Noninvasive prenatal diagnosis of fetal trisomy by allelic ratio analysis using targeted massively parallel sequencing

Abstract

Whether a fetus has an aneuploidy associated with a first chromosome is detected using ratios of alleles detected in a maternal sample having a mixture of maternal and fetal DNA. DNA from the sample is enriched for target regions associated with polymorphic loci and then sequenced. Polymorphic loci (e.g., single nucleotide polymorphisms) in the target regions with fetal-specific alleles are identified on a first chromosome and on one or more reference chromosomes. A first ratio of the fetal-specific alleles and shared alleles is determined for the loci on the first chromosome. A second ratio of the fetal-specific alleles and shared alleles is determined for the loci on the reference chromosome(s). A third ratio of the first and second ratio can be compared to a cutoff to determine whether an aneuploidy is present, and whether the aneuploidy is maternally-derived or paternally-derived.

What is claimed is: 
     
         1 . A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to analyze a biological sample from a female subject pregnant with a fetus to determine whether the fetus has an aneuploidy associated with a first chromosome, the biological sample containing a mixture of DNA molecules from the fetus and the female subject, the plurality of instructions comprising:
 receiving a plurality of sequence reads obtained from sequencing DNA molecules from the biological sample, where the biological sample is enriched for DNA molecules from a plurality of target regions that are known to have polymorphic loci;   analyzing the plurality of sequence reads, wherein analyzing a sequence read includes:
 identifying a location of the sequence read in a reference genome by aligning the sequence read to the reference genome; and 
 determining a respective allele of the sequence read; 
   identifying a plurality of first loci on the first chromosome, the plurality of first loci corresponding to a portion of the target regions;   identifying a plurality of second loci on one or more reference chromosomes, the plurality of second loci corresponding to a portion of the target regions, wherein the female subject is homozygous for a respective maternal allele at each of the first and second loci, and wherein the fetus is heterozygous for the respective maternal allele and a respective paternal allele at each of the first and second loci, the respective paternal alleles being different from the respective maternal alleles;   determining a first maternal amount of the respective maternal alleles at the plurality of first loci;   determining a first paternal amount of the respective paternal alleles at the plurality of first loci;   calculating a first ratio of the first maternal amount and the first paternal amount;   determining a second maternal amount of the respective maternal alleles at the plurality of second loci;   determining a second paternal amount of the respective paternal alleles at the plurality of second loci;   calculating a second ratio of the second maternal amount and the second paternal amount;   calculating a third ratio of the first ratio and the second ratio; and   comparing the third ratio to one or more cutoff values to determine whether the fetus has the aneuploidy associated with the first chromosome, wherein a first cutoff value of the one or more cutoff values corresponds to an aneuploidy that is paternally-derived.   
     
     
         2 . The computer product of  claim 1 , wherein:
 the third ratio is the first ratio divided by the second ratio, and   a second cutoff value of the one or more cutoff values corresponds to an aneuploidy that is maternally-derived.   
     
     
         3 . The computer product of  claim 2 , wherein the third ratio is approximately two when the aneuploidy is paternally-derived. 
     
     
         4 . The computer product of  claim 2 , wherein the third ratio is approximately 1−(f/2) when the aneuploidy is maternally-derived, where f is a fractional fetal DNA concentration in the mixture. 
     
     
         5 . The computer product of  claim 4 , the plurality of instructions further comprising:
 determining the fractional fetal DNA concentration f from the second paternal amount and the second maternal amount.   
     
     
         6 . The computer product of  claim 2 , wherein comparing the third ratio to one or more cutoff values includes:
 comparing the third ratio to the first cutoff value to determine whether the fetus has a paternally-derived aneuploidy, the plurality of instructions further comprising:   when the fetus does not have a paternally-derived aneuploidy:
 measuring a fractional fetal DNA concentration in the mixture; and 
   comparing the third ratio to the second cutoff value to determine whether the fetus has a maternally-derived aneuploidy, wherein the second cutoff value is determined using the fractional fetal DNA concentration.   
     
     
         7 . The computer product of  claim 1 , wherein the first ratio includes the first paternal amount divided by the first maternal amount, and the second ratio includes the second paternal amount divided by the second maternal amount. 
     
