Detecting Genetic Abnormalities

Abstract

directed to compositions and methods for detecting genetic abnormalities. The present invention encompasses methods and compositions for comparing alleles in a sample containing both maternal and fetal nucleic acids in order to identify genetic abnormalities.

Description

CROSS REFERENCE TO RELATED APPLICATIONS

[0001]This application claims the benefit of priority to U.S. Patent Application No. 61/106,435, filed Oct. 17, 2008, which is hereby incorporated by reference in its entirety. This application is a continuation-in-part of U.S. patent application Ser. No. 11/713,069, filed Feb. 28, 2007, which claims priority to U.S. Patent Application No. 60/777,865, filed Feb. 28, 2006, each of which is hereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

[0002]A majority of pregnant women receive some kind of test, including maternal serum screening and/or an ultrasound test, to determine risks for common birth defects, such as those resulting from trisomy 13, 18, and 21 (Down Syndrome). Both the sensitivity and specificity of these common non-invasive screening tools are extremely poor. The best current non-invasive tests lead to a false positive rate between 7 and 20%. This high false positive rate often causes individuals to opt for invasive diagnostic tests, such as chorionic villus sampling (CVS) and amniocentesis. Such invasive tests each carry a fetal loss rate of 0.5%-1% and account for the loss of thousands of normal fetuses annually. However, prenatal diagnosis can be critical for management of a pregnancy with chromosomal abnormalities and localized genetic abnormalities, because an accurate and early diagnosis allows for interventional care before or during delivery and can prevent devastating consequences for the neonate. The development of a non-invasive test for genetic abnormalities that is sensitive and specific with low false-positive and false-negative rates would be of benefit to the field of molecular diagnostics.

SUMMARY OF THE INVENTION

[0003]Accordingly, the present invention provides methods and compositions for detecting genetic abnormalities.

[0004]In one aspect, the present invention provides method for determining whether a fetus has at least one chromosomal abnormality. This method includes the step of comparing at least three alleles, and this comparing identifies the at least one chromosomal abnormality.

[0005]In a further aspect, the present invention provides a method for determining whether a fetus has at least one chromosomal abnormality. This method includes the steps of: (i) detecting a paternally-inherited fetal allele in a sample that includes both maternal and fetal nucleic acids, wherein that paternally-inherited fetal allele is not present in the maternal genome; (ii) detecting a first maternal allele and a second maternal allele in the sample; and (iii) comparing the paternally-inherited fetal allele to the first and second maternal alleles, where the comparing identifies the at least one chromosomal abnormality.

[0006]In an exemplary embodiment, comparing alleles according to the present invention includes detecting the number of molecules of each allele. In a further embodiment, detecting the number of molecules of each allele provides the allelic dosage of each allele.

[0007]In a still further exemplary embodiment, comparing alleles according to the present invention includes calculating a haplotype ratio. In a still further embodiment, the haplotype ratio is calculated according to the formula: HR=|P1-P2↑/P3, where P1 is the number of molecules of a first maternal allele, P2 is the number of molecules of a second maternal allele, and P3 is the number of molecules of a paternally-inherited fetal allele.

BRIEF DESCRIPTION OF THE DRAWINGS

[0008]FIG. 1 is a schematic illustration of an embodiment of an assay of the invention.

[0009]FIG. 2 is a schematic illustration of possible haplotypes in an exemplary embodiment of a tandem SNP.

[0010]FIG. 3 is a schematic illustration of an embodiment of an assay of the invention.

[0011]FIG. 4 is a schematic illustration of an embodiment of an assay of the invention.

[0012]FIG. 5A-B is a table of an exemplary list of tandem SNPs of the invention.

[0013]FIG. 6A-AO is a table of an exemplary list of tandem SNPs of the invention and primers directed to those tandem SNPs.

[0014]FIG. 7 provides a DNA melting map of a constant denaturant capillary electrophoresis target sequence covering a tandem SNP.

[0015]FIGS. 8A and B provides data of a haplotype ratio analysis.

[0016]FIG. 9A-C is a table of an exemplary list of tandem SNPs of the invention.

DETAILED DESCRIPTION OF THE INVENTION

[0017]The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such conventional techniques include polymer array synthesis, hybridization, ligation, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the example herein below. However, other equivalent conventional procedures can, of course, also be used. Such conventional techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press), Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York, Gait, "Oligonucleotide Synthesis: A Practical Approach" 1984, IRL Press, London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3^rd Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al. (2002) Biochemistry, 5^th Ed., W. H. Freeman Pub., New York, N.Y., all of which are herein incorporated in their entirety by reference for all purposes.

[0018]Note that as used herein and in the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a polymerase" refers to one agent or mixtures of such agents, and reference to "the method" includes reference to equivalent steps and methods known to those skilled in the art, and so forth.

[0019]Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing devices, compositions, formulations and methodologies which are described in the publication and which might be used in connection with the presently described invention.

[0020]Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either both of those included limits are also included in the invention.

[0021]In the following description, numerous specific details are set forth to provide a more thorough understanding of the present invention. However, it will be apparent to one of skill in the art that the present invention may be practiced without one or more of these specific details. In other instances, well-known features and procedures well known to those skilled in the art have not been described in order to avoid obscuring the invention.

[0022]Although the present invention is described primarily with reference to specific embodiments, it is also envisioned that other embodiments will become apparent to those skilled in the art upon reading the present disclosure, and it is intended that such embodiments be contained within the present inventive methods.

I. Overview of the Invention

[0023]The present invention is directed to methods and compositions for detecting genetic abnormalities. By "genetic abnormality" is meant any variation in one or more elements of an individual's genome in comparison to a general population. Genetic abnormalities can include without limitation chromosomal abnormalities, single point mutations, and any other variations that can result in changes in the levels of cDNA, RNA, mRNA, microRNA, and coding and non-coding RNA. Thus, the term "genetic abnormality" as used herein is interchangeable with the term "nucleic acid abnormality". "Chromosomal abnormalities" can include without limitation aneuploidy (including without limitation trisomy 13 (Patau Syndrome), trisomy 18 (Edward Syndrome) and sex chromosome aneuploidies such as XXY (Klinefelter's Syndrome), subchromosomal abnormalities, gross deletions, gross insertions, large deletions, large insertions, copy number variants, copy number variation, repeat variations, structural alterations, small deletions (<20 bp), small insertions (<20 bp), indels, small indels (<20 bp), and the like. Genetic abnormalities can be inherited, arise somatically, occur as de novo events, occur clonally, etc.

[0024]In general, methods and compositions of the present invention can be used to analyze a sample comprising genetic material from two or more individuals. "Genetic material" includes without limitation DNA (including full or partial chromosomes, cDNA and genetic DNA) and RNA (including mRNA, tRNA, siRNA, micro RNA, coding and non-coding RNA). Methods of the present invention include comparing alleles contained in the sample to detect and quantify differences between the genetic material from the two or more individuals. In some embodiments, such differences can be used to identify genetic abnormalities in one or more of the individuals. Although the description of the present invention is primarily provided herein in terms of DNA, it will be appreciated that these aspects and embodiments of the invention also encompass RNA, and that all methods and compositions of the present invention can be applied to any nucleic acid.

[0025]In a specific aspect, methods and compositions of the invention are used to analyze a sample containing fetal and maternal genetic material. In a further aspect, methods and compositions of the invention are used to compare alleles contained in such a sample to determine if the fetal genetic material comprises a genetic abnormality. As used herein, "allele" is a variant form of a sequence at a particular region on a chromosome. The variants in the sequence can come as a result of single nucleotide polymorphisms ("SNPs"), combinations of SNPs, haplotype methylation patterns, insertions, deletions, and the like. An allele may comprise the variant form of a single nucleotide, a variant form of a contiguous sequence of nucleotides from a region of interest on a chromosome, or a variant form of multiple single nucleotides (not necessarily all contiguous) from a region of interest on a chromosome.

[0026]The term "comparing alleles" as used herein refers to any analysis that identifies similarities and differences among the alleles of interest. For example, comparing alleles may involve detecting and/or identifying the different alleles of interest in a sample. Comparing alleles may also involve detecting and quantifying the number of molecules of each of the different alleles of interest in a sample. Comparing alleles may further involve determining the relative number of molecules of each of the different alleles with respect to each other or with respect to a reference sample. In addition, comparing alleles may involve a comparison of the concentrations or relative concentrations of each of the alleles in a sample. As will be discussed in further detail herein, comparing alleles in a sample can detect and identify genetic abnormalities.

[0027]Although the present invention is primarily discussed in terms of a comparison between fetal and maternal genetic material, the methods and compositions described herein can also be applied to other applications in which a comparison of the genetic material between two or more individuals is desired. Embodiments of such extensions to the described methods and compositions are discussed in further detail herein and are encompassed by the present invention.

II. Comparing and Quantifying Alleles

[0028]In one aspect, the present invention provides methods and compositions for comparing alleles in a sample.

[0029]A "sample" in accordance with the present invention may comprise any number of substances, including, but not limited to, bodily fluids (including, but not limited to, blood, urine, serum, lymph, saliva, anal and vaginal secretions, perspiration and semen, of virtually any organism, with mammalian samples being preferred and human samples being particularly preferred); environmental samples (including, but not limited to, air, agricultural, water and soil samples); biological warfare agent samples; research samples (i.e. in the case of nucleic acids, the sample may be the products of an amplification reaction, including both target and signal amplification as is generally described in PCT/US99/01705, such as PCR amplification reaction); purified samples, such as purified genomic DNA, RNA, proteins, etc.; raw samples (bacteria, virus, genomic DNA, etc.); as will be appreciated by those in the art, virtually any experimental manipulation may have been conducted on the sample.

[0030]In one aspect, samples of use in the present invention are obtained from a pregnant female. Such samples can include without limitation maternal blood, maternal urine, maternal sweat, maternal cells, or cell free DNA. In a further aspect, these maternal samples contain both maternal and fetal DNA.

[0031]Although the majority of the disclosure herein is directed to embodiments using DNA, it will be appreciated that any genetic material is contemplated for use and analysis in accordance with the present invention and is therefore encompassed by the present invention. In addition, the terms "chromosomal region" and "chromosome" are used interchangeably herein, and both refer to part or all of a chromosome unless otherwise specified.

[0032]In general, the present invention provides methods and compositions for comparing alleles in a sample. Comparing alleles in accordance with the invention includes detecting the identity of the different alleles present in the sample. Comparing alleles also includes detecting and/or quantifying the number of molecules of each allele of interest that is present in a sample. For example, a maternal sample containing both fetal and maternal DNA may contain three different alleles for a particular chromosomal region of interest. As discussed above, these three alleles would be variant sequences of the chromosomal region of interest. Methods known in the art and described further herein can be used to determine how many molecules of each of the three different alleles are present in the sample. In such an exemplary embodiment, comparing the three alleles would include comparing the number of molecules of each of the three alleles. Comparing alleles in further embodiments of the invention can include without limitation evaluating the concentration of alleles in a sample and evaluating relative concentrations and/or relative numbers of molecules of alleles in a sample.

[0033]In a further embodiment, evaluating relative concentrations or numbers of molecules in a sample includes calculating an "allelic ratio" among the alleles in a sample. This allelic ratio is the ratio of the amount of molecules of each of the alleles of interest present in the sample, and may be calculated in any number of ways known in the art and described further herein. For example, if a sample comprises two alleles A and B, and a standard method in the art (such as sequencing) shows that there are twice as many molecules of B as there are of A, then one embodiment of an allelic ratio may be the characterization of A:B as 1:2. In further embodiments, such as those containing a calculation of multiple alleles, the allelic ratio may be a standard ratio--for example, for three alleles A, B, and C, the allelic ratio may be expressed as the number of molecules of A:B:C. In further embodiments, a more complex relationship may be described as an allelic ratio, such as (A-B)/C. Such embodiments are discussed in further detail herein.

[0034]Methods for detecting and quantifying alleles or any other sequence of interest are known in the art. Such methods include without limitation any methods that detect DNA (including without limitation genomic and cDNA) and RNA (including without limitation mRNA, microRNA, and silent RNA). Such methods for detecting nucleic acids can include without limitation sequencing methods, gel electrophoresis, mass spectrometry, detection of methylation patterns, PCR methods, high performance liquid chromatography (HPLC) and the like. Methods for detecting and quantifying alleles in accordance with the present invention provide the sequence of the alleles present in the sample (or identify the presence of an allele of interest) and may also provide the number of molecules of each of the alleles in the sample. Methods for detecting and/or quantifying alleles that are of use in the present invention also include methods that quantify the relative amounts of two or more alleles of interest in a sample. By "relative amounts" is meant relative numbers of molecules and/or relative concentrations.

[0035]Sequencing methods of use for detecting and quantifying alleles of interest according to the present invention include without limitation single molecule sequencing, sequencing by synthesis, sequencing using arrays (hybridization and/or ligation), capillary sequencers, Sanger sequencing, constant denaturant capillary electrophoresis (CDCE), cycling temperature capillary electrophoresis (CTCE), polony sequencing, pyrosequencing, shot-gun sequencing, and the like. Commercial high throughput sequencing platforms for detecting and quantifying alleles of interest and such platforms are known in the art and can include without limitation: Illumina's GA, Life Technologies' SOLiD, Roche's 454, Pacific Biosciences single molecule sequencing platform, Oxford Nanopore, Ion Torrent, Complete Genomics, Nimblegen, Helicos Biosciences, Lingvitae, Nabsys, and Visigen Biotechnologies.

[0036]PCR methods of use for detecting and quantifying alleles of interest according to the present invention include without limitation digital PCR and competitive PCR.

[0037]Methods such as those described above and known in the art can be used to compare alleles in a sample by providing information on the identity (i.e., the sequence) of the alleles as well as the number of molecules of each allele present in the sample.

[0038]In general, methods of the invention include detecting alleles of a specific chromosomal region. As has been discussed above, the term "chromosomal region" refers to all or part of a chromosome. Detection of such alleles can be conducted using any method known in the art, including the sequencing and PCR methods described above. In some embodiments, the sample being analyzed is from a pregnant female and contains both maternal and fetal DNA. Detecting and/or quantifying the number of different alleles in the sample and the number of molecules of those alleles that are present in the sample can identify the presence of a chromosomal abnormality in a fetus.

[0039]In a further exemplary embodiment, a sample contains three alleles of a chromosomal region that is being analyzed. Two of the alleles are from a known source, while the third allele is expected to come from a separate source. Quantification of the number of molecules present in the sample of each allele allows comparison between the alleles from the known source and the third allele.

[0040]In a still further exemplary embodiment, the sample is a maternal sample containing both fetal and maternal nucleic acids. In this example, the sample again contains three alleles of a particular chromosomal region. If the maternal genome is heterozygous for this allele, then two of the three alleles detected in the sample are from the maternal germline DNA, while the third allele is expected from the paternal DNA contribution (if the paternal DNA contains an allele not present in the maternal genome). Quantification of the three alleles therefore allows comparisons between the two maternal alleles from the mother, allowing the determination of which allele and how many molecules were contributed by the mother to the fetus. Quantifying the number of molecules of the alleles also provides information on how many molecules of the third allele were contributed by the father to the fetus. Comparison of the maternally inherited and paternally inherited alleles further allows a quantification of the maternal and paternal contributions to the fetal DNA.

