the overhang corresponds to cytosine, which is complementary to guanine. Fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP is used to determine the sequence of both alleles.

[0727] Below, a schematic of the 5′ overhang for SNP TSC0195492 is shown. The entire DNA sequence is not reproduced, only the portion to demonstrate the overhang.

[0728]

	5′ ATCT
	3′ TAGA	R	A	C	A
Overhang position		1	2	3	4

[0729] The observed nucleotides at this site are cytosine and guanine (here depicted as the top strand). The second position in the 5′ overhang is adenine, which is complementary to thymidine, and the third position in the overhang corresponds to cytosine, which is complementary to guanine. Fluorescently labeled ddGTP in the presence of unlabeled dCTP, dTTP, and dATP is used to determine the sequence of both alleles.

[0730] As demonstrated above, the sequence of both alleles of the six SNPs can be determined by labeling with ddGTP in the presence of unlabeled dATP, dTTP, and dCTP. The following components were added to each fill in reaction: 1 μl of fluorescently labeled ddGTP, 0.5 μl of unlabeled dNTPs (40 μM), which contained all nucleotides except guanine, 2 μl of 10× sequenase buffer, 0.25 μl of Sequenase, and water as needed for a 20 μl reaction. The fill in reaction was performed at 40° C. for 10 min. Non-fluorescently labeled dNTP was purchased from Fermentas Inc. (Hanover, Md.). All other labeling reagents were obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565).

[0731] After labeling, each Streptawell was rinsed with 1×PBS (100 μl) three times. The “filled in” DNA fragments were then released from the Streptawells by digestion with the restriction enzyme EcoRI, according to the manufacturer's instructions that were supplied with the enzyme. Digestion was performed for 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

[0732] After release from the streptavidin matrix, the sample was loaded into a lane of a 36 cm 5% acrylamide (urea) gel (BioWhittaker Molecular Applications, Long Ranger Run Gel Packs, catalog number 50691). The sample was electrophoresed into the gel at 3000 volts for 3 min. The gel was run for 3 hours on a sequencing apparatus (Hoefer SQ3 Sequencer). The gel was removed from the apparatus and scanned on the Typhoon 9400 Variable Mode Imager. The incorporated labeled nucleotide was detected by fluorescence.

[0733] As shown in FIG. 11, the template DNA in lanes 1 and 2 for SNP TSC0837969 is homozygous for adenine. The following fill-in reaction was expected to occur if the individual was homozygous for adenine:

[0734] Homozygous for adenine at TSC 0837969:

[0735]

	5′ TTAA	A	T	G*
	3′ AATT	T	A	C	A
Overhang position		1	2	3	4

[0736] Unlabeled dATP was incorporated in the first position complementary to the overhang. Unlabeled dTTP was incorporated in the second position complementary to the overhang. Labeled ddGTP was incorporated in the third position complementary to the overhang. Only one band was seen, which migrated at about position 46 of the acrylamide gel. This indicated that adenine was the nucleotide filled in at position one. If the nucleotide guanine had been filled in, a band would be expected at position 44.

[0737] However, the template DNA in lanes 3 and 4 for SNP TSC0837969 was heterozygous. The following fill-in reactions were expected if the individual was heterozygous:

[0738] Heterozygous at TSC0837969:

[0739]

Allele 1	5′ TTAA	G*
	3′ AATT	C	A	C	A
Overhang position		1	2	3	4
Allele 2	5′ TTAA	A	T	G*
	3′ AATT	T	A	C	A
Overhang position		1	2	3	4

[0740] Two distinct bands were seen; one band corresponds to the molecules filled in with ddGTP at position 1 complementary to the overhang (the G allele), and the second band corresponds to molecules filled in with ddGTP at position 3 complementary to the overhang (the A allele). The two bands were separated based on the differences in molecular weight using gel electrophoresis. One fluorescently labeled nucleotide ddGTP was used to determine that an individual was heterozygous at a SNP site. This is the first use of a single nucleotide to effectively detect the presence of two different alleles.

[0741] For SNP TSC0034767, the template DNA in lanes 1 and 3 is heterozygous for cytosine and guanine, as evidenced by the two distinct bands. The lower band corresponded to ddGTP filled in at position 1 complementary to the overhang. The second band of slightly higher molecular weight corresponded to ddGTP filled in at position 3, indicating that the first position in the overhang was filled in with unlabeled dCTP, which allowed the polymerase to continue to incorporate nucleotides until it incorporated ddGTP at position 3 complementary to the overhang. The template DNA in lanes 2 and 4 was homozygous for guanine, as evidenced by a single band of higher molecular weight than if ddGTP had been filled in at the first position complementary to the overhang.

[0742] For SNP TSC1130902, the template DNA in lanes 1, 2, and 4 is homozygous for adenine at the variable site, as evidenced by a single higher molecular weight band migrating at about position 62 on the gel. The template DNA in lane 3 is heterozygous at the variable site, as indicated by the presence of two distinct bands. The lower band corresponds to molecules filled in with ddGTP at position 1 complementary to the overhang (the guanine allele). The higher molecular weight band corresponds to molecules filled in with ddGTP at position 3 complementary to the overhang (the adenine allele).

[0743] For SNP TSC0597888, the template DNA in lanes 1 and 4 was homozygous for cytosine at the variable site; the template DNA in lane 2 was heterozygous at the variable site, and the template DNA in lane 3 was homozygous for guanine. The expected fill-in reactions are diagrammed below:

[0744] Homozygous for Cytosine:

[0745]

Allele 1	T	C	T	G	ATTC 3′
		G*	A	C	TAAG 5′
	4	3	2	1		Overhang position
Allele 2	T	C	T	G	ATTC 3′
		G*	A	C	TAAG 5′
	4	3	2	1		Overhang position

[0746] Homozygous for Guanine:

[0747]

Allele 1	T	C	T	C	ATTC 3′
				G*	TAAG 5′
	4	3	2	1		Overhang position
Allele 2	T	C	T	C	ATTC 3′
				G*	TAAG 5′
	4	3	2	1		Overhang position

[0748] Heterozygous for Guanine/Cytosine:

[0749]

Allele 1	T	C	T	G	ATTC 3′
		G*	A	C	TAAG 5′
	4	3	2	1		Overhang position
Allele 2	T	C	T	C	ATTC 3′
				G*	TAAG 5′
	4	3	2	1		Overhang position

[0750] Template DNA homozygous for guanine at the variable site displayed a single band, which corresponded to the DNA molecules filled in with ddGTP at position 1 complementary to the overhang. These DNA molecules were of lower molecular weight compared to the DNA molecules filled in with ddGTP at position 3 of the overhang (see lane 3 for SNP TSC0597888). The DNA molecules differed by two bases in molecular weight.