     
         8 . The computer product of  claim 1 , wherein identifying a first locus of the plurality of first loci on the first chromosome includes:
 aligning the plurality of sequence reads to the first locus; and   identifying two alleles among the plurality of sequence reads aligned to the first locus.   
     
     
         9 . The computer product of  claim 8 , wherein the plurality of instructions further comprise:
 determining a first number of sequence reads corresponding to a first allele at the first locus;   determining a second number of sequence reads corresponding to a second allele at the first locus;   calculating an allelic ratio of the first number and the second number;   determining whether the allelic ratio is above a first threshold and below a second threshold.   
     
     
         10 . The computer product of  claim 1 , wherein identifying a first locus of the plurality of first loci on the first chromosome includes:
 identifying that the father of the fetus is homozygous for a first allele at the first locus; and   identifying that the female subject is homozygous for a second allele at the first locus.   
     
     
         11 . The computer product of  claim 10 , wherein identifying that the father of the fetus is homozygous for the first allele at the first locus comprises genotyping the father of the fetus at the first locus, and
 wherein identifying that the female subject is homozygous for the second allele at the first locus comprises genotyping the female subject at the first locus using a sample from the female subject.   
     
     
         12 . The computer product of  claim 11 , wherein the sample from the female subject includes blood cells from the female subject. 
     
     
         13 . The computer product of  claim 1 , wherein the first ratio is a first percentage as determined from the first maternal amount and the first paternal amount, and wherein the second ratio is a second percentage as determined from the second maternal amount and the second paternal amount. 
     
     
         14 . The computer product of  claim 1 , wherein the first ratio includes the first paternal amount divided by a sum of the first paternal amount and the first maternal amount. 
     
     
         15 . The computer product of  claim 1 , wherein the first chromosome is chromosome 21, chromosome 13, or chromosome 18. 
     
     
         16 . The computer product of  claim 1 , wherein at least one of the first loci is a SNP. 
     
     
         17 . The computer product of  claim 1 , wherein the plurality of second loci are located on a plurality of reference chromosomes. 
     
     
         18 . A system for determining whether a fetus has an aneuploidy associated with a first chromosome, the system comprising:
 a sequencing platform configured to generate a plurality of sequence reads by sequencing DNA molecules from a biological sample, the biological sample containing a mixture of DNA molecules from the fetus and the female subject, wherein the biological sample is enriched for DNA molecules from a plurality of target regions that are known to have polymorphic loci;   a computer system; and   a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control the computer system to analyze a biological sample from a female subject pregnant with the fetus to determine whether the fetus has the aneuploidy associated with a first chromosome, the plurality of instructions comprising:
 receiving the plurality of sequence reads; 
   analyzing the plurality of sequence reads, wherein analyzing a sequence read includes:
 identifying a location of the sequence read in a reference genome by aligning the sequence read to the reference genome; and 
 determining a respective allele of the sequence read; 
 identifying a plurality of first loci on the first chromosome, the plurality of first loci corresponding to a portion of the target regions; 
 identifying a plurality of second loci on one or more reference chromosomes, the plurality of second loci corresponding to a portion of the target regions, wherein the female subject is homozygous for a respective maternal allele at each of the first and second loci, and wherein the fetus is heterozygous for the respective maternal allele and a respective paternal allele at each of the first and second loci, the respective paternal alleles being different from the respective maternal alleles; 
 determining a first maternal amount of the respective maternal alleles at the plurality of first loci; 
 determining a first paternal amount of the respective paternal alleles at the plurality of first loci; 
 calculating a first ratio of the first maternal amount and the first paternal amount; 
 determining a second maternal amount of the respective maternal alleles at the plurality of second loci; 
 determining a second paternal amount of the respective paternal alleles at the plurality of second loci; 
 calculating a second ratio of the second maternal amount and the second paternal amount; 
 calculating a third ratio of the first ratio and the second ratio; and 
 comparing the third ratio to one or more cutoff values to determine whether the fetus has the aneuploidy associated with the first chromosome, wherein a first cutoff value of the one or more cutoff values corresponds to an aneuploidy that is paternally-derived. 
   
     
     
         19 . The system of  claim 18 , further comprising a system for enriching DNA molecules from the plurality of target regions.