[0041]FIG. 1 is a schematic representation of the comparisons that can be made between different alleles detected in a sample. In FIG. 1, a maternal sample in which three alleles are detected is shown. The peaks illustrated in FIG. 1 represent the number of molecules of each allele present in the sample. As discussed herein, these "peaks" (i.e., the number of molecules) can be determined using methods well known in the art and described herein. For example, the area under the peaks from an electropherogram from a CDCE analysis of a sample provides information on the number of molecules of each detected allele. Similarly, the output of a sequencing platform will provide a count of the number of molecules for each allele, which can also be depicted by the peaks in FIG. 1.

[0042]In an exemplary embodiment, genetic abnormalities, including chromosomal abnormalities, are detected by comparing the number of molecules of alleles in a sample. As is generally illustrated in FIG. 1, a sample comprising both fetal and maternal nucleic acids will be expected to show specific relationships between the number of molecules for alleles of a particular chromosome. For example, if the maternal genome is heterozygous for a particular chromosomal region, then two alleles detected in the sample will be the maternal contribution. Since the sample contains both fetal and maternal DNA, the number of molecules detected for those two alleles will include the numbers of molecules from the maternal DNA and the numbers of molecules for the maternally-inherited allele in the fetal DNA (also referred to herein as the "maternally-inherited fetal allele"). The fetal genome will contain maternally and paternally-inherited alleles. If the paternally-inherited allele in the fetal DNA (also referred to herein as the "paternally-inherited fetal allele") is not present in the maternal genome, then three different alleles will be detected in the sample containing both maternal and fetal DNA (the two alleles from the mother and the one paternally-inherited allele in the fetus). Comparing the number of molecules for each allele can then be used to detect a chromosomal abnormality.

[0043]In further embodiments, the present invention provides methods for detecting genetic abnormalities, including chromosomal abnormalities, in a fetus by detecting alleles for a location of interest on a chromosome (also referred to herein as a "genetic location"), where the maternal genome is heterozygous at that location of interest and the fetus inherits a different allele from the father at that same genetic location. In still further embodiments, methods of the invention detect a paternally-inherited fetal allele in a sample comprising both maternal and fetal nucleic acids, where that paternally-inherited fetal allele is not present in the maternal genome. Detection of such a paternally-inherited fetal allele will in such embodiments indicate that the fetus does have a genetic abnormality.

[0044]As will be appreciated, the term "maternal allele" may refer to the allele inherited by the fetus from the mother and/or the alleles in the maternal genome. In a sample comprising both fetal and maternal DNA, the molecules of "maternal allele" detected and quantified will include both molecules of the allele from the maternal DNA as well as molecules from the fetal DNA of the maternally-inherited fetal allele.

[0045]For example, in approximately 95% of trisomy cases, the fetus inherits two copies of the chromosome from the mother. In this situation, three alleles of that chromosome or a particular region of that chromosome are detected in the sample (represented by the three peaks in FIG. 1). As discussed above, if the mother is heterozygous, two of the alleles detected are the maternal alleles. The number of molecules detected for those two alleles will reflect the molecules from the maternal DNA in the sample plus the molecules of those same two alleles from the fetal DNA (i.e., the maternal alleles plus the maternally-inherited fetal alleles). The third allele detected will be the fetal allele that is paternally inherited and is not present in the maternal genome. In this example, trisomy is detected if the number of molecules for the two maternal alleles is equal (first trace of FIG. 1B) or if all three alleles are present in different numbers in the relationship of peak, x and peak+2x, where "peak" represents the number of molecules for one of the maternal alleles, "x" represents the number of molecules for the paternally-inherited fetal allele, and "peak+2x" is the number of molecules for the other maternal allele (right two traces of FIG. 1B). In the situation in which the two maternal alleles have equal numbers of molecules, trisomy is detected, because the numbers for the two maternal alleles are actually a sum of the maternal alleles and the maternally-inherited fetal alleles. The only way for the numbers for both maternal alleles to be equal in a sample comprising both fetal and maternal DNA is if the fetus inherited two alleles from the mother. The presence of the paternally inherited allele indicates that the fetus must then have trisomy, because it has both alleles from the mother and one from the father.

[0046]Similarly, in the situation in which all three alleles are present in the sample in the relationship of peak, x and peak+2x, this also indicates that the fetus has trisomy. The "peak" represents the number of molecules of maternal allele. "x" represents the number of molecules of the paternally-inherited fetal allele. "x" therefore represents a kind of internal standard of how much fetal DNA is present in the sample. The allele with the number of alleles "peak+2x" thus contains alleles from the mother as well as two copies of the allele from the fetus. These two copies are the maternally-inherited fetal DNA. Therefore, the fetus again has inherited two alleles from the mother and one from the father, which is an indication of trisomy.

[0047]The same analysis of the number and identity of the alleles in a sample can also be used to determine that the fetus does not have trisomy. As discussed above, this analysis must be conducted for an allele for which the maternal genome is heterozygous. If three alleles are detected in a sample containing both maternal and fetal DNA, then two of the alleles will be from the heterozygous mother, and the third allele is the paternally-inherited fetal allele. For a fetus without trisomy, the number of molecules of the three alleles will all be different, but unlike the case with trisomy above, the number of molecules of the three alleles will be in the relationship of "peak", "x" and "peak+x". "Peak" represents the number of molecules of one of the maternal alleles. "x" represents the number of molecules of the paternally-inherited fetal allele. "Peak+x" represents the number of molecules of the second maternal allele--this number includes both the number of molecules of the allele from the maternal DNA and the number of molecules of the maternally-inherited fetal allele. Thus, if the fetus has inherited only one chromosome from each parent, there should be a larger number of molecules for the allele the fetus inherited from the mother and a smaller number of molecules for the allele the fetus inherited from the father. Since the sample comprises maternal and fetal DNA but no paternal DNA, the only molecules of paternal alleles present in the sample are molecules of the paternally-inherited fetal allele. As a result, the number of molecules of the paternally-inherited fetal allele can provide an internal standard of how much fetal DNA is present in the sample relative to the maternal DNA.

[0048]In further embodiments, analysis of the number of molecules of alleles in a sample provides a measure of "allelic dosage". By "allelic dosage" as used herein is meant the number or concentration (or relative number or concentration) of molecules of each allele that is present in a sample. Thus, calculation of an "allelic ratio" as discussed above provides a mechanism to measure the dosage of each allele. Furthermore, in an analysis of a sample comprising both fetal and maternal nucleic acids, determining the number of molecules of paternally-inherited fetal alleles also provides a measure of the paternally-inherited fetal allelic dosage. This paternally-inherited fetal allelic dosage can serve as an internal standard that can be used to determine the maternally-inherited fetal allelic dosage. Thus, a calculation of allelic dosage provides a measure of the allelic dosage from each parent to the fetus. Calculations of allelic dosage can be used to detect a genetic abnormality using any of the methods described herein, because the relationships expected for maternal and paternal (and maternally-inherited and paternally-inherited) are equivalent to the relationships described herein for comparing alleles.

[0049]As will be appreciated, the above methods can also be used to compare alleles based on de novo deletions, insertions, and the like. For example, in the case of 22q11.2 deletion syndrome (the most common human deletion syndrome, which is typically a 3 million basepair deletion), the deletion is a de novo event in 75% of the cases. If the de novo event is a maternally-derived deletion in the fetal genome, three alleles would again be detectable in a sample comprising both maternal and fetal DNA. However, the number of molecules of the three alleles will show a relationship in which two of the alleles are present in equal numbers and the third allele will be present in smaller numbers. In other words, two fetal alleles will not be detected in the sample, because one of those alleles would be deleted. As discussed above, for a normal fetus, all three alleles should have different numbers of molecules present in the sample, with the numbers being in the relationship of "peak", "x" and "peak+x". In the case of a maternally-derived deletion, the numbers would instead be in the relationship of "peak", "peak" and "x".

[0050]Similarly, in the case of a de novo but paternally-derived 22q11.2 deletion in the fetal genome, a third allele would not be detected in a sample containing both maternal and fetal DNA, because it would be the paternally-inherited fetal allele that would be deleted. In further embodiments, multiple assays directed to the detection of different alleles can be conducted to confirm that the lack of a third fetal allele is the result of a deletion rather than the result of a non-informative assay (i.e., an assay in which the maternal genome is not heterozygous for an allele or the paternal genome has an allele in common with the maternal genome).

[0051]In further embodiments, methods of the present invention can be used to detect alleles that are inherited. In the maternally-derived and paternally-derived deletions discussed above, the maternal and paternal genomes are normal at the deletion/insertion site, but during meiosis, deletions or insertions occur and are passed to the fetus. In contrast, deletions and insertions and point mutations (which would include basepair substitutions), small (less than 20 base pairs) deletions or insertions (also referred to herein as "small-deletions" and "small-insertions" respectively) may occur in the maternal and/or paternal genomes and are passed on to the fetus. When a target sequence is larger than the small deletion or insertion, the same comparisons described above for allelic comparisons can be used to determine allelic dosage inheritance if a neighboring SNP can be encompassed by the target sequence. For example, the delta F508 deletion in the CFTR gene is a small deletion that can be passed on to the fetus by either the mother or the father. In the case where the mother is a carrier of the delta F508 deletion, it will appear as if she has two peaks. If the father contributes a normal allele and the fetus inherits the delta F508 deletion, the maternal plasma would show two peaks of equal area and height. It would not be clear if there was no fetal DNA present in the sample, or was at levels too low to be detected. However, if a neighboring SNP is encompassed, permitting at least three possible alleles in the target sequence, it would be possible to distinguish maternally inherited from paternally inherited alleles. The term "peaks" as used herein refers to the number of molecules of an allele and to a signal associated with the number of molecules of an allele.

[0052]In one aspect, the present invention provides methods and compositions for comparing alleles, where those alleles may be comprised of haplotypes. As used herein, the term "haplotypes" refers to groups or sets of markers (including without limitation SNPs, deletions, small deletions, insertions, small insertions, methylation, and short tandem repeats) that are inherited together as a unit. Thus, alleles detected and quantified as described herein encompass multiple markers, and thus different alleles comprise different combinations of these multiple markers. As will be discussed in further detail herein, alleles of use in the present invention may comprise multiple SNPs. These SNPs may be contiguous or non-contiguous. In further embodiments, alleles for comparison may include any combination of sites, including deletion sites, insertion sites, and sites which comprise variant sequences of two or more nucleotides in length. For example, alleles detected and compared in accordance with the present invention may include a deletion site and/or an insertion site and/or one or more SNPs and/or a variant sequence comprising two or more nucleotides. Such combinations increase the number of haplotypes that can be detected for a particular genetic location, thus increasing the informative of the comparative assays of the invention, as is discussed in more detail herein.

[0053]In a further aspect, multiple alleles are detected in a single reaction or assay. Thus, by identifying one or more SNPs, methylation patterns, or any other combination of markers that can compose an allele as described above, detecting multiple alleles (e.g., detecting both maternal alleles and a paternally-inherited fetal allele) in a single reaction or assay preserves phase information on the chromosome.

[0054]II(A). Amplification of Nucleic Acids Prior to Detection

[0055]In order to increase the signal of alleles of interest for a specific chromosome or chromosomal region, the nucleic acids in a sample are in many embodiments amplified using methods known in the art. Such amplification methods include polymerase chain reaction (PCR), strand displacement amplification (SDA), multiple displacement amplification (MDA), rolling circle amplification (RCA), rolling circle amplification (RCR) and other amplification (including whole genome amplification) methodologies. In certain embodiments, the chromosomes are amplified using primers directed to desired regions. This amplification enriches the sample for the allelic sequences for those specific chromosomal regions, and then methods known in the art for detecting those sequences can be used to detect and quantify the different alleles present in the sample. In some embodiments all nucleic acids in the sample are amplified, and then alleles of interest are detected using methods known in the art and described herein. In some embodiments, alleles of interest are amplified using primers with sequences such as those listed in FIGS. 5 and 6 and then detected using methods well known in the art and described herein.

[0056]The term "nucleic acid" refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, made of monomers (nucleotides) containing a sugar, phosphate and a base that is either a purine or pyrimidine. Unless specifically limited, the term encompasses nucleic acids containing known analogs of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues.

[0057]The term "nucleotide sequence" refers to a polymer of DNA or RNA which can be single-stranded or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases capable of incorporation into DNA or RNA polymers. The terms "nucleic acid," "nucleic acid molecule," or "polynucleotide" are used interchangeably herein.

[0058]In some embodiments, High-Fidelity (Hi-Fi) PCR is used to amplify alleles of interest in a sample. High-Fidelity PCR is an amplification method resulting in an error rate (in per basepair doubling) equal to or better than standard PCR. For example, Taq polymerase, which is not a high fidelity polymerase, has an error rate of ˜10^-4 per basepair doubling. In contrast, Pyrococcus furiosus (Pfu) is a high-fidelity polymerase, with a published error rate for Pfu is 1.3×10^-6 per basepair doubling (Cline et al, Nucleic Acids Res. 1996 Sep. 15; 24(18): 3546-3551). Examples of high-fidelity enzymes include Pfu and its derivations, or other enzymes with similar proofreading 3'->5' exonucleases. Mixed blends and fusions with enzymes with proof-reading capabilities can increase the fidelity of a polymerase. Use of such a high fidelity polymerase ensures that the alleles of interest are amplified efficiently and with minimal to no introduction of errors.

[0059]Methods for improving PCR fidelity and efficiency include, among others: A) using a high-fidelity polymerase enzyme; and B) the addition of chemical reagents (e.g., betaine) that can lower temperatures required during the PCR process. Lowering temperatures required during the PCR products can increase efficiency and prevent damage to the amplification products, because prolonged heating of DNA and nucleotides during PCR can lead to damaged products, such as deaminated cytosines (uracils) and thus lead to misincorporation errors and miscopying errors during PCR (Andre, Kim, Khrapko, Thilly. Genome Res. 1997 7: 843-852. Zheng, Khrapko, Coller, Thilly, Copeland. Mutat Res. 2006 Jul. 25; 599(1-2):11-20).

[0060]In certain embodiments of the invention, amplification using HiFi-PCR, is performed with primers present in molar excess (e.g., 10¹² copies/μl of primer vs 10⁶ or less of the template) so that it is more likely that primers will anneal with template DNA than with each other (see, e.g., Li-Sucholeiki X C, Thilly W G. Nucleic Acids Res. 2000 May 1; 28(9):E44; Thompson J R, Marcelino L, Polz M. Nucleic Acids Res. 2002 May 1; 30(9): 2083-2088.). This can significantly reduce the creation of heteroduplexes.

III. Tandem SNPs

[0061]In certain embodiments, comparisons of alleles as described above utilize alleles of tandem single nucleotide polymorphisms (referred to herein as "tandem SNPs"). A "single nucleotide polymorphism (SNP)" is a single basepair variation in a nucleic acid sequence. A "tandem SNP" is a variation in more than one nucleotide in a nucleic acid sequence, e.g. on a chromosome. In some embodiments, a tandem SNP is a pair of SNPs that are located in the nucleic acid sequence. In further embodiments, a tandem SNP comprises more than two SNPs. As will be appreciated, any number of SNPs can be contained in a tandem SNP, limited only by the total number of nucleotides present in the nucleic acid. In still further embodiments, a tandem SNP comprises from 2 to about 20 SNPs. In still further embodiments, a tandem SNP comprises from about 3 to about 19, about 4 to about 18, about 5 to about 17, about 6 to about 16, about 7 to about 15, about 8 to about 14, about 9 to about 13, and about 10 to about 12 SNPs. In yet further embodiments, a tandem SNP comprises between two SNPs and the maximum number of SNPS that can be assayed in a single reaction, which may depend on the detection platform (e.g., the read length of the sequencing technology). In still further embodiments, a tandem SNP comprises between two SNPs and the maximum number of SNPs contained within the segment of genetic material to be analyzed. For example, fetal DNA circulating in maternal serum is often fragmented and has a length of 200-400 bases--in such an exemplary embodiment, the number of SNPs contained in a tandem SNP would be limited by the maximum number of SNPs contained in that fragmented DNA.