[0751] Template DNA homozygous for cytosine at the variable site displayed a single band, which corresponds to the DNA molecules filled in with ddGTP at position 3 complementary to the overhang. These DNA molecules migrated at a higher molecular weight than DNA molecules filled in with ddGTP at position 1 (see lanes 1 and 4 for SNP TSC0597888).

[0752] Template DNA heterozygous at the variable site displayed two bands; one band corresponded to the DNA molecules filled in with ddGTP at position 1 complementary to the overhang and was of lower molecular weight, and the second band corresponded to DNA molecules filled in with ddGTP at position 3 complementary to the overhang, and was of higher molecular weight (see lane 3 for SNP TSC0597888).

[0753] For SNP TSC0195492, the template DNA in lanes 1 and 3 was heterozygous at the variable site, which was demonstrated by the presence of two distinct bands. The template DNA in lane 2 was homozygous for guanine at the variable site. The template DNA in lane 4 was homozygous for cytosine. Only one band was seen in lane 4 for this SNP, and it had a higher molecular weight than the DNA molecules filled in with ddGTP at position 1 complementary to the overhang (compare lanes 2, 3 and 4).

[0754] The observed alleles for SNP TSC0607185 are reported as cytosine or thymidine. For consistency, the SNP consortium denotes the observed alleles as they appear in the sense strand www.snp.cshl.org/shpsearch.shtml; website active as of Feb. 11, 2003). For this SNP, the second primer annealed upstream of the locus of interest, which allowed the fill-in reaction to occur on the antisense strand after digestion with BsmF I.

[0755] The template DNA in lanes 1 and 3 was heterozygous; the template DNA in lane 2 was homozygous for thymidine, and the template DNA in lane 4 was homozygous for cytosine. The antisense strand was filled in with ddGTP, so the nucleotide on the sense strand corresponded to cytosine.

[0756] Molecular weight markers can be used to identify the positions of the expected bands. Alternatively, for each SNP analyzed, a known heterozygous sample can be used, which will identify precisely the position of the two expected bands.

[0757] As demonstrated in FIG. 11, one nucleotide labeled with one fluorescent dye can be used to determine the identity of a variable site including but not limited to SNPs and single nucleotide mutations. Typically, to determine if an individual is homozygous or heterozygous at a SNP site, multiple reactions are performed using one nucleotide labeled with one dye and a second nucleotide labeled with a second dye. However, this introduces problems in comparing results because the two dyes have different quantum coefficients. Even if different nucleotides are labeled with the same dye, the quantum coefficients are different. The use of a single nucleotide labeled with one dye eliminates any errors from the quantum coefficients of different dyes.

[0758] In this example, fluorescently labeled ddGTP was used. However, the method is applicable for a nucleotide tagged with any signal generating moiety including but not limited to radioactive molecule, fluorescent molecule, antibody, antibody fragment, hapten, carbohydrate, biotin, derivative of biotin, phosphorescent moiety, luminescent moiety, electrochemiluminescent moiety, chromatic moiety, and moiety having a detectable electron spin resonance, electrical capacitance, dielectric constant or electrical conductivity. In addition, labeled ddATP, ddTTP, or ddCTP can be used.

[0759] The above example used the third position complementary to the overhang as an indicator of the second allele. However, the second or fourth position of the overhang can be used as well (see Section on Incorporation of Nucleotides). Furthermore, the overhang was generated with the type IIS enzyme BsmF I; however any enzymes that cuts DNA at a distance from its binding site can be used including but not limited to the enzymes listed in Table I.

[0760] Also, in the above example, the nucleotide immediately preceding the SNP site was not a guanine on the strand that was filled in. This eliminated any effects of the alternative cutting properties of the type IIS restriction enzyme to be removed. For example, at SNP TSC0837969, the nucleotide from the SNP site on the sense strand was an adenine. If BsmF I displayed alternate cutting properties, the following overhangs would be generated for the adenine allele and the guanine allele:

[0761]

G allele-11/15 Cut	5′ TTA
	3′ AAT	T	C	A	C
Overhang position		0	1	2	3
G allele after fill-in	5′ TTA	A	G*
	3′ AAT	T	C	A	C
Overhang position			0	1	2	3
A allele 11/15 Cut	5′ TTA
	3′ AAT	T	T	A	C
Overhang position		0	1	2	3
A allele after fill-in	5′ TTA	A	A	T	G*
	3′ AAT	T	T	A	C
Overhang position		0	1	2	3

[0762] For the guanine allele, the first position in the overhang would be filled in with dATP, which would allow the polymerase to incorporate ddGTP at position 2 complementary to the overhang. There would be no detectable difference between molecules cut at the 10/14 position or molecules cut at the 11/15 position.

[0763] For the adenine allele, the first position complementary to the overhang would be filled in with dATP, the second position would be filled in with dATP, the third position would be filled in with dTTP, and the fourth position would be filled in with ddGTP. There would be no difference in the molecular weights between molecules cut at 10/14 or molecules cut at 11/15. The only differences would correspond to whether the DNA molecules contained an adenine at the variable site or a guanine at the variable site.

[0764] As seen in FIG. 11, positioning the annealing region of the first primer allows multiple SNPs to be analyzed in a single lane of a gel. Also, when using the same nucleotide with the same dye, a single fill-in reaction can be performed. In this example, 6 SNPs were analyzed in one lane. However, any number of SNPs including but not limited to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-40, 40-50, 51-60, 61-70, 71-80, 81-100, 101-120, 121-140, 141-160, 161-180, 181-200, and greater than 200 can be analyzed in a single reaction.

