Systems and Methods for Detection of Aneuploidy

Abstract

Provided herein are improved methods for detecting aneuploidy in a sample. The methods in certain embodiments are used for the analysis of circulating DNA in serum samples, such as circulating fetal DNA or circulating tumor DNA. In certain embodiments, chromosome or chromosome segments of interest are used to set a bias model and/or a control value for a z-score determination, in illustrative examples without the use of a control chromosome.

What is claimed is: 
     
         1 . A method for detecting a presence or absence of aneuploidy of a chromosome or chromosome segment of interest in a test sample, comprising:
 obtaining genetic data for the chromosome or chromosome segment of interest from each sample in a set of samples comprising the test sample, wherein the genetic data is obtained from a parallel analysis of the samples, wherein the genetic data of the test sample are obtained by isolating a mixture of fetal cell-free genomic DNA and maternal cell-free genomic DNA from the test sample which is a blood sample of a pregnant woman, and amplifying and sequencing the mixture of fetal cell-free genomic DNA and maternal cell-free genomic DNA together;   determining whether aneuploidy is present in the test sample by a first method comprising:
 determining a depth of reads or a proportion of reads that map to the chromosome or chromosome segment of interest; 
 calculating a z-score for the depth of reads or the proportion of reads that map to the chromosome or chromosome segment of interest; and 
 determining whether the test sample is aneuploidy at the chromosome or chromosome segment of interest based on the z-score, thereby providing a first result; and 
   determining whether aneuploidy is present in the test sample by a second method comprising:
 creating a plurality of ploidy hypotheses wherein each ploidy hypothesis is associated with a specific copy number for the chromosome or chromosome segment of interest, 
 determining a ploidy probability value for each ploidy hypothesis, wherein the ploidy probability value indicates the likelihood that the test sample has the specific copy number for the chromosome or chromosome segment of interest that is associated with the ploidy hypothesis, and 
 determining which ploidy hypothesis is most likely to be correct by selecting the ploidy hypothesis with the maximum likelihood, thereby providing a second result, 
   wherein aneuploidy is detected by considering the first result and the second result.   
     
     
         2 . The method according to  claim 1 , wherein the genetic data comprises quantitative allelic data from a plurality of polymorphic loci in the set of loci, wherein each of the ploidy hypotheses specifies an expected distribution of quantitative allelic data at the plurality of polymorphic loci, and wherein the ploidy probability values are determined by calculating, for each of the ploidy hypotheses, the fit between the expected genetic data and the obtained genetic data. 
     
     
         3 . The method according to  claim 1 , wherein the genetic data comprises quantitative non-allelic data from a plurality of polymorphic loci in the set of loci, and wherein each of the ploidy hypotheses specifies an expected mean value of quantitative non-allelic data at the plurality of polymorphic loci, and wherein the ploidy probability values are determined by calculating, for each of the ploidy hypotheses, the fit between the expected genetic data and the obtained genetic data. 
     
     
         4 . The method according to  claim 1 , wherein the first result is determined by calculating a likelihood based on the z-score. 
     
     
         5 . The method according to  claim 4 , wherein aneuploidy is detected by combining the aneuploidy likelihoods from the first method and these second method using the following formula:
   Combined likelihood= R 1 R 2/[ R 1 R 2+(1− R 1)(1− R 2)].
   
     
     
         6 . The method according to  claim 1 , wherein the first result is determined by determining whether the z-score for the test sample is above a threshold value. 
     
     
         7 . The method according to  claim 1 , wherein the second method comprises a quantitative allelic method. 
     
     
         8 . The method according to  claim 7 , wherein the quantitative allelic method is het rate method. 
     
     
         9 . The method according to  claim 8 , wherein the het rate method is based on analysis of observed allele ratios at each SNP using a joint distribution model. 
     
     
         10 . The method according to  claim 1 , wherein the second method comprises a quantitative non-allelic method. 
     
     
         11 . The method according to  claim 10 , wherein the quantitative non-allelic method is QMM method. 
     
     
         12 . The method according to  claim 11 , wherein the QMM method is based on analysis of the number of sequencing reads at each SNP. 
     
     
         13 . The method according to  claim 1 , wherein the second method comprises both a quantitative allelic method and a quantitative non-allelic method. 
     
     
         14 . A method for determining a presence or absence of a fetal aneuploidy in a fetus for each of a plurality of maternal blood samples obtained from a plurality of different pregnant women, said maternal blood samples comprising fetal and maternal cell-free genomic DNA, said method comprising:
 determining a number of enumerated sequence reads corresponding to a chromosome or chromosome segment of interest for each of the plurality of samples;   determining a reference value of enumerated sequence reads from a diploid subset of between 1 and 50 samples of the plurality of samples or between 1-50% of samples of the plurality of samples having a number of enumerated sequence reads closest to the median number of enumerated sequence reads for the chromosome or chromosome segment of interest for the plurality of maternal blood samples, without using determining sequencing reads for a separate reference chromosome; and   comparing the enumerated sequence reads from each of the other samples of the plurality of samples that are not diploid samples, to the reference value, thereby determining the presence or absence of a fetal aneuploidy in the chromosome or chromosome segment of interest.   
     
     
         15 . The method according to  claim 14 , further comprising before the determining the number of enumerated sequence reads:
 obtaining a fetal and maternal cell-free genomic DNA sample from each of the plurality of maternal blood samples;   generating a library derived from each fetal and maternal cell-free genomic DNA sample,   performing massively parallel sequencing of polynucleotide sequences of the library from the chromosome or chromosome segment of interest; and   enumerating sequence reads corresponding to fetal and maternal polynucleotide sequences selected from the chromosome or chromosome segment of interest.   
     
     
         16 . The method according to  claim 14 , wherein the reference value of enumerated sequence reads is determined from a diploid subset of between 10 and 40 samples closest to the median. 
     
     
         17 . The method according to  claim 14 , wherein the reference value of enumerated sequence reads is determined from a diploid subset of between 15 and 40 samples closest to the median. 
     
     
         18 . The method according to  claim 14 , wherein each library of enriched and indexed fetal and maternal polynucleotide sequences includes an indexing nucleotide sequence which identifies a maternal blood sample of the plurality of maternal blood samples and pooling the libraries generated to produce a pool of enriched and indexed fetal and maternal non-random polynucleotide sequences. 
     
     
         19 . The method according to  claim 14 , wherein said plurality of polynucleotide sequences comprises at least 100 different non-random polynucleotide sequences, wherein each of said plurality of non-random polynucleotide sequences is from 10 to 1000 nucleotide bases in length. 
     
     
         20 . The method according to  claim 14 , wherein the method further comprises selectively enriching a plurality of non-random polynucleotide sequences of each fetal and maternal cell-free genomic DNA samples.