[0062]As will be appreciated, the two or more single SNPs in a tandem SNP may be of any distance apart. For tandem SNPs with more than two single SNPs, the multiple SNPs may be of equal distance apart, or there may be varying distances between them. In some embodiments, the distance between SNPs of a tandem SNP is generally about 350 basepairs or fewer. In still further embodiments, the SNPs of tandem SNPs are about 5 to about 300, about 10 to about 250, about 15 to about 200, about 20 to about 150, about 25 to about 140, about 30 to about 130, about 35 to about 120, about 40 to about 110, about 45 to about 100, about 50 to about 90, about 55 to about 80, and about 60 to about 70 base pairs apart.

[0063]Increasing the number of SNPs that make up tandem SNPs of the invention increases the potential number of haplotypes, and thereby increases the likelihood that an assay detecting alleles will be informative. For example, if a tandem SNP contains 3 SNP sites, the potential number of haplotypes is 8 and if it contains 4 SNP sites, the potential number of haplotypes is 16. This increases the likelihood that an assay will be informative, because the mother is more likely to be heterozygous at such a tandem SNP, and the paternal contribution to the fetus (also referred to herein as the "paternally-inherited fetal allele") is likely to be different from that present in the mother's genome. Thus, an assay that detects the alleles for this tandem SNP is likely to provide the at least three alleles that allows a comparison to be conducted for detection of a genetic abnormality, as is discussed in further detail herein.

[0064]Tandem SNPs provide a particularly powerful tool for comparing alleles in a sample, because tandem SNPs allow the detection and quantification of haplotypes. As will be discussed in further detail herein, the use of haplotypes in methods of the present invention provide an internal standard that eliminates the need for using reference markers across different chromosomes, thereby increasing specificity and/or minimizing or eliminating false positives.

[0065]As discussed herein, "haplotypes" are groups or sets of markers (including without limitation SNPs, deletions, small deletions, insertions, small insertions, methylation, and short tandem repeats) that are inherited together as a unit. Different alleles of a tandem SNP are thus haplotypes, and haplotypes can be assigned to a chromosome (i.e., the maternally inherited or paternally inherited chromosome). Comparing alleles of a tandem SNP comprises far more information than is possible from comparing individual SNPs, because comparing alleles of a tandem SNP provides a comparison of haplotypes.

[0066]An exemplary embodiment of a tandem SNP is schematically illustrated in FIG. 2. In this embodiment, the tandem SNP comprises a pair of SNPs. At SNP 1, two alleles are possible: G or T. At SNP 2, two alleles are possible: A or G. There are therefore four alleles possible for this tandem SNP, and these alleles are defined by the four possible haplotypes: G-A, T-A, G-G, or T-G. As will be appreciated, an individual may be heterozygous or homozygous for a tandem SNP, as is the case for a single SNP, but being heterozygous for a tandem SNP means that multiple different haplotypes are possible alleles for that tandem SNP. As will also be appreciated, for tandem SNPs containing three or more SNPs, the resultant number of possible haplotypes will also increase.

[0067]As discussed above, genetic abnormalities can be detected in a fetus by comparing the number of molecules of alleles between the fetal and maternal nucleic acids in a sample. By using tandem SNPs, the comparison can be used to both compare and quantify the differences between maternal and fetal DNA.

[0068]In an exemplary embodiment, detecting the alleles of tandem SNPs in a sample containing both maternal and fetal DNA can be used to calculate a haplotype ratio. As discussed above, these allele comparison assays are conducted for chromosomal regions of interest at which the maternal genome is heterozygous. In the case of tandem SNPs, the maternal genome being heterozygous means that it has two different haplotypes for that particular tandem SNP. Detecting the number of molecules of alleles of the tandem SNP present in a sample is thus a detection of the number of molecules of the different haplotypes are present in the sample.

[0069]If three alleles of a tandem SNP are detected in a sample containing both maternal and fetal DNA, the haplotype ratio (HR) can be calculated using the following formula:

HR=|P1-P2|/P3 (Formula I)

[0070]P1 and P2 represent the number of molecules of each of the maternal haplotypes, and P3 represents the number of molecules of a third haplotype that is not present in the maternal genome. P3 thus represents the number of molecules of the haplotype inherited by the fetus from the father. As discussed herein for comparing alleles, the calculation of the haplotype ratio provides a way to determine if the fetus has a chromosomal abnormality, including without limitation trisomy, monosomy, partial duplication, partial deletion, microduplication, microdeletion, and the like. As will be appreciated, the description of the number of molecules of alleles as relating to the terms "peak", and "x" are related to P1, P2 and P3 of Formula I. For example, P1 and P2 represent the maternal alleles--i.e., "peak+x" (or "peak+2x" in cases of trisomy) and "peak", whereas P3 of Formula I is equivalent to the paternally-inherited fetal allele, i.e., "x".

[0071]In exemplary embodiments, the haplotype ratio calculation will produce the discrete results of 1, 2, 0 or 0.5. These numbers are interpreted as follows:

TABLE-US-00001 TABLE 1 interpretation of haplotype ratio calculations for the detection of trisomy and/or partial duplications Haplotype ratio Interpretation |P1 - P2|/P3 = 1 Fetus has the normal number of chromosomes |P1 - P2|/P3 = 2 Fetus has trisomy, likely as result of a duplication during maternal meiosis II or paternal meiosis I |P1 - P2|/P3 = 0 Fetus has trisomy, likely as a result of a duplication during maternal meiosis I |P1 - P2|/P3 = 0.5 Fetus has trisomy, likely as a result of a duplication during paternal meiosis II

[0072]In a further embodiment, paternal non-disjunction, in which the fetus inherits two alleles from the father, may result in the haplotype ratios described in Table 1. In addition, if the two alleles from the father are both not found in the maternal genome, it would be possible to detect four alleles in a sample containing both maternal and fetal DNA--two alleles would again be from the maternal genome, and two would be paternally-inherited fetal alleles (see FIG. 3, lower panel for exemplary combinations of alleles).

[0073]In further embodiments, the haplotype ratio can be calculated according to the following formula:

HR=|P1-P2|/|P3+P4| (Formula II)

In this embodiment, P1 and P2 represent the number of molecules of each of the maternal haplotypes and P3 and P4 represent the number of molecules of a third and fourth haplotype that is not present in the maternal genome. As will be appreciated, Formula II is applicable to embodiments of paternal non-disjunction trisomy, in which two paternally-inherited fetal alleles are present in the sample. Formula II is also applicable to situations in which only one paternally-inherited fetal allele is present in the sample--in such situations, either P3 or P4=0. Thus, Formula II can be applied to calculate the haplotype ratio for any sample from a pregnant female carrying a single fetus.

[0074]For de novo deletions in the fetus (including partial deletions, microsomal deletions, large deletions, etc,), paternally inherited deletions in the fetus would result in an entire panel of tandem SNPs without an informative third allele being present in the maternal sample. In such a situation, haplotype ratios cannot be calculated. Thus, the absence of an informative third allele or third haplotype can indicate a de novo deletion in the paternally inherited chromosome and would be informative in and of itself.

[0075]Thus, calculation of the haplotype ratio provides discrete detection and quantification of fetal chromosomal/genetic abnormality/allelic dosage within a single measurement from a sample comprising both maternal and fetal DNA. Unlike traditional methods of using single SNPs to determine whether a fetus has a chromosomal abnormality, the present invention does not require measurements of alleles across different chromosomes in order to determine the amount of fetal DNA present in the sample in relation to the maternal DNA. As discussed above, the present invention has an internal standard for each measurement. Since the maternal genome is heterozygous for the particular tandem SNP being analyzed, detection of three alleles in a sample containing both maternal and fetal DNA means that one of the detected alleles is the paternally-inherited fetal allele. Since the molecules of the paternally-inherited fetal allele can only be from the fetal DNA, detection of the number of molecules of that paternally-inherited fetal allele provides a measurement of how much fetal DNA is present in the sample. This third allele serves as an internal standard of the amount of fetal DNA, and there is no need to compare the measurement of the number of molecules of fetal alleles against the number of molecules of fetal alleles present for another chromosome that is not expected to have an abnormality. Thus, in the present invention, a single measurement of the number of molecules of an allele of a particular chromosome (i.e., a chromosome expected to be subject to an abnormality) provides all the information needed to determine whether the fetus has a chromosomal abnormality.

[0076]A further advantage of the methods of the present invention, particularly the internal standard provided by detection of the third allele, is that the ratios of the alleles and the calculation of the haplotype ratio will not vary based on the concentration in the sample of fetal genetic material. Traditional methods for detecting chromosomal abnormalities must normalize calculations of ratios with respect to the amount of fetal genetic material present in the sample being analyzed. In contrast, the methods of the present invention do not require such normalization, because comparing the number of molecules of the paternally-inherited fetal allele to the number of molecules of the maternal alleles in accordance with the present invention allows a calculation of allelic ratios that is independent of the amount of the total amount of fetal genetic material present in the sample.

[0077]As will be appreciated, the above methods for calculating haplotype ratios can be conducted using a single tandem SNP or using multiple tandem SNPs (also referred to herein as "panels" of tandem SNPs). When multiple tandem SNPs are used in any methods in accordance with the present invention, they can be utilized one at a time, in specific groupings, or all possible tandem SNPs can be analyzed at the same time in a multiplex assay. In some embodiments of the invention, panels of tandem SNPs comprise between 2 and 200 tandem SNPs. As will be appreciated, each of these tandem SNPs define a haplotype and therefore may in turn comprise two or more SNPs. In further embodiments, panels of tandem SNPs comprising between about 2-150, 10-140, 15-130, 20-120, 25-110, 30-100, 35-90, 40-80, 45-70, and 50-60 tandem SNPs are used in accordance with the present invention.

[0078]Multiple tandem SNPs may be assayed individually for a sample or multiplexed into a single assay. In some embodiments, the number of SNPs applied in a single assay may depend on the amount of nucleic acids that are present in and/or can be obtained from a sample. In further embodiments, all or a selected portion of the nucleic acids in a sample are amplified, which will allow multiple tandem SNPs directed to one or more chromosomes to be applied in a single multiplexed assay. As will be appreciated, using multiple tandem SNPs, either sequentially or simultaneously, can be used in some embodiments to assay for abnormalities in multiple chromosomes. The number of chromosomes that can be assayed using methods of the invention is limited only by the number of chromosomes present in the organism from which the sample is obtained.

[0079]In many embodiments, a panel of tandem SNPs is assayed in a sample, but only a subset of the panel (anywhere from between 1 and up to the total number of tandem SNPs in the panel) is informative, meaning that not every tandem SNP in a panel will produce a "positive" result. A positive result in assays utilizing tandem SNPs is generally the detection of at least three alleles for a particular tandem SNP. For any particular sample, even a single positive result from a tandem SNP can allow detection of a genetic abnormality. Results from more than one tandem SNP can be used as further internal confirmation of an assay.

[0080]The analysis of the paternally inherited fetal allele, particularly analysis with respect to tandem SNPs, is of use in detecting non-chromosomal mutations. In the case of a point mutation that is present in the mother or father's genome (A* in FIG. 4), this can be combined with a nearby SNP site to create at least three potential haplotypes. The inheritance pattern of the point mutation(s) to the fetus can therefore be traced in accordance with the methods described herein.

[0081]As is schematically illustrated in FIG. 4, the use of tandem SNPs allows detection of a recessive mutation that would not be detectable in methods utilizing single SNPs. As shown in the left panel, detecting alleles for a single SNP in a sample comprising both maternal and fetal DNA does not allow one to determine whether the fetus has inherited the point mutation. However, using the haplotype analysis possible by detecting alleles of tandem SNPs (FIG. 4, right panel), it is possible to detect the third allele in the sample, which is the paternally-inherited fetal allele. If the paternally-inherited fetal haplotype comprises the recessive point mutation, detection of that third allele is informative. Although in this exemplary embodiment the tandem SNP comprises two single SNPs, as is discussed herein, tandem SNPs may comprise multiple single SNPs.

[0082]In the extremely rare situation that the point mutation occurs at a base pair which is known to have a SNP, the single site would be tri-allelic and therefore it may not be necessary to combine the point mutation site with a nearby SNP. Then a simple comparison of detected alleles as described in further detail above would allow detection of the mutant allele.

[0083]The ability to trace the inheritance pattern of point mutations has clinical importance in the case of recessive disorders. If both the mother and father are heterozygous at a point mutation site carrying a normal and mutated base, the use of haplotypes (point mutation+nearby SNP) allows one to determine whether the fetus is at risk for being homozygous for the recessive mutation. This is thus one embodiment of the tandem SNP analysis described herein. The combination of any mutation (e.g. point mutation, insertion, deletion, methylation) along with a nearby SNP is useful to determining the fetal risk of homozygosity for a recessive disorder.

[0084]In some embodiments, short tandem repeats (STRs) can be used as a tandem SNP or as part of a tandem SNP for comparing alleles. STRs are highly polymorphic regions in the genome, and many alleles can be present at a single STR site--for example, in many situations it is possible to have ten or more alleles at a given site. STRs generally arise in highly repetitive sequences which are error prone during amplification, resulting in their highly polymorphic state.

[0085]In some embodiments, tandem SNPs do not comprise STRs.

[0086]In some embodiments, the information gathered about the alleles of interest in a sample comprising both maternal and fetal DNA is compared to similar information gathered about the alleles of interest in a sample comprising maternal DNA but no fetal DNA. The sample containing only the maternal DNA can be used as a reference for the sample containing both maternal and fetal DNA. Although such a reference sample is not generally necessary, it can provide additional substantiation of the results from the assays discussed herein. In some embodiments, the sample comprising maternal DNA but no fetal DNA is obtained using methods known in the art. Such samples can be obtained from a number of sources, including without limitation: maternal buccal swabs, maternal cells, including maternal white blood cells, and the like.

[0087]III(A). Identifying Tandem SNPs

[0088]As will be appreciated, different samples will require the use of different tandem SNPs for detection of genetic abnormalities. This is because one requirement of the methods described herein, particularly methods involving tandem SNPs, is that the maternal genome must be heterozygous for the allele of interest in order to allow the detection of a third, paternally-inherited allele. In addition, tandem SNPs for which the paternal genome comprises the same haplotypes as the maternal genome will not be informative, because it is the detection of three alleles for a particular tandem SNP that provides the internal standard of the paternally-inherited fetal allele.

[0089]The present invention provides methods and compositions for identifying tandem SNPs. In some embodiments, a chromosomal region of interest is studied to identify potential markers (i.e., alleles) for use as tandem SNPs. Studying a chromosomal region of interest for identifying tandem SNPs in some embodiments involves analyzing a database comprising information on the occurrence of SNPs in one or more populations (such as the database from the International HapMap Project). In further embodiments, studying a chromosomal region of interest to identify tandem SNPs comprises collecting samples of nucleic acids for a number of individuals and amplifying the region of interest. The amplification product can then be sequenced or otherwise analyzed to identify potential markers for use as tandem SNPs.