[0765] Furthermore, one labeled nucleotide used to detect both alleles can be mixed with a second labeled nucleotide used to detect a different set of SNPs provided that neither of the nucleotides that are labeled occur immediately before the variable site (complementary to nucleotide at position 0 of the 11/15 cut). For example, suppose SNP X can be guanine or thymidine at the variable site and has the following 5′ overhang generated after digestion with BsmF I:

[0766]

SNP X 10/14	5′ TTGAC
G allele	3′ AACTG	C	A	C	T
Overhang position		1	2	3	4
SNP X 11/15	5′ TTGA
G allele	3′ AACT	G	C	A	C
Overhang position		0	1	2	3
SNP X 10/14	5′ TTGAC
T allele	3′ AACTG	A	A	C	T
Overhang position		1	2	3	4
SNP X 11/15	5′ TTGA
T allele	3′ AACT	G	A	A	C
Overhang position		0	1	2	3

[0767] After the fill-in reaction with labeled ddGTP, unlabeled dATP, dCTP, and dTTP, the following molecules would be generated:

[0768]

SNP X 10/14	5′ TTGAC	G*
G allele	3′ AACTG	C	A	C	T
Overhang position		1	2	3	4
SNP X 11/15	5′ TTGA	C	G*
G allele	3′ AACT	G	C	A	C
Overhang position		0	1	2	3
SNP X 10/14	5′ TTGAC	T	T	G*
T allele	3′ AACTG	A	A	C	T
Overhang position		1	2	3	4
SNP X 11/15	5′ TTGA	C	T	T	G*
T allele	3′ AACT	G	A	A	C
Overhang position		0	1	2	3

[0769] Now suppose SNP Y can be adenine or thymidine at the variable site, and has the following 5′ overhangs generated after digestion with BsmF I.

[0770]

SNP Y 10/14	5′ GTTT
A allele	3′ CAAA	T	G	T	A
Overhang position		1	2	3	4
SNP Y 11/15	5′ GTT
A allele	3′ CAA	A	T	G	T
Overhang position		0	1	2	3
SNP Y 10/14	5′ GTTT
T allele	3′ CAAA	A	G	T	A
Overhang position		1	2	3	4
SNP Y 11/15	5′ GTT
T allele	3′ CAA	A	A	G	T
Overhang position		0	1	2	3

[0771] After fill-in with labeled ddATP and unlabeled dCTP, dGTP, and dTTP, the following molecules would be generated:

[0772]

SNP Y 10/14	5′ GTTT	A*
A allele	3′ CAAA	T	G	T	A
Overhang position		1	2	3	4
SNP Y 11/15	5′ GTT	T	A*
A allele	3′ CAA	A	T	G	T
Overhang position		0	1	2	3
SNP Y 10/14	5′ GTTT	T	C	A*
T allele	3′ CAAA	A	G	T	A
Overhang position		1	2	3	4
SNP Y 11/15	5′ GTT	T	T	C	A*
T allele	3′ CAA	A	A	G	T
Overhang position		0	1	2	3

[0773] In this example, labeled ddGTP and labeled ddATP are used to determine the identity of both alleles of SNP X and SNP Y respectively. The nucleotide immediately preceding (the complementary nucleotide to position 0 of the overhang from the 11/15 cut SNP X is not guanine or adenine on the strand that is filled-in. Likewise, the nucleotide immediately preceding SNPY is not guanine or adenine on the strand that is filled-in. This allows the fill-in reaction for both SNPs to occur in a single reaction with labeled ddGTP, labeled ddATP, and unlabeled dCTP and dTTP. This reduces the number of reactions that need to be performed and increases the number of SNPs that can be analyzed in one reaction.

[0774] The first primers for each SNP can be designed to anneal at different distances from the locus of interest, which allows the SNPs to migrate at different positions on the gel. For example, the first primer used to amplify SNP X can anneal at 30 bases from the locus of interest, and the first primer used to amplify SNP Y can anneal at 35 bases from the locus of interest. Also, the nucleotides can be labeled with fluorescent dyes that emit at spectrums that do not overlap. After running the gel, the gel can be scanned at one wavelength specific for one dye. Only those molecules labeled with that dye will emit a signal. The gel then can be scanned at the wavelength for the second dye. Only those molecules labeled with that dye will emit a signal. This method allows maximum compression for the number of SNPs that can be analyzed in a single reaction.

[0775] In this example, the nucleotide preceding the variable site on the strand that was filled-in was not adenine or guanine, and the nucleotide following the variable site can not be adenine or guanine on the sense strand. This method can work with any combination of labeled nucleotides, and the skilled artisan would understand which labeling reactions can be mixed and those that can not. For instance, if one SNP is labeled with thymidine and a second SNP is labeled with cytosine, the SNPs can be labeled in a single reaction if the nucleotide immediately preceding each variable site is not thymidine or cytosine on the sense strand and the nucleotide immediately after the variable site is not thymidine or cytosine on the sense strand.

[0776] This method allows the signals from one allele to be compared to the signal from a second allele without the added complexity of determining the degree of alternate cutting, or having to correct for the quantum coefficients of the dyes. This method is especially useful when trying to quantitate a ratio for one allele to another. For example, this method is useful for detecting chromosomal abnormalities. The ratio of alleles at a heterozygous site is expected to be about 1:1 (one A allele and one G allele). However, if an extra chromosome is present the ratio is expected to be about 1:2 (one A allele and 2 G alleles or 2 A alleles and 1 G allele). This method is especially useful when trying to detect fetal DNA in the presence of maternal DNA.

[0777] In addition, this method is useful for detecting two genetic signals in one sample. For example, this method can detect mutant cells in the presence of wild type cells (see Example 5). If a mutant cell contains a mutation in the DNA sequence of a particular gene, this method can be used to detect both the mutant signal and the wild type signal. This method can be used to detect the mutant DNA sequence in the presence of the wild type DNA sequence. The ratio of mutant DNA to wild type DNA can be quantitated because a single nucleotide labeled with one signal generating moiety is used.

[0778] Non-invasive methods for the detection of various types of cancer have the potential to reduce morbidity and mortality from the disease. Several techniques for the early detection of colorectal tumors have been developed including colonoscopy, barium enemas, and sigmoidoscopy; however the techniques are limited in use because they are invasive, which causes a low rate of patient compliance. Non-invasive genetic tests may be useful in identifying early stage colorectal tumors.

[0779] In 1991, researchers identified the Adenomatous Polyposis Coli gene (APC), which plays a critical role in the formation of colorectal tumors (Kinzler et al., Science 253:661-665, 1991). The APC gene resides on chromosome 5q21-22 and a total of 15 exons code for an RNA molecule of 8529 nucleotides, which produces a 300 Kd APC protein. The protein is expressed in numerous cell types and is essential for cell adhesion.

