Fetal aneuploidy detection by sequencing

Abstract

The present invention provides apparatus and methods for enriching components or cells from a sample and conducting genetic analysis, such as SNP genotyping to provide diagnostic results for fetal disorders or conditions.

1 . A method of determining a likelihood of the presence or absence of a fetal aneuploidy in a fetus using a maternal sample derived from a pregnant human female comprising fetal and maternal DNA, the method comprising:
 (a) selectively amplifying a plurality of single nucleotide polymorphism (SNP) sites of a first chromosome selected from the group consisting of chromosomes 13, 18, 21, X, and Y in the maternal sample comprising fetal and maternal DNA;   (b) sequencing the amplified plurality of SNP sites of the fetal and maternal DNA of (a) and determining abundances of alleles at the plurality of SNP sites to obtain a first set of genotype data;   (c) selectively amplifying the plurality of SNP sites of the first chromosome in a maternal-only sample comprising maternal DNA, wherein the maternal-only sample is essentially free of fetal DNA;   (d) sequencing the amplified plurality of SNP sites of the first chromosome of the maternal DNA of (c) and determining abundances of alleles at the plurality of SNP sites to obtain a second set of genotype data;   (e) creating model sets corresponding to a plurality of fetal ploidy states using the second set of genotype data;   (f) comparing the first set of genotype data to the model sets and selecting from the model sets a model that provides a best fit to the first set of genotype data; and   (g) determining the likelihood of the presence or absence of a fetal aneuploidy of the first chromosome using the selected model that provides the best fit to the first set of genotype data.   
     
     
         2 . The method of  claim 1 , wherein (a) and (b) each comprise selectively amplifying at least 100 SNP sites of the first chromosome. 
     
     
         3 . The method of  claim 1 , wherein the fetal aneuploidy comprises a trisomy of the first chromosome. 
     
     
         4 . The method of  claim 3 , wherein the fetal aneuploidy comprises trisomy 13, trisomy 18, or trisomy 21. 
     
     
         5 . The method of  claim 1 , wherein the fetal aneuploidy comprises an aneuploidy of chromosome X. 
     
     
         6 . The method of  claim 5 , wherein the fetal aneuploidy comprises monosomy X. 
     
     
         7 . The method of  claim 1 , wherein the fetal aneuploidy comprises an aneuploidy of chromosome Y. 
     
     
         8 . The method of  claim 1 , wherein the fetal aneuploidy comprises XXX, XXY, or XYY. 
     
     
         9 . The method of  claim 1 , wherein selectively amplifying the plurality of SNP sites of the first chromosome of (a) comprises performing polymerase chain reaction (PCR) amplification. 
     
     
         10 . The method of  claim 1 , wherein selectively amplifying the plurality of SNP sites of the first chromosome of (c) comprises performing polymerase chain reaction (PCR) amplification. 
     
     
         11 . The method of  claim 1 , wherein the plurality of SNP sites of (a) are amplified in parallel. 
     
     
         12 . The method of  claim 1 , wherein the plurality of SNP sites of (c) are amplified in parallel. 
     
     
         13 . The method of  claim 2 , wherein the at least 100 SNP sites of each of (a) and (c) are amplified in parallel. 
     
     
         14 . The method of  claim 1 , wherein (a) further comprises selectively amplifying a plurality of SNP sites of a second chromosome that is different from the first chromosome selected from the group consisting of chromosomes 13, 18, 21, X, and Y. 
     
     
         15 . The method of  claim 1 , wherein (c) further comprises selectively amplifying a plurality of SNP sites of a second chromosome that is different from the first chromosome selected from the group consisting of chromosomes 13, 18, 21, X, and Y. 
     
     
         16 . The method of  claim 1 , wherein sequencing of (b) and sequencing of (d) each comprise sequencing millions of molecules in parallel. 
     
     
         17 . The method of  claim 1 , wherein steps (c) and (d) are performed prior to steps (a) and (b). 
     
     
         18 . The method of  claim 1 , further comprising performing paternal genotyping to obtain a third set of genotype data. 
     
     
         19 . The method of  claim 18 , wherein (e) further comprises creating model sets corresponding to a plurality of fetal ploidy states using the second and third sets of genotype data. 
     
     
         20 . The method of  claim 1 , wherein the plurality of fetal chromosomal ploidy states comprise disomy, trisomy, and monosomy. 
     
     
         21 . A method of determining a likelihood of the presence or absence of a fetal aneuploidy in a fetus using a maternal sample derived from a pregnant human female comprising fetal and maternal DNA, the method comprising:
 (a) amplifying by PCR amplification a plurality of selected genomic DNA regions comprising of a first chromosome selected from the group consisting of chromosomes 13, 18, 21, X, and Y in the maternal sample comprising fetal and maternal DNA, and amplifying by PCR amplification a plurality of selected genomic DNA regions of SNPs of the first chromosome in a maternal-only sample comprising maternal DNA, wherein the maternal-only sample is essentially free of fetal DNA, and wherein each genomic DNA region comprises a locus comprising one or more single nucleotide polymorphism (SNP) positions of interest;   (b) sequencing the amplified plurality of selected genomic DNA regions of the fetal and maternal DNA of the maternal sample and determining abundances of alleles at one or more SNP positions to obtain a first set of genotype data, and sequencing the amplified plurality of selected genomic DNA of the maternal DNA of the maternal-only sample and determining abundances of alleles at one or more SNP positions to obtain a second set of genotype data;   (c) creating model sets corresponding to a plurality of fetal ploidy states using the second set of genotype data;   (d) comparing the first set of genotype data to the model sets and selecting from the model sets a model that provides a best fit to the first set of genotype data; and   (e) determining the likelihood of the presence or absence of a fetal aneuploidy of the first chromosome using the selected model that provides the best fit to the first set of genotype data.   
     
     
         22 . The method of  claim 21 , wherein (c) comprises amplifying a plurality of selected genomic DNA regions of a second chromosome that is different from the first chromosome and is selected from the group consisting of chromosomes 13, 18, 21, X, and Y. 
     
     
         23 . The method of  claim 21 , wherein the plurality of fetal chromosomal ploidy states comprise disomy, trisomy, and monosomy. 
     
     
         24 . The method of  claim 23 , wherein the fetal aneuploidy comprises trisomy 13, trisomy 18, trisomy 21, or monosomy X. 
     
     
         25 . The method of  claim 21 , wherein (a) comprises amplifying a plurality of selected genomic DNA regions of each of chromosomes 13, 18, 21, X, and Y. 
     
     
         26 . The method of  claim 21 , wherein at least one SNP position comprises an informative SNP.