[0090]In some embodiments, a tandem SNP is chosen by identifying two or more neighboring SNPs. Such SNPs may be separated by any range of distances, and as will be appreciated, the distances between neighboring SNPs is limited only by the size of the chromosomal region of interest. In some embodiments, the two or more SNPs in a tandem SNP may be separated by a distance of about 5 to about 400 base pairs. In further embodiments, the two or more SNPs in a tandem SNP may be separated by a distance of about 10 to about 350, about 20 to about 300, about 30 to about 250, about 40 to about 200, about 50 to about 150, about 50 to about 140, about 60 to about 130, about 70 to about 120, about 80 to about 110, and about 80 to about 100 base pairs. In embodiments in which more than two SNPs are in a tandem SNP, each individual SNP may be of equal distance from the other SNPs, or the SNPs may be at varying distances from each other. Although the description herein of tandem SNPs is primarily in terms of two or more SNPs, a tandem SNP may also include any combination of SNPs, deletions, insertions, and sequence variants of two nucleotides or greater, and descriptions of tandem SNPs herein applies to all such combinations. As will be appreciated, "neighboring" SNPs as described herein may have one or more SNPs (or deletions, insertions, sequence variants) that occur in the region between the SNPs that are part of a particular tandem SNP. Thus, in an exemplary embodiment, if SNPs A, B and C occur in that order along a chromosomal region in a population, a tandem SNP may be chosen such that A and C are the "neighboring" SNPs, and B is a SNP located in the intervening region between A and C.

[0091]In further embodiments, tandem SNPs of the invention are selected such that the combination of SNPs (and/or deletions, insertions and sequence variants) results in more than two haplotypes being present in a population. In still further embodiments, tandem SNPs are chosen that result in more than two haplotypes present in populations across different ethnic groups--as will be appreciated, such information can be generated from publicly available databases (such as the HapMap database) or from direct investigation of samples collected from multiple individuals.

[0092]In still further embodiments, tandem SNPs of the invention are chosen such that their component SNPs, deletions, insertions and sequence variants do not lie within a common, non-disease related CNV (copy number variation) region, such as those present in the Database of Genomic Variants from The Centre for Applied Genomics at http://projects.tcag.ca/variation/.)

[0093]In further embodiments, methods for identifying tandem SNPs utilize maternal buccal samples (or any other samples that contain maternal DNA but no fetal DNA) in order to identify regions at which the maternal genome is heterozygous.

[0094]In an exemplary embodiment, tandem SNPs are identified from population data files (such as the HapMap database). In this exemplary embodiment, highly heterozygous (i.e., greater than 10% or more or "common") SNPs are identified. In some embodiments, only those SNPs that are highly heterozygous in all populations contained in the database are chosen as likely candidates. In other embodiments, likely candidates are chosen from SNPs that are highly heterozygous in a subset of the populations contained in the database. Tandem SNPs can then be provisionally selected by choosing highly heterozygous SNPs that are at a desired distance from each other, as is discussed above. As is also discussed herein, likely tandem SNPs may comprise a wide range of individual SNPs.

[0095]In still further embodiment, any likely tandem SNPs that occur in the list of SNPs from common CNV regions are removed from further consideration. In still further embodiments, tandem SNPs that lie in regions with long stretches of homopolymeric sequences (i.e. 6 or greater) are also removed from further consideration.

[0096]In yet further embodiments, primers are designed to amplify regions containing likely tandem SNPs. In some embodiments, these primers are optimized for efficiency and specificity using methods known in the art. In further embodiments, primers are tested to determine if they preferentially amplify one or more alleles of the likely tandem SNPs over others.

[0097]As will be appreciated, tandem SNPs of use in accordance with the present invention can be chosen using any combination of the above methods and characteristics. In some exemplary embodiments, tandem SNPs are chosen based solely on distance between each component. A "component" of a tandem SNP as used herein refers to individual SNPs, deletions, insertions, or sequence variations that make up a tandem SNP.

[0098]In some embodiments, a chromosomal region of interest can be directly sequenced from one or more samples to identify potential tandem SNPs. In further embodiments, genetic material from a number of individuals, (e.g., 8 individuals, 10 individuals, 96 individuals, even 20,000 individuals) can be collected and amplified for a given target sequence of interest. The alleles present in this amplified sample can then be detected and quantified to identify sequences that can serve as tandem SNPs. In some embodiments, the genomic DNA from these individuals are pooled together and a target sequence of interest is amplified in a single PCR reaction. If three or more alleles occur in this pooled sample, and at least three of these alleles occur at high percentages (>10%) in the pooled sample, then the target sequence is a likely candidate for use as a tandem SNP in accordance with the present invention.

[0099]As will be appreciated, tandem SNPs can be identified for any chromosome. Exemplary tandem SNPs identified in accordance with the present invention for chromosome 21 are provided in FIG. 5. FIG. 6 shows tandem SNPs for chromosome 21 as well as primers that can be used for amplification and detection of these tandem SNPs. Exemplary tandem SNPs identified in accordance with the present invention for chromosomes 13, 18 and 22 are provided in FIG. 9. Tandem SNPs identified in accordance with the present invention for any other chromosome are also encompassed by the present invention, as are tandem SNPs other than those in FIGS. 5, 6 and 9. As will be appreciated, sequences that have at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99% sequence identity to the sequences provided in FIGS. 5-6 and 9 are also encompassed by the present invention.

IV. Uses Beyond Detecting Genetic Abnormalities

[0100]Although the above description has been provided in terms primarily of genetic abnormalities, the same detection and quantification of alleles, including alleles of tandem SNPs, can be used in other applications.

[0101]In some embodiments, the present methods and compositions of the present invention can be used to evaluate tissue rejection in a patient who has received a tissue transplant. In such embodiments, if the host is heterozygous, detection of a third (and possibly fourth) allele frequency may come from the graft at the time of transplant. The levels of allelic dosage at the time of transplant can then be compared to levels at later time points to determine if the graft is being rejected. Such comparisons can be conducted by calculating allelic and/or haplotype ratios as discussed herein. An advantage of using tandem SNPs in this embodiment, particularly with tandem SNPs comprising more than two SNPs or other components, is that the likelihood of having an informative assay (i.e., one in which at least three alleles can be detected) is increased, and it would be possible to quantitatively measure both the maternally inherited and the paternally inherited alleles from both the recipient and the graft by calculating a Haplotype Ratio. Such information can not be obtained from studies in which only individual SNPs are used to compare between the genetic material of the recipient and the graft.

[0102]In still further embodiments, the methods and compositions can be used in transfusions, to determine if a donor is a match for the recipient. As with the analysis for detecting tissue rejection, the allelic dosage can be calculated to determine if the transfusion is acceptable to the recipient.

[0103]In further embodiments, the methods and compositions of the present invention can be used in forensic analysis by identifying samples through a comparison of alleles for a particular chromosomal region. Methods of the present invention for detecting and comparing alleles, including alleles of tandem SNPs, will provide information as to whether a particular forensic sample comprises samples from one or more individuals. Such forensic analysis may be used in cases of sexual assault, for determining paternity, as well as other forensic applications that would benefit from the ability to compare allelic dosage in a sample.

EXAMPLES

Example 1

Tandem SNPs for Chromosome 21

[0104]Allelic markers on chromosome 21 were selected by examining tandem SNPs. These tandem SNPs covered both q and p arms of the chromosome. Using heterozygosity data available through dbSNP, DCC Genotype Database and through the HapMap Project, SNPs that appeared to be promising for high heterozygosity (≧25%) were selected. Because all four possibilities may not exist in nature due to haplotype blocks in regions of low recombination, those that suggested less than three haplotypes were screened out.

[0105]Target sequences covering tandem SNPs were designed using Vector NTI and WinMelt software. As an example, the melting map of a CDCE or CTCE target covering two tandem SNPs (dbSNP rs2839416 and rs2839417) on chromosome 21 was calculated using WinMelt according to the algorithm of Lerman and Silverstein (Lerman et al., Methods Enzymol, 1987. 155: p. 482-501) and is depicted in FIG. 7.

[0106]FIG. 7 depicts a DNA melting map of a CDCE or CTCE target sequence covering tandem SNPs. All four haplotypes can be theoretically separated according to DNA melting temperature. The curves for the four different haplotypes (haplotype 1 (G,A); haplotype 2 (T,A); haplotype 3 (G,G); and haplotype 4 (T,G)) are identified on the figure.

[0107]HiFi PCR optimization for each target sequence was performed using Pfu polymerase. One of primers flanking the target sequence was ˜20 bases in length and labeled 5' with a fluorescein molecule. The other primer was about 74 bases including a ˜20-base target specific sequence and the 54-base clamp sequence. A standard HiFi PCR condition was applied to all target sequences, varying only annealing temperatures. These PCR amplicons were subjected to CDCE or CTCE electrophoretic separation. The resulting electropherograms were analyzed for yield and purity of the PCR products. The purity was evaluated by comparing the peak area of the desired products to that of the byproducts and nonspecific amplification. Target sequences that could be amplified with a high PCR efficiency (≧45% per cycle) and low levels of byproducts and nonspecific amplification 0.1% of the desired products) were subjected to CDCE or CTCE optimization. For those target sequences that did not have acceptable PCR products in the first stage, increasing amounts of Mg⁺² concentrations (up to about 7 mM) in combination with different annealing temperatures were tested. For the remaining target sequences that still did not work, primer positions were changed and the entire optimization process is repeated.

[0108]For CDCE or CTCE optimization, the relevant haplotypes were created for the targets using pools of 96 individuals. The optimal separation condition for each haplotype should provide the greatest resolution among the observed peaks. Initial optimization is done around the theoretical melting temperature (T_m) in a 2° C. temperature range in increments of 0.2° C. which covers (T_m-1° C.±a predetermined offset) to (T_m+1° C.±a predetermined offset).

[0109]Electropherogram and peak measurements were transferred to a spreadsheet for analysis. To ensure the quality of the data, minimum and maximum peak heights were used. Individual markers were failed if electrophoretic spikes occur. Peak areas were used to calculate allele ratios. A check for allelic preferential amplification was performed on all 96 tandem SNPs.

[0110]In the fall of 2005, the International HapMap Project publicly released genotypes and frequencies from 270 people of four ethnic populations. Chromosome 21 haplotype data from approximately 40,000 SNPs genotyped across four populations, including U.S. residents with northern and western European ancestry, residents of Ibadan, Nigeria, of Tokyo, Japan, and of Beijing, China, were downloaded (2005-10-24: HapMap Public Release #19) and converted to the + orientation. Tandem SNP candidates fell within 100 basepairs from each other and at least three haplotypes existed in all four ethnic populations. CDCE or CTCE target sequences and primers were designed for the tandem SNPs identified through the HapMap Project. The neighboring sequences for each of the tandem SNPs were imported into a software program, e.g., Sequencher (Gene Codes, Ann Arbor, Mich.) and/or Vector NTI (Invitrogen, Carlsbad, Calif.) for sequence alignment and primer design, and into Winmelt (Medprobe, Oslo, Norway) or Poland software (available at biophys.uniduesseldorf.de/local/POLAND/poland.html) where the algorithm for computing DNA melting temperatures given the Gotoh-Tagashira values for the enthalpy of melting DNA sequences were used to calculate melting temperatures of target sequences. CDCE or CTCE candidates generally have a high melting region adjacent to a low melting region, lie in a low melting region, melting temperatures of the low melting region fall below 80° C., and no "valleys" occur between the high melting region and the low melting region.

[0111]All of the 40,000 genotypes on chromosome 21 were analyzed for tandem SNP/CDCE/CTCE marker suitability. 118 tandem SNPs/CDCE/CTCE targets meeting requirements have been identified (see FIG. 5 for the first 42 identified and FIG. 6 for all 118).

[0112]Primer sequences for these 118 tandem SNP/CDCE/CTCE targets were designed. These were optimized as described herein using HiFi PCR and CDCE or CTCE. These optimizations included the creation of relevant haplotypes for all targets, a check for allelic preferential amplification during HiFi PCR, and obtaining the greatest resolution among peaks during CDCE or CTCE. Haplotypes may be separated as homoduplex peaks. However, if certain targets cannot be separated out as homoduplexes, maternal DNA can be separated from fetal DNA as heteroduplexes.

Example 2

Determining Heterozygosity of Tandem SNPs

[0113]Genomic DNA samples from 300 anonymous subjects were obtained from healthy young adults who were less than 35 years old. The samples were anonymous as the only data obtained were the geographic location of the Red Cross blood donor center, donor gender, and whether or not the donor was 35 and under. These samples were reviewed to ensure that at least three haplotypes were present for a given target sequence of interest. These results were compared to haplotypes identified through analysis of the database from the HapMap project as described in Example 1, and it was found that the same or similar haplotypes were identified using both methods.

Example 3

Detecting Fetal DNA in Maternal Serum

[0114]A cohort of subjects confirmed to have trisomy 21 by traditional karyotype analysis was examined. Tandem SNPs were used to demonstrate detection of trisomy in subjects. DNA from 20 subjects who were characterized by traditional karyotype analysis to have trisomy 21 were analyzed with the tandem SNP panel.

[0115]Biological samples, including a buccal (cheek) swab and a blood sample were collected from a cohort of pregnant women. Maternal buccal swab samples were compared to maternal serum to demonstrate that a third (paternal) peak was observed in several of the tandem SNP assays. Approximately 20 maternal buccal swab to maternal serum comparisons were made. To control for experimental artifacts, genomic DNA samples from maternal buccal swabs were utilized for each target sequence. The buccal samples were subjected to the process in parallel with the maternal blood sample. Any artifacts generated by the CDCE/CTCE/HiFi-PCR procedure (including nonspecific PCR amplification and polymerase-induced mutations) were revealed as background peaks in the buccal swab samples.

Example 4

Detecting Fetal Chromosomal Abnormalities

[0116]A blinded study is performed where the goal is to detect 20 known trisomy 21 fetuses by assaying maternal serum from 40 patients (previously determined by amniocentesis or CVS) (see FIG. 3).

[0117]FIG. 1A depicts a schematic illustration of the output of detecting alleles in a sample from maternal buccal swab. Markers exhibiting two alleles were pursued. A baby with trisomy is expected to show either three alleles, evident by three peaks in a 1:1:1 ratio or two alleles in a 2:1 ratio. FIG. 1B depicts a sample from maternal serum. Markers exhibiting three alleles are informative. Maternal serum from a woman carrying a baby with trisomy is expected to exhibit three alleles, evident by two equal peaks with a third smaller peak if the trisomy occurred during meiosis I (75% of T21 cases) or three alleles with different areas if the trisomy occurred during meiosis II (20% of T21 cases) where areas are: peak, x, and peak+2x. FIG. 1C is a schematic illustration of the analysis of a sample from maternal serum. Markers exhibiting three alleles are informative. Maternal serum from a woman with a normal baby with three alleles has three different areas where areas are: peak, x, and peak+x.

[0118]FIG. 8 shows data from a CDCE experiment for two different samples. In the top sample, the mother is carrying a non-trisomy 21 fetus. As expected, the haplotype ratio calculated from comparing the peaks in the output (which each represent a different allele, and the area under each of which provides the number of molecules for each allele) is within a margin of error to 1, the haplotype ratio expected for a normal fetus (see FIG. 8A). FIG. 8B shows the results for a mother carrying a fetus with trisomy 21. The haplotype ratio calculated from these data was within a margin of error to 2, which is one of the haplotype ratios expected for a fetus with a chromosomal abnormality.