[0780] Mutations in the APC gene generally initiate colorectal neoplasia (Tsao, J. et al., Am, J. Pathol. 145:531-534, 1994). Approximately 95% of the mutations in the APC gene result in nonsense/frameshift mutations. The most common mutations occur at codons 1061 and 1309; mutations at these codons account for 1/3 of all germline mutations. With regard to somatic mutations, 60% occur within codons 1286-1513, which is about 10% of the coding sequence. This region is termed the mutation Cluster Region (MCR). Numerous types of mutations have been identified in the APC gene including nucleotide substitutions (see Table VII), splicing errors (see Table VIII), small deletions (see Table IX), small insertions (see Table X), small insertions/deletions (see Table XI), gross deletions (see Table XII), gross insertions (see Table XIII), and complex rearrangements (see Table XIV).

[0781] Researchers have attempted to identify cells harboring mutations in the APC gene in stool samples (Traverso, G. et al., New England Journal of Medicine, Vol 346:311-320, 2002). While APC mutations are found in nearly all tumors, about 1 in 250 cells in the stool sample has a mutation in the APC gene; most of the cells are normal cells that have been shed into the feces. Furthermore, human DNA represents about one-billionth of the total DNA found in stool samples; the majority of DNA is bacterial. The technique employed by Traverso et al. only detects mutations that result in a truncated protein.

[0782] As discussed above, numerous mutations in the APC gene have been implicated in the formation of colorectal tumors. Thus, a need still exists for a highly sensitive, non-invasive technique for the detection of colorectal tumors. Below, methods are described for detection of two mutations in the APC gene. However, any number of mutations can be analyzed using the methods described herein.

Preparation of Template DNA

[0783] The template DNA is purified from a sample containing colon cells including but not limited to a stool sample. The template DNA is purified using the procedures described by Ahlquist et al. (Gastroenterology, 119:1219-1227, 2000). If stool samples are frozen, the samples are thawed at room temperature, and homogenized with an Exactor stool shaker (Exact Laboratories, Maynard, Mass.) Following homogenization, a 4 gram stool equivalent of each sample is centrifuged at 2536×g for 5 minutes. The samples are centrifuged a second time at 16, 500×g for 10 minutes. Supernatants are incubated with 20 μl of RNase (0.5 mg per milliliter) for 1 hour at 37° C. DNA is precipitated with 1/10 volume of 3 mol of sodium acetate per liter and an equal volume of isopropanol. The DNA is dissolved in 5 ml of TRIS-EDTA (0.01 mol of Tris per liter (pH 7.4) and 0.001 mole of EDTA per liter.

Design of Primers

[0784] To determine if a mutation resides at codon 1370, the following primers are used:

[0785]

First primer:
5′ GTGCAAAGGCCTGAATTCCCAGGCACAAAGCTGTTGAA 3′	(SEQ ID NO: 42)
Second primer:
5′ TGAAGCGAACTAGGGACTCAGGTGGACTT 3′	(SEQ ID NO: 43)

[0786] The first primer contains a biotin tag at the extreme 5′ end, and the nucleotide sequence for the restriction enzyme EcoRI. The second primer contains the nucleotide sequence for the restriction enzyme BsmF I.

[0787] To determine if a small deletion exists at codon 1302, the following primers are used:

[0788]

First primer:
5′ GATTCCGTAAACGAATTCAGTTCATTATCATCTTTGTC 3′	(SEQ ID NO: 44)
Second primer:
5′ CCATTGTTAAGCGGGACTTCTGCTATTTG 3′	(SEQ ID NO: 45)

[0789] The first primer has a biotin tag at the 5′ end and contains a restriction enzyme recognition site for EcoRI. The second primer contains a restriction enzyme recognition site for BsmF I.

PCR Reaction

[0790] The loci of interest are amplified from the template genomic DNA using the polymerase chain reaction (PCR, U.S. Pat. Nos. 4,683,195 and 4,683,202, incorporated herein by reference). The loci of interest are amplified in separate reaction tubes; they can also be amplified together in a single PCR reaction. For increased specificity, a “hot-start” PCR reaction is used, e.g. by using the HotStarTaq Master Mix Kit supplied by QIAGEN (catalog number 203443). The amount of template DNA and primer per reaction are optimized for each locus of interest but in this example, 40 ng of template human genomic DNA and 5 μM of each primer are used. Forty cycles of PCR are performed. The following PCR conditions are used:

[0791] (1) 95° C. for 15 minutes and 15 seconds;

[0792] (2) 37° C. for 30 seconds;

[0793] (3) 95° C. for 30 seconds;

[0794] (4) 57° C. for 30 seconds;

[0795] (5) 95° C. for 30 seconds;

[0796] (6) 64° C. for 30 seconds;

[0797] (7) 95° C. for 30 seconds;

[0798] (8) Repeat steps 6 and 7 thirty nine (39) times;

[0799] (9) 72° C. for 5 minutes.

[0800] In the first cycle of PCR, the annealing temperature is about the melting temperature of the 3′ annealing region of the second primers, which is 37° C. The annealing temperature in the second cycle of PCR is about the melting temperature of the 3′ region, which anneals to the template DNA, of the first primer, which is 57° C. The annealing temperature in the third cycle of PCR is about the melting temperature of the entire sequence of the second primer, which is 64° C. The annealing temperature for the remaining cycles is 64° C. Escalating the annealing temperature from TM1 to TM2 to TM3 in the first three cycles of PCR greatly improves specificity. These annealing temperatures are representative, and the skilled artisan understands that the annealing temperatures for each cycle are dependent on the specific primers used.

[0801] The temperatures and times for denaturing, annealing, and extension, are optimized by trying various settings and using the parameters that yield the best results.

Purification of Fragment of Interest

[0802] The PCR products are separated from the genomic template DNA. Each PCR product is divided into four separate reaction wells of a Streptawell, transparent, High-Bind plate from Roche Diagnostics GmbH (catalog number 1 645 692, as listed in Roche Molecular Biochemicals, 2001 Biochemicals Catalog). The first primers contain a 5′ biotin tag so the PCR products bound to the Streptavidin coated wells while the genomic template DNA does not. The streptavidin binding reaction is performed using a Thermomixer (Eppendorf) at 1000 rpm for 20 min. at 37° C. Each well is aspirated to remove unbound material, and washed three times with 1×PBS, with gentle mixing (Kandpal et al., Nucl. Acids Res. 18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., Nucl. Acids Res. 18:6163-6164 (1990)).

[0803] Alternatively, the PCR products are placed into a single well of a streptavidin plate to perform the nucleotide incorporation reaction in a single well.