[0119]For the case of the minimum heterozygosity, where both SNP1 and SNP2 are heterozygous at their respective loci at a rate of 25%, if 96 tandem SNPs are assayed, an average of 43 markers (44.5%) are expected to be heterozygous (two haplotypes) in the mother. The mother's expected heterozygosity is calculated using the following formula:

H=1-Σp_i² (Formula III)

wherein l=1 to k alleles and pi=estimated allele frequency.

[0120]The allele frequencies at each SNP loci are expected to be 85% and 15% for the majority and minority alleles, respectively, assuming Hardy-Weinberg equilibrium. The desired third haplotype is expected to be present at an average of 6.4 markers (15%) of per maternal-fetal sample tested. Because most loci have a heterozygosity value greater than 25%, for every maternal-fetal sample tested using the panel of 96 tandem SNP assays, greater than about 6.4 markers are most informative. Thus, while a panel of 96 tandem SNPs may be used, 6 or 7 of those tandem SNPs may be informative for any one specific maternal-fetal sample tested, and a `positive` result from any one of those tandem SNPs is informative.

[0121]Finally, in order to diagnose a trisomy, a "positive" tandem SNPs should be identified on both the p and the q arm of chromosome 21. Because of the comparative nature of the basic approach, the tandem SNP assay is predicted to have a detection rate of 95% (those that occur during maternal meiosis) for trisomy 21. If paternal samples are available, non-disjunctions that occur during paternal meiosis can also be detected. Thus, detection rates would be higher (about ˜99%) with a 0% false positive rate.

Example 5

Identification of Patients with Trisomy 21

[0122]A study was approved by the Institutional Review Board for Human Research at the Medical College of Wisconsin. 27 high risk pregnant patients who were scheduled to undergo amniocentesis or CVS or had already had either of these procedures were recruited as subjects at Froedtert Hospital. Informed consent was obtained from each participant before blood draws and buccal swabs were obtained.

[0123]Karyotype analysis confirmed 7 pregnancies carried a trisomy 21 fetus while 20 pregnancies carried a disomy 21 fetus. The gestational week and maternal age varied from 9-36.1 weeks and 22-43 years respectively. The gestational age ranged from first to third trimesters and the race and ethnicity of the subjects were (White (non-Hispanic), White (other), Asian, Other, and unknown).

[0124]The results from the study are shown in the table below:

TABLE-US-00002 TABLE 2 RESULTS OF STUDY CONFIRMED BY KARYOTYPE ANALYSIS Fetal % of fetal Chromosome 21 Haplotype ratio DNA (paternal Subject status (HR) CV contribution) Subject 1 Disomy 1.21 0.39 7.4% Subject 2 Disomy 1.19 0.06 10.8% Subject 3 Trisomy 2.29 0.17 4.4% Subject 4 Trisomy 2.55 0.22 1.3% Subject 5 Trisomy 2.09 0.08 5.0% Subject 6 Trisomy 2.33 0.26 3.3% Subject 7 Trisomy 2.29 0.56 1.7% Subject 8 Trisomy 0.05 0.05 7.1% Subject 9 Disomy 0.95 0.16 5.5% Subject 10 Disomy 1.04 0.05 19.7% Subject 11 Disomy 1.00 0.05 8.0% Subject 12 Disomy 0.99 0.31 6.8% Subject 13 Disomy 0.90 0.26 7.3% Subject 14 Disomy 1.04 0.05 24.0% Subject 15 Disomy 1.15 0.12 4.0% Subject 16 Disomy 1.06 0.11 2.9% Subject 17 Disomy 0.92 0.26 4.0% Subject 18 Disomy 1.35 0.02 11.7% Subject 19 Disomy 0.95 0.13 9.2% Subject 20 Disomy 1.29 0.23 3.7% Subject 21 Disomy 1.46 0.07 7.0% Subject 22 Disomy 1.21 0.14 6.4% Subject 23 Trisomy 2.07 0.13 6.8% Subject 24 Disomy 1.29 0.25 7.3% Subject 25 Disomy 1.01 0.10 4.2% Subject 26 Disomy 0.85 0.04 13.7% Subject 27 Disomy 1.20 0.21 9.7%

[0125]As is apparent from the above table, calculation of the haplotype ratio correctly identified each subject carrying a baby with trisomy and the haplotype ratio calculation was also able to correctly identify all normal pregnancies.

[0126]The present specification provides a complete description of the methodologies, systems and/or structures and uses thereof in example aspects of the presently-described technology. Although various aspects of this technology have been described above with a certain degree of particularity, or with reference to one or more individual aspects, those skilled in the art could make numerous alterations to the disclosed aspects without departing from the spirit or scope of the technology hereof. Since many aspects can be made without departing from the spirit and scope of the presently described technology, the appropriate scope resides in the claims hereinafter appended. Other aspects are therefore contemplated. Furthermore, it should be understood that any operations may be performed in any order, unless explicitly claimed otherwise or a specific order is inherently necessitated by the claim language. It is intended that all matter contained in the above description and shown in the accompanying drawings shall be interpreted as illustrative only of particular aspects and are not limiting to the embodiments shown. Unless otherwise clear from the context or expressly stated, any concentration values provided herein are generally given in terms of admixture values or percentages without regard to any conversion that occurs upon or following addition of the particular component of the mixture. To the extent not already expressly incorporated herein, all published references and patent documents referred to in this disclosure are incorporated herein by reference in their entirety for all purposes. Changes in detail or structure may be made without departing from the basic elements of the present technology as defined in the following claims.

Sequence CWU 1

3571127DNAHomo sapiens 1aacaaatctt catcttggaa tagcctgtga gaatgcctaa tcatctacga atgttacttt 60ggcaccatct actggacaga ttaaataaca accaactcac tgtggattag acctacttct 120atttcag 127220DNAHomo sapiens 2atagcctgtg agaatgccta 20320DNAHomo sapiens 3atccacagtg agttggttgt 20484DNAHomo sapiens 4ttcctggaaa acaaaagtat ttctttcata gcccagctag catgataaat cagcgagtca 60gaattctagc tttgttgtaa ggtt 84520DNAHomo sapiens 5tcctggaaaa caaaagtatt 20621DNAHomo sapiens 6aaccttacaa caaagctaga a 21771DNAHomo sapiens 7cactaagcct tggggatcca gctgcttaag gactaagacc gtatctagct ccttttagta 60tttccacagc a 71820DNAHomo sapiens 8actaagcctt ggggatccag 20921DNAHomo sapiens 9tgctgtggaa atactaaaag g 2110155DNAHomo sapiens 10tcctccagag gtaatcctgt gatcagcact aacaccacat accagccctt tcatcagctt 60gttggagaag catctttact tcccgccaag cagtgaccta gataccatct cacaccagtt 120agaatcagga tcattaaaaa gtcaagaaaa aacag 1551120DNAHomo sapiens 11ctccagaggt aatcctgtga 201221DNAHomo sapiens 12tggtgtgaga tggtatctag g 2113146DNAHomo sapiens 13tccaagtata atccatgaat cttgtttaaa tatagatcaa ataaaccact ataccaaaaa 60catcaaaaga caactgggta aattttttaa atgactagct atttgatgtt aaggaagtaa 120tgttactctc ttatatacaa tttgaa 1461422DNAHomo sapiens 14gtataatcca tgaatcttgt tt 221522DNAHomo sapiens 15ttcaaattgt atataagaga gt 2216132DNAHomo sapiens 16atggaaccga aacttcaagt agtttcatac gtatcacatt gacagttttc tctaagtttt 60ctggtcttat gactcgttgt ttcattatta aaactgtgcc agtgtatgca tagggcttag 120aaatttttta at 1321718DNAHomo sapiens 17atggaaccga aacttcaa 181822DNAHomo sapiens 18ttaataatga aacaacgagt ca 2219157DNAHomo sapiens 19acaggatcct tcctgaagac accaccttgg ggagggtgaa ggataaagaa tttgatcaga 60aatcaagggt ggtgagatac atgttaagga tgaataaact ggccttttag gattcttgct 120aaaattagac aatgcagagg caaccacaga gtccaag 1572019DNAHomo sapiens 20ttcctgaaga caccacctt 192118DNAHomo sapiens 21cttggactct gtggttgc 1822173DNAHomo sapiens 22aatttccatt aaatcttgtt cgttgcttta ctgaggcact gaagttacca atgttccact 60ggttgacctg cggggctatc tctaggttat gttactccag aaaatgaatt gtgtataaaa 120gaggccttgg aggaaggcgt tttattcaca tcagttgttt tgcacattgc tta 1732320DNAHomo sapiens 23actgaggcac tgaagttacc 202420DNAHomo sapiens 24taagcaatgt gcaaaacaac 2025191DNAHomo sapiens 25tcggtttcag caggaaagtt atttttaata acttccctgt atttcttggt ttcagttatt 60aattaactca ttaatgctaa actttgtgat cctaggttaa aaaacatatt caagatagct 120tcagaatgtt tggtatacaa gtaggtctgg ctaaatataa gtgttagctt tctcaagcat 180ctaaatgctg g 1912620DNAHomo sapiens 26gcaggaaagt tatttttaat 202721DNAHomo sapiens 27tgcttgagaa agctaacact t 2128166DNAHomo sapiens 28aagttatttt taataacttc cctgtatttc ttggtttcag ttattaatta actcattaat 60gctaaacttt gtgatcctag gttaaaaaac atattcaaga tagcttcaga atgtttggta 120tacaagtagg tctggctaaa tataagtgtt agctttctca agcatc 1662920DNAHomo sapiens 29atttttaata acttccctgt 203020DNAHomo sapiens 30cacttatatt tagccagacc 2031152DNAHomo sapiens 31attcattgtg tagaaagtgc ctgactcagt gtttggaaat tgtctgactt ttcctcatat 60atagtgtggt ttcatgttat tgtatataag aactgacatg aactctgttt acaataatct 120cccagtgcca taaagaccat aataaataat at 1523220DNAHomo sapiens 32cagtgtttgg aaattgtctg 203320DNAHomo sapiens 33ggcactggga gattattgta 2034163DNAHomo sapiens 34cactgggtcc tgttgttaag tacacataat accacacagg agaaaatcag gctaattgta 60aatgggcaac ctacttaatt gtttcattaa aaagcataca gattacattt acactatagc 120tagtcttgtt tgttttttta ttttgcaaaa gtaattacgg ccc 1633520DNAHomo sapiens 35tcctgttgtt aagtacacat 203618DNAHomo sapiens 36gggccgtaat tacttttg 1837108DNAHomo sapiens 37ctactcagta ggcactttgt gtctagaaac ttctgtgtca acggttttcc ctctctctgg 60aattcatcag gacagaagtg attggtgtgg tggaagaggg ttgtgsta 1083821DNAHomo sapiens 38actcagtagg cactttgtgt c 213918DNAHomo sapiens 39tcttccacca caccaatc 1840144DNAHomo sapiens 40tggcttttca aaggtaaaat ttactaagtg tattaatatt ttaccaattt ccagccagga 60gagtatgaat gttgcattat tacattgctt tgaaacaaag cattagtctt aattcagaag 120tttaaattca gatgttaacg ttgc 1444119DNAHomo sapiens 41tggcttttca aaggtaaaa 194221DNAHomo sapiens 42gcaacgttaa catctgaatt t 2143110DNAHomo sapiens 43taagtattga agaaaggaga atttaaatta cttcatatac ctgataaagg aaaacatata 60caaggcaaat aaacatctta gatcatgaca tataaaataa tagattatta 1104420DNAHomo sapiens 44ttgaagaaag gagaatttaa 204522DNAHomo sapiens 45attttatatg tcatgatcta ag 2246165DNAHomo sapiens 46tgcagagatt acaggtgtga gccaccgtgc ccagcctcat aaccgtttca actacttttt 60cacttgacaa gcagatgtga agttaacaaa gtcacccata tttgaaataa agatagtata 120ttcctggggt aggcagaggc agttgaggat catgaaataa ctatg 1654719DNAHomo sapiens 47agagattaca ggtgtgagc 194819DNAHomo sapiens 48atgatcctca actgcctct 1949178DNAHomo sapiens 49tgcaatgaaa ctcaaaagag aaaagttaac aggtgcaaaa ggtagtttta ttataaaagg 60agggtaggca acaagaatat gtttaatttt tcttcctttt catgagtaag gacaagagtg 120tcatatatgt gaatattttt atttaatttt aagtagaaat ctgtttttaa aatatggg 1785020DNAHomo sapiens 50tgaaactcaa aagagaaaag 205120DNAHomo sapiens 51acagatttct acttaaaatt 2052102DNAHomo sapiens 52ccaccattca tcaaaacttt gatactggac tcaattgtga atttgacttg aaatttgata 60atgcttttgt tttactgttc tgctcagcaa aatagtacat gt 1025320DNAHomo sapiens 53caaaactttg atactggact 205419DNAHomo sapiens 54acatgtacta ttttgctga 1955166DNAHomo sapiens 55gcctgcataa agtgaggatg gtgtagtaat tgggtatctc cagttataaa cacaaaaagc 60atgatagagc tgggactgtg attgcaggaa agcaatagtc actccaaaag gagatcctca 120tgatatgaat acggaagaaa caatatttcc tgctaatgta gtagcc 1665620DNAHomo sapiens 56cctgcataaa gtgaggatgg 205721DNAHomo sapiens 57tgaggatctc cttttggagt g 2158154DNAHomo sapiens 58gcaaaggggt actctatgta atgaacatga cctggcagta ctgacatctc ctgagggact 60gttagaagtg cagactcttg tatcttttct caagtctatg aaatctagac ttcattttaa 120caagatgacc cgatatttac atacacatta aagt 1545920DNAHomo sapiens 59gcaaaggggt actctatgta 206020DNAHomo sapiens 60tatcgggtca tcttgttaaa 2061174DNAHomo sapiens 61gtatctaaca aagctctgtc caaaattttg aatttctcgt taaaagcatc atgattatag 60aacagaggtt acaatcaatt attcagtcac acaatcactc tcatcagtca ttaaggtgcg 120tacctggtgt tccagttatt cagtgtggta taacaaacta cctggaactt aatg 1746222DNAHomo sapiens 62tctaacaaag ctctgtccaa aa 226321DNAHomo sapiens 63ccacactgaa taactggaac a 2164202DNAHomo sapiens 64agagtggtta agtgacttga tcaattcctc aggtggggat tcaagctctt aaagctgtag 60actatgtcgt ccaaacaaac actgacatga atatgacttc caataggcaa gaaaagaggc 120ctaggtcgag atactgcaag acatgcaagc aatctagtaa tggcataaaa cctgctatcc 180gaattggcta aaattatgta tt 2026520DNAHomo sapiens 65ggtggggatt caagctctta 206622DNAHomo sapiens 66ggatagcagg ttttatgcca tt 2267156DNAHomo sapiens 67ttctttctca cacaatgggt tccattccca ctactactcc attcaaattg aagtgccttc 60aatgattatt aaaaaactct ctttaaaata gctcacgtaa ccttacatcc tttgactgag 120gctcaactca tgtcaatgct tcagtatcaa cttttc 1566821DNAHomo sapiens 68aatgggttcc attcccacta c 216920DNAHomo sapiens 69tgagcctcag tcaaaggatg 2070202DNAHomo sapiens 70atttgtaata acatttagta agtatttatt tgaggagttt gaattttgtt cttgtttatc 60ttgttctctt tcttcgtaga ttagttggtg ttaacatcaa taggataacc ctttctttca 120gcatatgtga atgaaataaa ccaattattg ccactttcca ggttaaccag aatatacata 180gatacgagga cagtggactg tt 2027122DNAHomo sapiens 71ttgaggagtt tgaattttgt tc 227220DNAHomo sapiens 72aacctggaaa gtggcaataa 2073171DNAHomo sapiens 73tagggcagag agagcaagca agctctctac cttctcatat aagggcacta atcccaccat 60gaaggcgcca ctgtcatgac ctgattatgt cacaaagacc ccggggcaaa tattaccact 120gtgaggagta cagttttagc atgtgaattt tggaagaaca caaacattta g 1717421DNAHomo sapiens 74gcaagcaagc tctctacctt c 217522DNAHomo sapiens 75tgttcttcca aaattcacat gc 2276195DNAHomo sapiens 76attctaattt taaatatcat tgatgtagaa cattctattt cactattcct tcattttatt 60attatgggaa attatataca gttctccaga tttttaaagc cttgctaaca tgttttaagt 120cacacaaata ttctcctgtg ggaaaatgac agtaatttag tgtgcaacaa ttatatagaa 180ctatttttca aactt 1957721DNAHomo sapiens 77atttcactat tccttcattt t 217822DNAHomo sapiens 78taattgttgc acactaaatt ac 2279138DNAHomo sapiens 79actgtcatgg acttaaacaa ttgtctttga attgtctttt ttcatacttt tatttgcatc 60tttccactaa aaagatggca caaagtaatc ctagtttaca ttttttacca tgtaattcca 120tattactttt tcctgaaa 1388020DNAHomo sapiens 80actgtcatgg acttaaacaa 208122DNAHomo sapiens 81ttcaggaaaa agtaatatgg aa 2282119DNAHomo sapiens 82aaagaaaaaa aagccacaga aatcagtcct agagaaaacc gatctatgag ctgcctgaaa 60ataattataa aataactatc ataaaaatgc ccagtgagat ataagaaaac acagacaac 1198321DNAHomo sapiens 83aaaaagccac agaaatcagt c 218422DNAHomo sapiens 84ttcttatatc tcactgggca tt 2285143DNAHomo sapiens 85caaggtcaga gaagttatct tggatggtag aagagaagaa aggagaagaa aggataagca 60gaaaatcaaa aagggcataa aaaaattact ggggaaaata attcttagtc actcaccatt 120tcttatgttt gtgaaaacag aaa 1438622DNAHomo sapiens 86ggatggtaga agagaagaaa gg 228722DNAHomo sapiens 87tcacaaacat aagaaatggt ga 2288136DNAHomo sapiens 88gaccacaatt cacaaatgca aagatgcaga accaacctaa gtggccactg actaatgaga 60ggataaagaa gatgtggcat atatatatca gggactacta ctcagccatt acaaggaaca 120aaataatgtc ttttgc 1368920DNAHomo sapiens 89tgcaaagatg cagaaccaac 209022DNAHomo sapiens 90ttttgttcct tgtaatggct ga 2291160DNAHomo sapiens 91gaccacaatt cacaaatgca aagatgcaga accaacctaa gtggccactg actaatgaga 60ggataaagaa gatgtggcat atatacatca gggactactt ctcagccatt acaaggaaca 120aaataatgtc ttttgcaaca acttggatag agctggaggc 1609220DNAHomo sapiens 92tgcaaagatg cagaaccaac 209321DNAHomo sapiens 93gcctccagct ctatccaagt t 2194160DNAHomo sapiens 94aatcctagac cttggattgc aagagactcc ttaatatctt cccatgtcca catttccttc 60acatagtttg aatgtggctt ctattatata cagatacaag attcaaatcc aacctctatg 120atgactggtc ttgtgaataa gcagaagagg cactaacaat 1609522DNAHomo sapiens 95ccttaatatc ttcccatgtc ca 229622DNAHomo sapiens 96attgttagtg cctcttctgc tt 2297162DNAHomo sapiens 97aagagaagtg aggtcagcag ctgcaagcca cctccgtcat ttagaaaagc ttcatgatgt 60agtgtgtcgt ttcgatgtga cactgtctca cagagttaaa atgatgttaa ggaactgttc 120aatggaaatt tagaaatttc tctttttctc aattttagtg ta 1629820DNAHomo sapiens 98gagaagtgag gtcagcagct 209922DNAHomo sapiens 99tttctaaatt tccattgaac ag 22100160DNAHomo sapiens 100atggctgaat agtattccct tgtgtatata tctatttatc cttttattca ttgatggaca 60cttaggctga ttttctctct tctcatggct ggcttctcat caccctttgg tcctcctgta 120tcctcgtgta ataaagctct tccccaatat ctcgatagat 16010122DNAHomo sapiens 101ggctgaatag tattcccttg tg 2210220DNAHomo sapiens 102tcgagatatt ggggaagagc 20103199DNAHomo sapiens 103cattttaact tgattacctc cacaaagact attccagaat aaggttatgt tctgaggtat 60taggggttac aacttcaaca tatgaatttt gagtggacac aattcaaccc atagcacctc 120cgtgtaagag ctgggaaggg aaagtggcta agttgtgcaa atgtgcacat tggttggaga 180tgattaactt ctggcatgt 19910422DNAHomo sapiens 104cctccacaaa gactattcca ga 2210520DNAHomo sapiens 105cactttccct tcccagctct 20106157DNAHomo sapiens 106agggggaaat tggcaatctg attctaaaat tcatacggaa aaaaacaatg gagttagaat 60aactaaaaca agtccgaaaa agaaaaagaa atggaggact aatgctacct gatttcaagt 120cttatcttat aaatctacat caataaagga caagttg 15710720DNAHomo sapiens 107gaaattggca atctgattct 2010821DNAHomo sapiens 108caacttgtcc tttattgatg t 21109173DNAHomo sapiens 109tctgtgtttg tctatgttga taaaacattg aaatgccaaa tagctcaaag gtcattcact 60taagaaatct aagtactgat aacatcttag ccccgattct tcataggcat tgttaagcct 120attataattt tggttcagag agaaggtaaa ctatattcca gacaggcata taa 17311022DNAHomo sapiens 110ctatgttgat aaaacattga aa 2211120DNAHomo sapiens 111gcctgtctgg aatatagttt 20112126DNAHomo sapiens 112tgcagggcat ataatctaag ctgtaaacgt cctgtcagaa gacaacatat tcatcttgct 60aaggtttaag ctatatgact ggcactgtgc tcaactcaga gtcattgaat gaacagtatt 120tattta 12611322DNAHomo sapiens 113cagggcatat aatctaagct gt 2211421DNAHomo sapiens 114caatgactct gagttgagca c 21115132DNAHomo sapiens 115ttcacattat tcccttaaaa taaactctct ccctcccctc tcccgtctca accttgtccc 60tttctttata taatgggtaa ttcgttaatg tcagcagaat agttttgggg ccataatggc 120aagtatcacg tg 13211619DNAHomo sapiens 116aactctctcc ctcccctct 1911720DNAHomo sapiens 117tatggcccca aaactattct 20118110DNAHomo sapiens 118tcaggaagca acaagtactg ggcagattga tactgtagct aggctctagc tctatacctc 60tagaataaat gttacaaact agcaacttga aagctaaacc tggcccacag 11011920DNAHomo sapiens 119acaagtactg ggcagattga 2012020DNAHomo sapiens 120gccaggttta gctttcaagt 20121106DNAHomo sapiens 121tggttcttga gaattttata tcaggagaaa cactgtcagt ctgtattgaa aggaacagag 60aaaattcgaa attaaagaag actattaaac ctccaaaatt ctggca 10612222DNAHomo sapiens 122ttttatatca ggagaaacac tg 2212321DNAHomo sapiens 123ccagaatttt ggaggtttaa t 21124171DNAHomo sapiens 124gcatcaaact acacactgtc attcctcctt tatctccaaa agcttgaaaa ttcctcactt 60gtatctcatt ctttctctct tagaaaactg atcacctctg atgaattaga acggaatgac 120caagctttgg gagaggcaaa agaatctcgg tgttaaagac tcagagttta a 17112522DNAHomo sapiens 125tgtcattcct cctttatctc ca 2212620DNAHomo sapiens 126ttcttttgcc tctcccaaag 20127163DNAHomo sapiens 127ttgaaaatta agaaaccctg gcacagtgtt gactggagcc acttacctta atagaaaata 60aagctcacat atatccataa tgaaaagcag agaccagcac