Restriction Enzyme Digestion of Isolated Fragments

[0804] The purified PCR products are digested with the restriction enzyme BsmF I (New England Biolabs catalog number R0572S), which binds to the recognition site incorporated into the PCR products from the second primer. The digests are performed in the Streptawells following the instructions supplied with the restriction enzyme. After digestion with the appropriate restriction enzyme, the wells are washed three times with PBS to remove the cleaved fragments.

Incorporation of Labeled Nucleotide

[0805] The restriction enzyme digest described above yields a DNA fragment with a 5′ overhang, which contains the locus of interest and a 3′ recessed end. The 5′ overhang functions as a template allowing incorporation of a nucleotide or nucleotides in the presence of a DNA polymerase.

[0806] For each locus of interest, four separate fill in reactions are performed; each of the four reactions contains a different fluorescently labeled ddNTP (ddATP, ddTTP, ddGTP, or ddCTP). The following components are added to each fill in reaction: 1 μl of a fluorescently labeled ddNTP, 0.5 μl of unlabeled ddNTPs (40 μM), which contains all nucleotides except the nucleotide that is fluorescently labeled, 2 μl of 10× sequenase buffer, 0.25 μl of Sequenase, and water as needed for a 20 μl reaction. The fill are performed in reactions at 40° C. for 10 min. Non-fluorescently labeled ddNTP are purchased from Fermentas Inc. (Hanover, Md.). All other labeling reagents are obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565). In the presence of fluorescently labeled ddNTPs, the 3′ recessed end is extended by one base, which corresponds to the locus of interest.

[0807] A mixture of labeled ddNTPs and unlabeled dNTPs also can be used for the fill-in reaction. The “fill in” conditions are as described above except that a mixture containing 40 μM unlabeled dNTPs, 1 μl fluorescently labeled ddATP, 1 μl fluorescently labeled ddTTP, 1 μl fluorescently labeled ddCTP, and 1 μl ddGTP are used. The fluorescent ddNTPs are obtained from Amersham (Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565; Amersham does not publish the concentrations of the fluorescent nucleotides). The locus of interest is digested with the restriction enzyme BsmF I, which generates a 5′ overhang of four bases. If the first nucleotide incorporated is a labeled ddNTP, the 3′ recessed end is filled in by one base, allowing detection of the locus of interest. However, if the first nucleotide incorporated is a dNTP, the polymerase continues to incorporate nucleotides until a ddNTP is filled in. For example, the first two nucleotides may be filled in with dNTPs, and the third nucleotide with a ddNTP, allowing detection of the third nucleotide in the overhang. Thus, the sequence of the entire 5′ overhang is determined, which increases the information obtained from each SNP or locus of interest. This type of fill in reaction is especially useful when detecting the presence of insertions, deletions, insertions and deletions, rearrangements, and translocations.

[0808] Alternatively, one nucleotide labeled with a single dye is used to determine the sequence of the locus of interest. See Example 6. This method eliminates any potential errors when using different dyes, which have different quantum coefficients.

[0809] After labeling, each Streptawell is rinsed with 1×PBS (100 μl) three times. The “filled in” DNA fragments are released from the Streptawells by digesting with the restriction enzyme EcoRI, according to the manufacturer's instructions that are supplied with the enzyme. The digestion is performed for 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

[0810] After release from the streptavidin matrix, the sample is loaded into a lane of a 36 cm 5% acrylamide (urea) gel (BioWhittaker Molecular Applications, Long Ranger Run Gel Packs, catalog number 50691). The sample is electrophoresed into the gel at 3000 volts for 3 min. The gel is run for 3 hours using a sequencing apparatus (Hoefer SQ3 Sequencer). The incorporated labeled nucleotide is detected by fluorescence.

[0811] To determine if any cells contain mutations at codon 1370 of the APC gene when separate fill-in reactions are performed, the lanes of the gel that correspond to the fill-in reaction for ddATP and ddTTP are analyzed. If only normal cells are present, the lane corresponding to the fill in reaction with ddATP is a bright signal. No signal is detected for the “fill-in” reaction with ddTTP. However, if the patient sample contains cells with mutations at codon 1370 of the APC gene, the lane corresponding to the fill in reaction with ddATP is a bright signal, and a signal is detected from the lane corresponding to the fill in reaction with ddTTP. The intensity of the signal from the lane corresponding to the fill in reaction with ddTTP is indicative of the number of mutant cells in the sample.

[0812] Alternatively, one labeled nucleotide is used to determine the sequence of the alleles at codon 1370 of the APC gene. At codon 1370, the normal sequence is AAA, which codes for the amino acid lysine. However, a nucleotide substitution has been identified at codon 1370, which is associated with colorectal tumors. Specifically, a change from A to T (AAA-TAA) typically is found at codon 1370, which results in a stop codon. A single fill-in reaction is performed using labeled ddATP, and unlabeled dTTP, dCTP, and dGTP. A single nucleotide labeled with one fluorescent dye is used to determine the presence of both the normal and mutant DNA sequence that codes for codon 1370. The relevant DNA sequence is depicted below with the sequence corresponding to codon 1370 in bold:

[0813]

	5′ CCCAAAAGTCCACCTGA	(SEQ ID NO: 46)
	3′ GGGTTTTCAGGTGGACT	(SEQ ID NO: 47)

[0814] After digest with BsmF I, the following overhang is produced:

[0815]

	5′ CCC
	3′ GGG	T	T	T	T
Overhang position		1	2	3	4

[0816] If the patient sample has no cells harboring a mutation at codon 1370, one signal is seen corresponding to incorporation of labeled ddATP.

[0817]

	5′ CCC	A*
	3′ GGG	T	T	T	T
Overhang position		1	2	3	4

[0818] However, if the patient sample has cells with mutations at codon 1370 of the APC gene, one signal is seen, which corresponds to the normal sequence at codon 1370, and a second signal is seen, which corresponds to the mutant sequence at codon 1370. The signals clearly are identified as they differ in molecular weight.

[0819]

Overhang of normal DNA sequence:	CCC
	GGG	T	T	T	T
Overhang position		1	2	3	4
Normal DNA sequence after fill-in:	CCC	A*
	GGG	T	T	T	T
Overhang position		1	2	3	4
Overhang of mutant DNA sequence:	CCC
	GGG	A	T	T	T
Overhang position		1	2	3	4
Mutant DNA sequence after fill-in:	CCC	T	A*
	GGG	A	T	T	T
Overhang position		1	2	3	4

[0820] Two signals are seen when the mutant allele is present. The mutant DNA molecules are filled in one base after the wild type DNA molecules. The two signals are separated using any method that discriminates based on molecular weight. One labeled nucleotide (ddATP) is used to detect the presence of both the wild type DNA sequence and the mutant DNA sequence. This method of labeling reduces the number of reactions that need to be performed and allows accurate quantitation for the number of mutant cells in the patient sample. The number of mutant cells in the sample is used to determine patient prognosis, the degree and the severity of the disease. This method of labeling eliminates the complications associated with using different dyes, which have distinct quantum coefficients. This method of labeling also eliminates errors associated with pipetting reactions.

[0821] To determine if any cells contain mutations at codon 1302 of the APC gene when separate fill-in reactions are performed, the lanes of the gel that correspond to the fill-in reaction for ddTTP and ddCTP are analyzed. The normal DNA sequence is depicted below with sequence coding for codon 1302 in bold type-face.

[0822]

	Normal Sequence:
	5′ ACCCTGCAAATAGCAGAA	(SEQ ID NO: 48)
	3′ TGGGACGTTTATCGTCTT	(SEQ ID NO: 49)

[0823] After digest, the following 5′ overhang is produced:

[0824]

	5′ ACCC
	3′ TGGG	A	C	G	T
Overhang position		1	2	3	4

[0825] After the fill-in reaction, labeled ddTTP is incorporated.

[0826]

	5′ ACCC	T*
	3′ TGGG	A	C	G	T
Overhang position		1	2	3	4

[0827] A deletion of a single base of the APC sequence, which typically codes for codon 1302, has been associated with colorectal tumors. The mutant DNA sequence is depicted below with the relevant sequence in bold:

[0828]

	Mutant Sequence:
	5′ ACCCGCAAATAGCAGAA	(SEQ ID NO: 50)
	3′ TGGGCGTTTATCGTCTT	(SEQ ID NO: 51)
After digest:
	5′ ACC
	3′ TGG	G	C	G	T
Overhang position		1	2	3	4
After fill-in:
	5′ ACC	C*
	3′ TGG	G	C	G	T
Overhang position		1	2	3	4

[0829] If there are no mutations in the APC gene, signal is not detected for the fill in reaction with ddCTP*, but a bright signal is detected for the fill-in reaction with ddTTP*. However, if there are cells in the patient sample that have mutations in the APC gene, signals are seen for the fill-in reactions with ddCTP* and ddTTP*.

[0830] Alternatively, a single fill-in reaction is performed using a mixture containing unlabeled dNTPs, fluorescently labeled ddATP, fluorescently labeled ddTTP, fluorescently labeled ddCTP, and fluorescently labeled ddGTP. If there is no deletion, labeled ddTTP is incorporated.

[0831]

	5′ ACCC	T*
	3′ TGGG	A	C	G	T
Overhang position		1	2	3	4

[0832] However, if the T has been deleted, labeled ddCTP* is incorporated.

[0833]

	5′ ACCC*
	3′ TGGG	C	G	T
Overhang position		1	2	3	4

[0834] The two signals are separated by molecular weight because of the deletion of the thymidine nucleotide. If mutant cells are present, two signals are generated in the same lane but are separated by a single base pair (this principle is demonstrated in FIG. 9D). The deletion causes a change in the molecular weight of the DNA fragments, which allows a single fill in reaction to be used to detect the presence of both normal and mutant cells.

[0835] In the above example, methods for the detection of a nucleotide substitution and a small deletion are described. However, the methods can be used for the detection of any type of mutation including but not limited to nucleotide substitutions (see Table VII), splicing errors (see Table VIII), small deletions (see Table IX), small insertions (see Table X), small insertions/deletions (see Table XI), gross deletions (see Table XII), gross insertions (see Table XIII), and complex rearrangements (see Table XIV).

[0836] In addition, the above-described methods are used for the detection of any type of disease including but not limited to those listed in Table IV. Furthermore, any type of mutant gene is detected using the inventions described herein including but not limited to the genes associated with the diseases listed in Table IV, BRCA1, BRCA2, MSH6, MSH2, MLH1, RET, PTEN, ATM, H-RAS, p53, ELAC2, CDH1, APC, AR, PMS2, MLH3, CYP1A1, GSTP1, GSTM1, AXIN2, CYP19, MET, NAT1, CDKN2A, NQ01, trc8, RAD51, PMS1, TGFBR2, VHL, MC4R, POMC, NROB2, UCP2, PCSK1, PPARG, ADRB2, UCP3, glur1, cart, SORBS1, LEP, LEPR, SIM1, TNF, IL-6, IL-1, IL-2, IL-3, IL1A, TAP2, THPO, THRB, NBS1, RBM15, LIF, MPL, RUNX1, Her-2, glucocorticoid receptor, estrogen receptor, thyroid receptor, p21, p27, K-RAS, N-RAS, retinoblastoma protein, Wiskott-Aldrich (WAS) gene, Factor V Leiden, Factor II (prothrombin), methylene tetrahydrofolate reductase, cystic fibrosis, LDL receptor, HDL receptor, superoxide dismutase gene, SHOX gene, genes involved in nitric oxide regulation, genes involved in cell cycle regulation, tumor suppressor genes, oncogenes, genes associated with neurodegeneration, genes associated with obesity. Abbreviations correspond to the proteins as listed on the Human Gene Mutation Database, which is incorporated herein by reference www.archive.uwcm.ac.uk./uwcm; website address active as of Feb. 12, 2003).

[0837] The above-example demonstrates the detection of mutant cells and mutant alleles from a fecal sample. However, the methods described herein are used for detection of mutant cells from any biological sample including but not limited to blood sample, serum sample, plasma sample, urine sample, spinal fluid, lymphatic fluid, semen, vaginal secretion, ascitic fluid, saliva, mucosa secretion, peritoneal fluid, fecal sample, body exudates, breast fluid, lung aspirates, cells, tissues, individual cells or extracts of the such sources that contain the nucleic acid of the same, and subcellular structures such as mitochondria or chloroplasts. In addition, the methods described herein are used for the detection of mutant cells and mutated DNA from any number of nucleic acid containing sources including but not limited to forensic, food, archeological, agricultural or inorganic samples.

[0838] The above example is directed to detection of mutations in the APC gene. However, the inventions described herein are used for the detection of mutations in any gene that is associated with or predisposes to disease (see Table XV).

[0839] For example, hypermethylation of the glutathione S-transferase P1 (GSTP1) promoter is the most common DNA alteration in prostrate cancer. The methylation state of the promoter is determined using sodium bisulfite and the methods described herein.