aaccatagtc acctgacagt 120tttaaaatcc aaggccagga tcttctcaac tcaggcccac tca 16312820DNAHomo sapiens 128accctggcac agtgttgact 2012920DNAHomo sapiens 129tgggcctgag ttgagaagat 2013020DNAHomo sapiens 130tttttcccat ttccaactct 20131122DNAHomo sapiens 131aaaaaaaaag atgagacagg caggtgcgaa agaaataaaa gtcaaaactg atccagttgg 60gaaactcaga attgacagtt acgtgtcctt tcatttattg atattttgag attcacaggg 120gt 12213220DNAHomo sapiens 132aaaagatgag acaggcaggt 2013320DNAHomo sapiens 133acccctgtga atctcaaaat 20134150DNAHomo sapiens 134gagttaaata aagcacttgc ttctattgtt tgtacctaaa cttaacagaa cacagtaagt 60aacaagtcat tgggatgcag aaaagaaaaa agagagtgaa ggaaggagaa aaggtgaagg 120gagaatggaa gagaggaagg gagggaggaa 15013521DNAHomo sapiens 135gcacttgctt ctattgtttg t 2113620DNAHomo sapiens 136cccttcctct cttccattct 20137129DNAHomo sapiens 137aaacgagcca ccagtgggag cactgcaggt atctgtgtga gacccgtact tcacaactcc 60tgctttccct ccataaagta gcttgcattt tccacattga ctttgcagtt ctttggtatc 120tgtattggt 12913818DNAHomo sapiens 138gtgggagcac tgcaggta 1813921DNAHomo sapiens 139acagatacca aagaactgca a 21140145DNAHomo sapiens 140tggacacctt tcaacttaga aatcataaac agattcattt ccttaaagtt aatgaaaaga 60attaacagac cctcctcaaa aaagacatat atgcagccta caatcatatg aaaaaaagtt 120caacattact gttcagcaaa tcaaa 14514120DNAHomo sapiens 141tggacacctt tcaacttaga 2014222DNAHomo sapiens 142gaacagtaat gttgaacttt tt 22143155DNAHomo sapiens 143tggatacatt cctagaaata gatggaaact gctcttgcaa aaagcttagc acatgttaaa 60aattttagaa acaatttgcc aaagtttatt tagtctagtg attttgacag gttaaatgga 120ccctttgaga tcttttttcc tcaagtacaa aggct 15514421DNAHomo sapiens 144tcttgcaaaa agcttagcac a 2114521DNAHomo sapiens 145aaaaagatct caaagggtcc a 21146119DNAHomo sapiens 146gcttttgctg aacatcaagt ggtgagccag gactcaaagc cagatcttct tgtttccctg 60ttaggtgttt gtagcacaac tggtatctgc agactatgct gctggaaggg ctagccgtc 11914720DNAHomo sapiens 147gcttttgctg aacatcaagt 2014819DNAHomo sapiens 148ccttccagca gcatagtct 19149161DNAHomo sapiens 149actgtcctag aaaatccagg atgtgcagtg atcatgtatg aatgcatgga cctgcacaca 60caggagtgaa caaaagaccc acccctgcca ggtcaccact catatctcac cccagcccac 120gctagctcac actcctcccc acacaccact gacctcatca t 16115018DNAHomo sapiens 150aaatccagga tgtgcagt 1815119DNAHomo sapiens 151atgatgaggt cagtggtgt 19152124DNAHomo sapiens 152cacatcacag atcatagtaa atggctttaa ttttttaacg aaatctcact actgcaaatg 60cattgttgtc ctagctaatg aatgcataga gtattgcctg caaaataata attgagattc 120tatt 12415322DNAHomo sapiens 153catcacagat catagtaaat gg 2215421DNAHomo sapiens 154aattattatt ttgcaggcaa t 21155151DNAHomo sapiens 155ttatcctcca catcctcatg aggcaaacac ctttcctacc ttaccgctcc ccagtggcct 60ccctgttgcc ttcttattca agactaagac tctctagaat gttctttatc ctgagtccag 120ctgattgtct atactaatat cagtacgggg t 15115620DNAHomo sapiens 156catgaggcaa acacctttcc 2015722DNAHomo sapiens 157gctggactca ggataaagaa ca 22158145DNAHomo sapiens 158agggtgcagc actttattat ggaagcctga gctgactaat acaggtgtct ctatatctca 60ctgagggaaa gtgacaggaa agtaagaacc atttatgtcc aagagtccag aggagtcaac 120cagattctgg gggaaaagaa ggtac 14515920DNAHomo sapiens 159tggaagcctg agctgactaa 2016020DNAHomo sapiens 160ccttcttttc ccccagaatc 20161154DNAHomo sapiens 161tgagaattta ggagaacaga agatcagagg gctgcacagg ctaaactaga caatgagccc 60atgcaagtaa gttaagagga gaagcgggta agtatgcacc tgctttgtct aggtgaccag 120caagcattta gcaatagtct tttcaaaaca acag 15416222DNAHomo sapiens 162ttaggagaac agaagatcag ag 2216322DNAHomo sapiens 163aaagactatt gctaaatgct tg 22164106DNAHomo sapiens 164aaacaggcaa aataagcgta gggctgtgtg tgcaacagtt aatcataaag ccatcaccag 60gagacgtcac tgggcgcctt ctggagtcta tccgtcctaa ctttgc 10616520DNAHomo sapiens 165taagcgtagg gctgtgtgtg 2016621DNAHomo sapiens 166ggacggatag actccagaag g 21167105DNAHomo sapiens 167gaatgacctt ggcactttta tcaaacatca actggccaca cacaggtgag tctacttctg 60gacacttatc ctgttccatt catctgtata tctctatcct tacac 10516823DNAHomo sapiens 168gaatgacctt ggcactttta tca 2316927DNAHomo sapiens 169aaggatagag atatacagat gaatgga 27170129DNAHomo sapiens 170ctgctggaat aggctgcttg gccatgttct tggaagctac caccatatca aggtaatttc 60ccacacaaca ttccagcccc tgctttcctc tctggcctta tctagggcca ttccccaact 120caggtgaat 12917120DNAHomo sapiens 171ggccatgttc ttggaagcta 2017220DNAHomo sapiens 172ttcacctgag ttggggaatg 20173138DNAHomo sapiens 173acctttgttc catgcaccgc gcaaatacct gggaaccctt attgcccaac tcaagagcca 60gagtcctctg tcatcatttt gcctctctcc taagtgagag gactgagtgc agacttggtg 120tttgtgggtg aggcatgt 13817418DNAHomo sapiens 174catgcaccgc gcaaatac 1817519DNAHomo sapiens 175atgcctcacc cacaaacac 19176159DNAHomo sapiens 176ctcctgagtc caagcccttc tcactcacct ctttcttgaa ctaatttctt cctgtttttt 60tccagtcctc ccttctgttc atgtctctcc tctgcacact tccattttgt ggttcagaaa 120atgtcaccgt cccagtcaca cttgccttat ggctgttgt 15917720DNAHomo sapiens 177tccaagccct tctcactcac 2017820DNAHomo sapiens 178ctgggacggt gacattttct 20179132DNAHomo sapiens 179cccaggaaga gtggaaagat taacctttgt gagccaaacc agtgacactt gattacttga 60cagaactaat ccttctgtcc tgatgacaga acttcaacta cacaggtaca tgcaagctaa 120tatctgttgt aa 13218021DNAHomo sapiens 180cccaggaaga gtggaaagat t 2118121DNAHomo sapiens 181ttagcttgca tgtacctgtg t 21182165DNAHomo sapiens 182gcctggcaag ctagatgggg tgaattttca cctgccacag ccgcaagtca aagccaccgg 60cttctctctt ctccctccca ttgctcctga cagccagggt taatattttg cctcatgtaa 120acagggaggc atccacccga gaatctcccc tcagcccaca taagc 16518320DNAHomo sapiens 183agctagatgg ggtgaatttt 2018418DNAHomo sapiens 184tgggctgagg ggagattc 18185160DNAHomo sapiens 185atcaagctaa ttaatgttat ctatcacttc acatagttca accttttttt gtggtgagag 60tactgaagat ctactctctt agcaattttc aaatctaaaa tacattatta ttaacacagt 120cactgtgccg tacgttagct ctgaggacct tattcatttt 16018622DNAHomo sapiens 186atcaagctaa ttaatgttat ct 2218720DNAHomo sapiens 187aatgaataag gtcctcagag 20188124DNAHomo sapiens 188tttaatctga tcattgccct atgaggtagg gagtattctg attcccattt tataaataag 60gaacccgagg cttagagagc atcagtgact tgttcaaggt cacccacagc tgtcaagtga 120caga 12418921DNAHomo sapiens 189tttaatctga tcattgccct a 2119018DNAHomo sapiens 190agctgtgggt gaccttga 18191128DNAHomo sapiens 191tgtcccacca ttgtgtatta ggtttgtaga gcgtagacaa cttgcctttt tagtttgtag 60gtttctgtat caagagaaga tgtgtgtggg cctaacctag attacaggat cctggacttc 120aagtctga 12819220DNAHomo sapiens 192tgtcccacca ttgtgtatta 2019320DNAHomo sapiens 193tcagacttga agtccaggat 20194128DNAHomo sapiens 194tcatttgcta aggtcggata gctcctaatt ggcaaagtca cgatgggatc ccagggattc 60tgaggatgaa gcctgtgttt aataactatt atgccaagtg agcattttca aatatatgag 120agaaatta 12819519DNAHomo sapiens 195catttgctaa ggtcggata 1919620DNAHomo sapiens 196tatttgaaaa tgctcacttg 20197159DNAHomo sapiens 197cattgcttca ggggtgttag ttttgtgttc acaactagat tataaactcc tcttgcattc 60ctgatggcag tgacttgaag gcatttattt gaagaataat agacatacag aaaggggcac 120atgtcataaa ggtacagctg gacgactttt cacaaagtg 15919820DNAHomo sapiens 198gcttcagggg tgttagtttt 2019920DNAHomo sapiens 199ctttgtgaaa agtcgtccag 20200117DNAHomo sapiens 200gagaggatgg tgccatcatg gaaagcatgg ggcagtcatg gagatgacgg agtagctcat 60ggagaagata atgccatcat ggaaggcata gtgcagtcat ggagatgatg gtgcagc 11720118DNAHomo sapiens 201ccatcatgga aagcatgg 1820220DNAHomo sapiens 202tcatctccat gactgcacta 20203167DNAHomo sapiens 203atggggcagt catggagatg acggagtagc tcatggagaa aataatgcca tcatggaagg 60catagtgcag tcatggagat gatggtgcag ctcatggaga agatggtgcc atcatggaag 120gcatggtgca atcatggagt agacagtgca gctgggccaa gattctc 16720420DNAHomo sapiens 204gagatgacgg agtagctcat 2020518DNAHomo sapiens 205cccagctgca ctgtctac 18206128DNAHomo sapiens 206gatgtgcctc tcttgttcca atcacaggac aggggtataa ctaggggcac tgtctatact 60ggctgcactc tggccagtgc tgtcccaggt agattcatca gggtctagag cttcagctaa 120cagcatga 12820720DNAHomo sapiens 207tcttgttcca atcacaggac 2020820DNAHomo sapiens 208atgctgttag ctgaagctct 20209109DNAHomo sapiens 209ttttattcat taagttgaaa gctcctaaag cagagggacc atatttttat gtcccaactc 60tccttaaggc cttgcctatg atagcacatc tcttcaatag aattgtcct 10921020DNAHomo sapiens 210tgaaagctcc taaagcagag 2021120DNAHomo sapiens 211ttgaagagat gtgctatcat 20212163DNAHomo sapiens 212cacataacta ataaatttgt aagtatgtgc aacggctcac acttgcttcc agaatggcac 60ctaaaaaaca gatttacctc tccccaaatt cagatatgga attaaatgta atgtcaggaa 120aactgtctaa gagttggaaa tgggaaaaaa atgttctttt ggt 16321321DNAHomo sapiens 213aatttgtaag tatgtgcaac g 21214207DNAHomo sapiens 214aaagaccagc ttttagctga acatcagggc tgccttcaga gtttaattac cgccctcccc 60atggggccaa atgagccatc gactcctccc aagggggttc ggcttggtac tgatctttaa 120gtaagtaaac gctaaaccag ctcatcttaa agcgcccaca tctgatttcc tgctctgctg 180caagacagta ggtgactggt aatgacc 20721520DNAHomo sapiens 215agggctgcct tcagagttta 2021620DNAHomo sapiens 216gcgctttaag atgagctggt 20217192DNAHomo sapiens 217actctgctcc cagtgtgaac atggggaaag ttgattaaac tctctgactt cagattcctc 60atgtaaaatg tggggaaaca gctctgactt aatggtgtca ctgtgaggag taaatgaggt 120agcatattta aaggattttg tatagtgctg gtgacagtaa ccagccaata gatgatatag 180ctagtaatag ca 19221820DNAHomo sapiens 218tgaacatggg gaaagttgat 2021922DNAHomo sapiens 219tcaccagcac tatacaaaat cc 22220170DNAHomo sapiens 220cttcactgac cacttcctta actgtccact ccgaaacacc ccttcttcct gttcttccaa 60tacaccaaac tctttcttgc ctctgtgtgc ttgcccatgc tgttccttct ggcttcttcc 120ttcacattca agtcttgact tagatgtcac ttgccaaggg agaccttgga 17022121DNAHomo sapiens 221acttccttaa ctgtccactc c 2122219DNAHomo sapiens 222ccttggcaag tgacatcta 19223181DNAHomo sapiens 223aaacatccca atagacaaaa ctccaagaag agtcaaaaca agaataaagt acaggtcatc 60ttttcttttg cactcctgac agcactttgt acatggtaat aataatctac caattaacta 120cataagccac atggttttat catagtgtga agctttgtat ccagaaagga gagaaggctc 180c 18122422DNAHomo sapiens 224ccaagaagag tcaaaacaag aa 2222521DNAHomo sapiens 225tctcctttct ggatacaaag c 21226149DNAHomo sapiens 226ggcagaggca tggggtgcat agggatatgg ggtgggccag tttgctcctc agaccagaag 60gggtgcagga ctccccccga tcaggatcat ggagaaaggt gtggacagag gaagggaggg 120agggagaaat ggcagctgcc ctgcagtgg 14922720DNAHomo sapiens 227ttgctcctca gaccagaagg 2022820DNAHomo sapiens 228ctcccttcct ctgtccacac 20229165DNAHomo sapiens 229cagggactaa gtgtctctga caatacattc agccactact acagtatgaa gccagcccct 60catccccacc ttcagagacc cctggtgcct cagattcctc ggccattctg gagctgctgt 120gcccgaggct tgtgtagttg gagatcattt tggcagtcag tgctg 16523022DNAHomo sapiens 230tgtctctgac aatacattca gc 2223120DNAHomo sapiens 231ctgactgcca aaatgatctc 20232181DNAHomo sapiens 232cctgtctccg tgcgtgaaag ccggctccaa agtgccttct gtcctatctg ccttccgcac 60ctggctttcc tgaaagaaag aaaacgcgtg gcttatcttt tcacggcacg ccaccttcac 120tctcactttt tcttttctaa taaatacctc tggatgggtt agtggtaatc tctcctcaaa 180c 18123320DNAHomo sapiens 233gctccaaagt gccttctgtc 2023420DNAHomo sapiens 234ccactaaccc atccagaggt 20235198DNAHomo sapiens 235gggagcacaa cctaggcccc tcctggggag gtggtggagt cagaatcacg taagagacaa 60agttccagtc cctcagtgcc ggctccattg tcccctggac ttcccttaca aaccacagat 120gcaaagagag cacttctcgg aatctccaca cagccacggt ggagcactca acccacgcga 180ccctcgggcg caggtgct 19823620DNAHomo sapiens 236ctggggaggt ggtggagtca 2023720DNAHomo sapiens 237gagtgctcca ccgtggctgt 20238161DNAHomo sapiens 238cctgagaagc ttccagcaaa gcaccagcac gaaccgcccc acctccccac ctccccgcaa 60gcgttgccgg gactgacaga ttacagagct ctggtccctc tgcactcctg ctctgccacc 120cccagggtgt cagaatgtgc cccccacaca gtttccaaaa g 16123918DNAHomo sapiens 239aaagcaccag cacgaacc 1824018DNAHomo sapiens 240ggggcacatt ctgacacc 18241162DNAHomo sapiens 241atggagctgc tgcgccggcc tgagctctga tccctcctcc gacccagcct caccctgcaa 60gcagcaccat gtggggctca gaatggggat cttaagggac cctccccaca acctcccgat 120aagcctttcc acggagggcc caagcggaga caggagaaca ct 16224219DNAHomo sapiens 242ctgagctctg atccctcct 1924318DNAHomo sapiens 243ttctcctgtc tccgcttg 18244194DNAHomo sapiens 244actttcagaa tgtgctgcct tccacgtgtg aaccagactg agctcctttc tgccactgat 60gttgaattgt ccatttgctc acatcagtgt ccacgtggca aatccacagg gcgtgggtgg 120gatcctgcag tctagacaaa gccaaggagc accgctggag gccacgttgg gcttcccaat 180ccacatgcaa accc 19424520DNAHomo sapiens 245cctttctgcc actgatgttg 2024619DNAHomo sapiens 246ttgcatgtgg attgggaag 19247213DNAHomo sapiens 247tctccagcca gcgtgtcaca aagccgctca cctgctcgtg tgagtgtctg aatgcacgtg 60tttgagtgtc agaggcgtgt gaaccacagc aactcaatct tgaatagggg ctgggtaaag 120tgaggctgag acctcccggg gctgcattcc cagatggtta aggcattcta agtcacaaga 180tgagatagga agttcgcaca agacactggt cat 21324820DNAHomo sapiens 248tcacctgctc gtgtgagtgt 2024920DNAHomo sapiens 249ccttaaccat ctgggaatgc 20250152DNAHomo sapiens 250ttgagtcctc ttaagtagtt actatagtgg agaacttgag tcattctttg tagcgtgctt 60cgtagagcag cgtgtttgtt agaaggattt gttaatcctg tatagggtct ttacgaaggc 120tgttttcatg gaagcttctc tttgttgact cc 15225122DNAHomo sapiens 251tggagaactt gagtcattct tt 2225219DNAHomo sapiens