[0840] Treatment with sodium bisulfite converts unmethylated cytosine residues into uracil, and leaving the methylated cytosines unchanged. Using the methods described herein, a first and second primer are designed to amplify the regions of the GSTP1 promoter that are often methylated. Below, a region of the GSTP1 promoter is shown prior to sodium bisulfite treatment:

[0841]

	Before Sodium Bisulfite treatment:
	5′ ACCGCTACA
	3′ TGGCGATCA

[0842] Below, a region of the GSTP1 promoter is shown after sodium bisulfite treatment, PCR amplification, and digestion with the type IIS restriction enzyme BsmF I:

[0843]

Unmethylated
	5′ ACC
	3′ TGG	U	G	A	T
Overhang position		1	2	3	4
Methylated
	5′ ACC
	3′ TGG	C	G	A	T
Overhang position		1	2	3	4

[0844] Labeled ddATP, unlabeled dCTP, dGTP, and dTTP are used to fill-in the 5′ overhangs. The following molecules are generated:

[0845]

Unmethylated
	5′ ACC	A*
	3′ TGG	U	G	A	T
Overhang position		1	2	3	4
Methylated
	5′ ACC	G	C	T	A*
	3′ TGG	C	G	A	T
Overhang position		1	2	3	4

[0846] Two signals are seen; one corresponds to DNA molecules filled in with ddATP at position one complementary to the overhang (unmethylated), and the other corresponds to the DNA molecules filled in with ddATP at position 4 complementary to the overhang (methylated). The two signals are separated based on molecular weight. Alternatively, the fill-in reactions are performed in separate reactions using labeled ddGTP in one reaction and labeled ddATP in another reaction.

[0847] The methods described herein are used to screen for prostate cancer and also to monitor the progression and severity of the disease. The use of a single nucleotide to detect both the methylated and unmethylated sequences allows accurate quantitation and provides a high level of sensitivity for the methylated sequences, which is a useful tool for earlier detection of the disease.

[0848] The information contained in Tables VII-XIV was obtained from the Human Gene Mutation Database. With the information provided herein, the skilled artisan will understand how to apply these methods for determining the sequence of the alleles for any gene. A large number of genes and there associated mutations can be found at the following website: www.archive.uwcm.ac.uk./uwcm.

[0849]