252ggagtcaaca aagagaagc 19253174DNAHomo sapiens 253cattctctcc agctgcaaac tttcttcaac tttcctaaat tcttactaaa ttcagaggaa 60taggataaag atcacttaga gaaagggtgc ttatggacat agcctgagtt tcctttaacc 120tctctgcaat gggtgctttt aactagcttc tacatggcaa gctgtttcag tttg 17425421DNAHomo sapiens 254ctttcttcaa ctttcctaaa t 2125519DNAHomo sapiens 255ttgccatgta gaagctagt 19256175DNAHomo sapiens 256ggacatctgg aactgcacca gcacagaacc gacacgttgt tactcatcgt cactcggcag 60ggctgaagac caccagaact catgacaggc agacgtgcct ggcccagttg aggatgtagc 120ttcagagcca agcgccagtc ctgttggcca cgtgggctgg gggcaggata gacca 17525719DNAHomo sapiens 257accagcacag aaccgacac 1925818DNAHomo sapiens 258aacaggactg gcgcttgg 18259182DNAHomo sapiens 259ggctggttct gcccttggga ggtggttcct ttggctggac cagaatgtct gaagatgatc 60aggagagggc caagggttgg ggggtgcccc atgtgcaccc tgagaattgc accaggcaca 120gtgagcaact tcagccctcc ttgtgcagag ctgcagcgta cagtgccagc cctcgctggc 180cc 18226020DNAHomo sapiens 260cttgggaggt ggttcctttg 2026118DNAHomo sapiens 261ctgcacaagg agggctga 18262155DNAHomo sapiens 262gttctcactt tactgagaaa cctggcagct tctcaggcca ccgcccaggt cacctgctca 60ccagcaacgt gaaccacagg aactgaggct gtgcgggagg cggctctgct ctgtgctggg 120cccccctcct cctcactcac cctcttcagt caaag 15526320DNAHomo sapiens 263tactgagaaa cctggcagct 2026420DNAHomo sapiens 264ctttgactga agagggtgag 20265180DNAHomo sapiens 265ttagtattat tattttcata tatatttttt ataataatca tatattcaat tttatcatca 60agaaaaaagt tttaaaattc aaaatccttt catgtgcact gttttaaact taggtagaag 120aaaaaaagtc actgaaaatc caagatgtaa taaacaggcc caacaaaggc caacaaactt 18026620DNAHomo sapiens 266ttcaatttta tcatcaagaa 2026720DNAHomo sapiens 267ttgggcctgt ttattacatc 20268196DNAHomo sapiens 268agggaacatg gccttgccca cacagatttc agacatctgg ctccagaact gtgggaggac 60acatttctgt tgtttagaac tgcatgtttt ttatactttg ttatggctgc cctaggcaac 120taatacagat attattttcc acttctgaac ttagcaaaat atttttaaaa tgaaaattct 180taaatgttgg cacagt 19626920DNAHomo sapiens 269ttgcccacac agatttcaga 2027022DNAHomo sapiens 270tgctaagttc agaagtggaa aa 22271120DNAHomo sapiens 271ctggataaag gatgctacac gtccctggtg ggacagagca ggacggcagg ggatttcatt 60acgccactca gaatggcagg caattgaaaa aacttataaa ttgtttattt ccagaatttt 12027220DNAHomo sapiens 272ggataaagga tgctacacgt 2027320DNAHomo sapiens 273aaaattctgg aaataaacaa 20274224DNAHomo sapiens 274tgtcagtggt gtaatccgac tgtgaaagat cagtctaaca aaacagcggg gagagagagg 60gctgaatcag agcaactagg tccaaagccg agggaaccac caacagatcc cctggtgacc 120caacaagaaa tgctcacagt ctggacccag tcagagtctg caggacacag cagacattct 180ggaagttaca acagccagga gcaagaggac gcatggcctg actg 22427520DNAHomo sapiens 275gggagagaga gggctgaatc 2027621DNAHomo sapiens 276gctcctggct gttgtaactt c 21277174DNAHomo sapiens 277cgccagagca ccccttctca gaacagaaag cgtctctaca aagtgatccg gaagtgagtg 60tgtgagggcg ctgcgtcctc cctgctcccc ttggagttgc cctttcttgc tcagatctgg 120gtgccttggc cttgtcctgg gcccttccgc agcccccggg gtgatccccg ctag 17427819DNAHomo sapiens 278ccagagcacc ccttctcag 1927918DNAHomo sapiens 279ggaagggccc aggacaag 18280201DNAHomo sapiens 280tatcttacgg atttgtcaac atcatttgag aagaagtcca taggctcagc agatttttat 60gccaggtggg ccatggcata aaaatgtgaa gaatgtgctc acttagacaa tacctgtgct 120aaaattggaa caatacagag aagattagca aattaaaaca atgttaggaa gtcagtgtgg 180tgaggtacgg tgcctcatgc c 20128121DNAHomo sapiens 281cagcagattt ttatgccagg t 2128220DNAHomo sapiens 282caccgtacct caccacactg 20283275DNAHomo sapiens 283aggcagggcc ctccttgcca catgtaaagc tgcacagagc ggtcactata tgtgtttcca 60tatttgcaat ccaaccacca ccaactgagt gtgcgtcctg atcagccgag cctgcccacg 120gtggccacag gccctctaca ttctaatctc gagagcctga gcatgtacaa attaaacgaa 180gcaaaacgac accacccagt tctggccgta ctataggagg tttccaggaa gggtttgtga 240acataaacat aagctaggta acactccttt ctgaa 27528420DNAHomo sapiens 284aaccaccacc aactgagtgt 2028520DNAHomo sapiens 285cctcctatag tacggccaga 20286230DNAHomo sapiens 286tcagagcatc gcctcagtgg ccatcaatag ctcgggggac tggattgctt ttggctgttc 60aggtttgtcc ccagcctggg tggtagagat ggactcccca ttagggacca gtgctgcccg 120gctacaggct tacttgacag ccacccactg ggggtgccct cccctccccc agttgtcttc 180catggggtgc cctctccccc agccgccttt cagaaggggc cctcccctcc 23028720DNAHomo sapiens 287tggattgctt ttggctgttc 2028820DNAHomo sapiens 288caccccatgg aagacaactg 20289199DNAHomo sapiens 289ctcatgctta catccttagc tgatcattaa actttgtgac catttcatgc tcactgcttt 60cttgcccggg agctaatggt gaggaaaggt cactgggaac cagcgcacca acctcagaca 120tcgattttgt tccagccttt tttcctgggc aggggtggct atcacctgct ggtaggcagc 180ggcaggccca ctgtcctgc 19929021DNAHomo sapiens 290ttaaactttg tgaccatttc a 2129118DNAHomo sapiens 291taccagcagg tgatagcc 18292181DNAHomo sapiens 292tgacagaaaa gtctcagagc agtgccttct gagctcttct acaccaagca ggcagaatgt 60tcactgctaa tgaggctgga gctggtcccc agcagtggta ggaagcttcc aacaggctca 120ggctgtgggt gcttgcaggg gcacagtgtg acggccacgg gcctcagagc tctggtgggc 180t 18129320DNAHomo sapiens 293gacagaaaag tctcagagca 2029418DNAHomo sapiens 294caagcaccca cagcctga 18295187DNAHomo sapiens 295acatctttct caaataaaga taacagcgat gtattttcac aaaagcaaga gcttagaaag 60tactccaccc aggtatccct cttggaaaaa atacttaagg aaatatgaca aatggcaaag 120tgattgttat ggatggaatg tttgtatcct cccaaaattc acatgttgag accctaattc 180caatatg 18729620DNAHomo sapiens 296attttcacaa aagcaagagc 2029720DNAHomo sapiens 297ttgggaggat acaaacattc 20298180DNAHomo sapiens 298aggggcattc tacaaaacac ccaaccggtc aaggtcgctg aggccaagga gagattgggc 60aaccgtcaca aaccagagaa gccgaggaga cctttcagcc aacgccatgt ggggtcctga 120gcaggaccca ccggaagttg gtgcagctgc ctaaagaccg tcctggctga gaagaaacag 18029918DNAHomo sapiens 299aaggagagat tgggcaac 1830019DNAHomo sapiens 300gtttcttctc agccaggac 19301228DNAHomo sapiens 301tggccctgac ctgccagagc tgttggcctc cagctggcgg gtaaaaccca cggccttctc 60agaacaggtt tctcaacaca tgagacagaa cacaccagac ttccaagggg aacacctgga 120tggagctggt tacccagatc gttcaacacc gaggggcagc ggcttgaggg tctttccacg 180aaggcttgga ttaacaagag gagcasrggt ctctccagga tgggccca 22830220DNAHomo sapiens 302catgagacag aacacaccag 2030320DNAHomo sapiens 303tcttgttaat ccaagccttc 20304223DNAHomo sapiens 304ccacccagtg tcacgtcacg gccccggcac gccatccacg gaccctggat ggagcccagc 60tgcctccagg agcgcagttt aactacaaag gagccctggc tgcccgcccc gcccagacgc 120actgacctgt tgttctctgt ggctgctgat ggcccatccc caaccactgg tgactcttcc 180ctggggcccc aagctcagcc cctaaccccc tgttgctgga agt 22330518DNAHomo sapiens 305cacggaccct ggatggag 1830618DNAHomo sapiens 306cagggaagag tcaccagt 18307186DNAHomo sapiens 307cagaggactg ggctgcgggg tcaggaatgg gcacacttcc taactgcagg acactctaag 60ggctttggtc atgcacacgc agccaagaga aggtgtcgct gacacacagc cttccaggag 120cggacttgga gacctcgcca aggaccagga ctccccagca ctcacactcc cttaggcgct 180gaagtc 18630820DNAHomo sapiens 308actctaaggg ctttggtcat 2030920DNAHomo sapiens 309ctaagggagt gtgagtgctg 20310185DNAHomo sapiens 310gaagaggaca acacggggct gtctgcagag cacctgccac gcgccaggct ctgtgtccac 60aagcacggcg gctgctccca catgacagag ctcgtgcggc agctccagga ctgtctggtg 120ccagagcccc agctctccgc cagccccagg ccactgtgcg aggccctcag tgaagagggg 180gccgt 18531118DNAHomo sapiens 311cgccaggctc tgtgtcca 1831218DNAHomo sapiens 312ggccccctct tcactgag 18313173DNAHomo sapiens 313tctaaataat gttaatgatc aaatttagtc agatctcaat cttcatatgt tagttgcctt 60cttaataaat attctgtttt ctttatcgtt ctttatttgt atctccacct tcatttctga 120ttaaattaag aagttttgtc tcttccattt aataattaat gtatttaata acc 17331422DNAHomo sapiens 314tttagtcaga tctcaatctt ca 2231522DNAHomo sapiens 315aatggaagag acaaaacttc tt 22316194DNAHomo sapiens 316cacactccac actggcccca cgcgggtggc gaaggactca gccagagcct ggcaggatcc 60tggggtgtct atttccaagg aatgttctgg aagaaacata cacacatact tgtttgccag 120atttacctgt gtggtcttcc agatgagaag cagcctgtgt cactccataa gggagagtgc 180gtgcagcatt gaga 19431718DNAHomo sapiens 317gaaggactca gccagagc 1831820DNAHomo sapiens 318ctctccctta tggagtgaca 20319225DNAHomo sapiens 319aagaaactcc caaggaacgc attgtcccaa gttgctgcac cagtcagtgt acattcccac 60aaacagtgca tgagagttcc tgttgcttgt gaaataaatg gtcagcattc agtgttgtca 120gcttttaaaa ttttctcctt tctagtgggc atgtaatggt ctcacattat agttttaatt 180tgcattttcc tggtgacatg tgatacggaa ccttcctccc atgct 22532019DNAHomo sapiens 320accagtcagt gtacattcc 1932119DNAHomo sapiens 321ggaaaatgca aattaaaac 19322170DNAHomo sapiens 322gtgcaattta attacaaacg cttaaatggg gaggtcaggg gcagagggat gatgtcacaa 60acacacccac gtgtgcttgg tgcaaaacag taaaacaaac agcaagaagg tccatgaagg 120aaagatcgcc tctgtcagtg ggagtaatga gagtggctga tggacaggtg 17032320DNAHomo sapiens 323cgcttaaatg gggaggtcag 2032420DNAHomo sapiens 324cctgtccatc agccactctc 20325189DNAHomo sapiens 325acgccaagca ggagatgcca gacacagagt ccatcctgag agagtctgtt cctgtccaag 60ctcagaaaca caggaagcca cctgtgctgt agcagcacac ggagatgcat cctttctggt 120ccaccccacg gccctcattg cagtcaggga tcctctccca gaaagtccct gctgccagcc 180cctgccctt 18932620DNAHomo sapiens 326agcaggagat gccagacaca 2032720DNAHomo sapiens 327ggtggaccag aaaggatgca 20328170DNAHomo sapiens 328catgagaaag actttgttcc catgagaaca acaagagaaa ctcaaacaaa attaaaattg 60tacttttcta aaagaccggg gtgggggtcg tggtcaggca gcagcatgaa gaaagccttg 120agaactgaat tccagaaaga aacaagcata ggcaagaaag agagatgaca 17032922DNAHomo sapiens 329cccatgagaa caacaagaga aa 2233020DNAHomo sapiens 330ctctttcttg cctatgcttg 20331167DNAHomo sapiens 331aagatttaga acagctgaag cagcgagaaa aaacccagca tgagtcagaa ctggagcaac 60tgaggattta ttttgaaaag aagttaaggg atgctgagaa aacttaccaa gaagacctaa 120ccctgttaca gcagaggctg cagggggcga gggaagatgc tcttctg 16733221DNAHomo sapiens 332cagctgaagc agcgagaaaa a 2133319DNAHomo sapiens 333cccctgcagc ctctgctgt 19334174DNAHomo sapiens 334gggaaactga cttggctttt gcaagggtca ttgcttcctg atgcatgttt aactgtcctg 60tgttcacttt gttgccgcag gtttttagag gaacgtaaag agatcaccga gaaattcagt 120gcggaacaag atgccttcct gcaggaggcc caggagcagc atgcccgtga gctg 17433522DNAHomo sapiens 335gggaaactga cttggctttt gc 2233620DNAHomo sapiens 336ggcatcttgt tccgcactga 20337175DNAHomo sapiens 337ccctgcacac tgacctgcat gccctcgtca cctgcactct gcatgctcac catctgacgg 60actcctgcga cgggcatggg aaggtcgccg ccgccggcag ccttgcgagc actttggatg 120tgtgcacccg gcatgccagg cccgagtcaa cagactggcc gaccttggcg tcctg 17533820DNAHomo sapiens 338gccctcgtca cctgcactct 2033920DNAHomo sapiens 339ccaaggtcgg ccagtctgtt 20340155DNAHomo sapiens 340tttattgctg agtggtattc cattttatgg gtccattata gtttatttgt ccagacactt 60catggaaaga catcagtgtt tcctgttttt caatcataaa ttgatgttta attttaaaat 120tttggaattg tagaagaaat gcaattcttt tttcc 15534122DNAHomo sapiens 341tgggtccatt atagtttatt tg 2234222DNAHomo sapiens 342tgcatttctt ctacaattcc aa 22343208DNAHomo sapiens 343ctttggtgca gaatcatgct gcaggcaagg tgggcccacc tccctggaat ttcatccccc 60ccgtcagtta aacccatggt ggttttattt tctaggccac ctgatctggg aggaccacct 120ccaagaaaag cagtcctatc gatgaacggt ctaagttatg gtgttatcag agtggatact 180gaagaaaagt tgtcagtcct tactgttc 20834420DNAHomo sapiens 344ggcccacctc cctggaattt 2034522DNAHomo sapiens 345tccactctga taacaccata ac 22346232DNAHomo sapiens 346atcacctggt ttggtgcatc ctcgcagaaa gagagccata cagtgaagtg gaaacacacc 60caaaagctct gcaatattcc tagaagttct cgaatctcct ccttaacaga gctgcagaag 120ggaaacacag acaggaagca cctgtttgac tcagacagca gccctaatgc agtgccactc 180aggagcattc cctcatttga agacccccca attacatgaa attatcaacc cc 23234720DNAHomo sapiens 347acacccaaaa gctctgcaat 2034820DNAHomo sapiens 348caaatgaggg aatgctcctg 20349240DNAHomo sapiens 349ggaactgcag gagatccctg ctgccttcca gttcatggga tgatggcctc cacttctgcc 60cctgtttgct tctcctttca aatcttacat gaaggtatac agtttgaaga agccagtttg 120actccaatat ctgtgcaatg gaatactgct cattaaaaag gaattaaact attgatacac 180acaacatggg tgaagatcaa actgtctcct tccctttgat tcaagggaat ctgagaaatg 24035019DNAHomo sapiens 350acttctgccc ctgtttgct 1935121DNAHomo sapiens 351tgatcttcac ccatgttgtg t 21352187DNAHomo sapiens 352tggagaaagt tgttgcaaac tgcccagaga ccctgggagt cactccagtt ttctgaaacc 60cagatatttc agtgcctcag gagagacaag tcctgacctt ctctcctcca gctctcccag 120gagataggca agcccctaac tccctaacta agcccttcag acctgaaatc cattgagtgg 180cttcttt 18735318DNAHomo sapiens 353gcaaactgcc cagagacc 1835420DNAHomo sapiens 354ttagggagtt aggggcttgc 20355184DNAHomo sapiens 355agggccatgg gatgatgcag gtggagactg gagtgctaca gctgcaagca aatacatttc 60tgtgctgtga agccacccat ttggtggtac tacgttaaaa cagctctagg aaattaatac 120agatgttgcc tgtatttttg tttctcatat tactactcat tgttttaatg atgactgttt 180tatt 18435620DNAHomo sapiens 356aggtggagac tggagtgcta 2035722DNAHomo sapiens 357agaaacaaaa atacaggcaa ca 22

Claims

1. A method for determining whether a fetus has at least one genetic abnormality, said method comprising comparing at least three alleles, wherein said comparing identifies said at least one genetic abnormality.

2. A method according to claim 1, wherein said comparing comprises detecting the number of molecules of each of said at least three alleles.

3. A method according to claim 1, wherein said three alleles are alleles of a tandem single nucleotide polymorphism (SNP).

4. A method according to claim 2, wherein said comparing comprises calculating a haplotype ratio.

5. A method according to claim 1, wherein two of said at least three alleles are maternal alleles and one of said at least three alleles is a paternal allele that is not present in the maternal genome.

6. A method according to claim 5, wherein said comparing comprises determining the number of molecules of each of said at least three alleles in said sample, and wherein if the number of molecules of said two maternal alleles is equal, said fetus has at least one genetic abnormality.

7. A method according to claim 5, wherein said comparing comprises determining the number of molecules present in said sample for each of said at least three alleles, and wherein if the number of molecules of the three alleles is in the relationship of peak, x and peak+2x, the fetus has at least one genetic abnormality.

8. A method according to claim 5, wherein said comparing comprises determining the number of molecules present in said sample for each of said at least three alleles, and wherein if the number of molecules of the three alleles is in the relationship of peak, x and peak+x, the fetus does not have a genetic abnormality.

9. A method according to claim 1, wherein one of said at least three alleles is a paternally-inherited fetal allele.

10. A method according to claim 9, wherein said comparing comprises calculating an allelic ratio, and wherein said paternally-inherited fetal allele serves as an internal standard for said allelic ratio.

11. A method according to claim 1, wherein said at least three alleles comprise a member selected from:a deletion, an insertion, a variant sequence, methylation, and any combination thereof.

Images