TABLE VII
NUCLEOTIDE SUBSTITUTIONS
Codon	Nucleotide	Amino acid	Phenotype
99	CGG-TGG	Arg-Trp	Adenomatous polyposis coli
121	AGA-TGA	Arg-Term	Adenomatous polyposis coli
157	TGG-TAG	Trp-Term	Adenomatous polyposis coli
159	TAC-TAG	Tyr-Term	Adenomatous polyposis coli
163	CAG-TAG	Gln-Term	Adenomatous polyposis coli
168	AGA-TGA	Arg-Term	Adenomatous polyposis coli
171	AGT-ATT	Ser-Ile	Adenomatous polyposis coli
181	CAA-TAA	Gln-Term	Adenomatous polyposis coli
190	GAA-TAA	Glu-Term	Adenomatous polyposis coli
202	GAA-TAA	Glu-Term	Adenomatous polyposis coli
208	CAG-CGG	Gln-Arg	Adenomatous polyposis coli
208	CAG-TAG	Gln-Term	Adenomatous polyposis coli
213	CGA-TGA	Arg-Term	Adenomatous polyposis coli
215	CAG-TAG	Gln-Term	Adenomatous polyposis coli
216	CGA-TGA	Arg-Term	Adenomatous polyposis coli
232	CGA-TGA	Arg-Term	Adenomatous polyposis coli
233	CAG-TAG	Gln-Term	Adenomatous polyposis coli
247	CAG-TAG	Gln-Term	Adenomatous polyposis coli
267	GGA-TGA	Gly-Term	Adenomatous polyposis coli
278	CAG-TAG	Gln-Term	Adenomatous polyposis coli
280	TCA-TGA	Ser-Term	Adenomatous polyposis coli
280	TCA-TAA	Ser-Term	Adenomatous polyposis coli
283	CGA-TGA	Arg-Term	Adenomatous polyposis coli
302	CGA-TGA	Arg-Term	Adenomatous polyposis coli
332	CGA-TGA	Arg-Term	Adenomatous polyposis coli
358	CAG-TAG	Gln-Term	Adenomatous polyposis coli
405	CGA-TGA	Arg-Term	Adenomatous polyposis coli
414	CGC-TGC	Arg-Cys	Adenomatous polyposis coli
422	GAG-TAG	Glu-Term	Adenomatous polyposis coli
423	TGG-TAG	Trp-Term	Adenomatous polyposis coli
424	CAG-TAG	Gln-Term	Adenomatous polyposis coli
433	CAG-TAG	Gln-Term	Adenomatous polyposis coli
443	GAA-TAA	Glu-Term	Adenomatous polyposis coli
457	TCA-TAA	Ser-Term	Adenomatous polyposis coli
473	CAG-TAG	Gln-Term	Adenomatous polyposis coli
486	TAC-TAG	Tyr-Term	Adenomatous polyposis coli
499	CGA-TGA	Arg-Term	Adenomatous polyposis coli
500	TAT-TAG	Tyr-Term	Adenomatous polyposis coli
541	CAG-TAG	Gln-Term	Adenomatous polyposis coli
553	TGG-TAG	Trp-Term	Adenomatous polyposis coli
554	CGA-TGA	Arg-Term	Adenomatous polyposis coli
564	CGA-TGA	Arg-Term	Adenomatous polyposis coli
577	TTA-TAA	Leu-Term	Adenomatous polyposis coli
586	AAA-TAA	Lys-Term	Adenomatous polyposis coli
592	TTA-TGA	Leu-Term	Adenomatous polyposis coli
593	TGG-TAG	Trp-Term	Adenomatous polyposis coli
593	TGG-TGA	Trp-Term	Adenomatous polyposis coli
622	TAC-TAA	Tyr-Term	Adenomatous polyposis coli
625	CAG-TAG	Gln-Term	Adenomatous polyposis coli
629	TTA-TAA	Leu-Term	Adenomatous polyposis coli
650	GAG-TAG	Glu-Term	Adenomatous polyposis coli
684	TTG-TAG	Leu-Term	Adenomatous polyposis coli
685	TGG-TGA	Trp-Term	Adenomatous polyposis coli
695	CAG-TAG	Gln-Term	Adenomatous polyposis coli
699	TGG-TGA	Trp-Term	Adenomatous polyposis coli
699	TGG-TAG	Trp-Term	Adenomatous polyposis coli
713	TCA-TGA	Ser-Term	Adenomatous polyposis coli
722	AGT-GGT	Ser-Gly	Adenomatous polyposis coli
747	TCA-TGA	Ser-Term	Adenomatous polyposis coli
764	TTA-TAA	Leu-Term	Adenomatous polyposis coli
784	TCT-ACT	Ser-Thr	Adenomatous polyposis coli
805	CGA-TGA	Arg-Term	Adenomatous polyposis coli
811	TCA-TGA	Ser-Term	Adenomatous polyposis coli
848	AAA-TAA	Lys-Term	Adenomatous polyposis coli
876	CGA-TGA	Arg-Term	Adenomatous polyposis coli
879	CAG-TAG	Gln-Term	Adenomatous polyposis coli
893	GAA-TAA	Glu-Term	Adenomatous polyposis coli
932	TCA-TAA	Ser-Term	Adenomatous polyposis coli
932	TCA-TGA	Ser-Term	Adenomatous polyposis coli
935	TAC-TAG	Tyr-Term	Adenomatous polyposis coli
935	TAC-TAA	Tyr-Term	Adenomatous polyposis coli
995	TGC-TGA	Cys-Term	Adenomatous polyposis coli
997	TAT-TAG	Tyr-Term	Adenomatous polyposis coli
999	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1000	TAC-TAA	Tyr-Term	Adenomatous polyposis coli
1020	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1032	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1041	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1044	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1045	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1049	TGG-TGA	Trp-Term	Adenomatous polyposis coli
1067	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1071	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1075	TAT-TAA	Tyr-Term	Adenomatous polyposis coli
1075	TAT-TAG	Tyr-Term	Adenomatous polyposis coli
1102	TAC-TAG	Tyr-Term	Adenomatous polyposis coli
1110	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1114	CGA-TGA	Arg-Term	Adenomatous polyposis coli
1123	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1135	TAT-TAG	Tyr-Term	Adenomatous polyposis coli
1152	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1155	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1168	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1175	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1176	CCT-CTT	Pro-Leu	Adenomatous polyposis coli
1184	GCC-CCC	Ala-Pro	Adenomatous polyposis coli
1193	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1194	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1198	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1201	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1228	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1230	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1244	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1249	TGC-TGA	Cys-Term	Adenomatous polyposis coli
1256	CAA-TAA	Gln-Term	Adenomatous polyposis coli
1262	TAT-TAA	Tyr-Term	Adenomatous polyposis coli
1270	TGT-TGA	Cys-Term	Adenomatous polyposis coli
1276	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1278	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1286	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1289	TGT-TGA	Cys-Term	Adenomatous polyposis coli
1294	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1307	ATA-AAA	Ile-Lys	Colorectal cancer,
			predisposition to,
			association
1309	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1317	GAA-CAA	Glu-Gln	Colorectal cancer,
			predisposition to
1328	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1338	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1342	TTA-TAA	Leu-Term	Adenomatous polyposis coli
1342	TTA-TGA	Leu-Term	Adenomatous polyposis coli
1348	AGG-TGG	Arg-Trp	Adenomatous polyposis coli
1357	GGA-TGA	Gly-Term	Adenomatous polyposis coli
1367	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1370	AAA-TAA	Lys-Term	Adenomatous polyposis coli
1392	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1392	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1397	GAG-TAG	Glu-Term	Adenomatous polyposis coli
1449	AAG-TAG	Lys-Term	Adenomatous polyposis coli
1450	CGA-TGA	Arg-Term	Adenomatous polyposis coli
1451	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1503	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1517	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1529	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1539	TCA-TAA	Ser-Term	Adenomatous polyposis coli
1541	CAG-TAG	Gln-Term	Adenomatous polyposis coli
1564	TTA-TAA	Leu-Term	Adenomatous polyposis coli
1567	TCA-TGA	Ser-Term	Adenomatous polyposis coli
1640	CGG-TGG	Arg-Trp	Adenomatous polyposis coli
1693	GAA-TAA	Glu-Term	Adenomatous polyposis coli
1822	GAC-GTC	Asp-Val	Adenomatous polyposis coli,
			association with ?
2038	CTG-GTG	Leu-Val	Adenomatous polyposis coli
2040	CAG-TAG	Gln-Term	Adenomatous polyposis coli
2566	AGA-AAA	Arg-Lys	Adenomatous polyposis coli
2621	TCT-TGT	Ser-Cys	Adenomatous polyposis coli
2839	CTT-TTT	Leu-Phe	Adenomatous polyposis coli

[0850]

TABLE VIII
NUCLEOTIDE SUBSTITUTIONS
Donor/	Relative
Acceptor	location	Substitution	Phenotype
ds	−1	G-C	Adenomatous polyposis coli
as	−1	G-A	Adenomatous polyposis coli
as	−1	G-C	Adenomatous polyposis coli
ds	+2	T-A	Adenomatous polyposis coli
as	−1	G-C	Adenomatous polyposis coli
as	−1	G-T	Adenomatous polyposis coli
as	−1	G-A	Adenomatous polyposis coli
as	−2	A-C	Adenomatous polyposis coli
as	−5	A-G	Adenomatous polyposis coli
ds	+3	A-C	Adenomatous polyposis coli
as	−1	G-A	Adenomatous polyposis coli
ds	+1	G-A	Adenomatous polyposis coli
as	−1	G-T	Adenomatous polyposis coli
ds	+1	G-A	Adenomatous polyposis coli
as	−1	G-A	Adenomatous polyposis coli
ds	+1	G-A	Adenomatous polyposis coli
ds	+3	A-G	Adenomatous polyposis coli
ds	+5	G-T	Adenomatous polyposis coli
as	−1	G-A	Adenomatous polyposis coli
as	−6	A-G	Adenomatous polyposis coli
as	−5	A-G	Adenomatous polyposis coli
as	−2	A-G	Adenomatous polyposis coli
ds	+2	T-C	Adenomatous polyposis coli
as	−2	A-G	Adenomatous polyposis coli
ds	+1	G-A	Adenomatous polyposis coli
ds	+1	G-T	Adenomatous polyposis coli
ds	+2	T-G	Adenomatous polyposis coli

Table IX: APC Small Deletions