Systems and methods for detection of aneuploidy
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.
1. A method for preparing a non-naturally occurring composition of amplified DNA from a test sample useful for determining the likelihood of aneuploidy of a chromosome or chromosome segment of interest in the test sample, comprising:
a. extracting 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;
b. preparing a non-naturally occurring composition of amplified DNA extracted in a. by performing amplification of at least 100 polymorphic loci on the chromosome or chromosome segment of interest in a single reaction from the mixture of fetal cell-free genomic DNA and maternal cell-free genomic DNA; and
c. analyzing the non-naturally occurring composition of amplified DNA produced in b. by performing sequencing to generate genetic data for the chromosome or chromosome segment of interest from each sample in a set of samples comprising the test sample and at least one diploid sample, wherein the genetic data is obtained from a parallel analysis of the samples, and wherein the analyzing comprises:
(i) setting a first bias model using the genetic data for the chromosome or chromosome segment of interest from the at least one diploid sample determined to be disomic for the chromosome or chromosome segment of interest,
(ii) normalizing the genetic data for the chromosome or chromosome segment of interest for the test sample using the first bias model, and
(iii) determining the likelihood of aneuploidy for the chromosome or chromosome segment of interest in the test sample using the normalized data, wherein the normalized data comprise quantitative allelic data from a plurality of polymorphic loci in the chromosome or chromosome segment of interest and quantitative non-allelic data from a plurality of polymorphic and/or non-polymorphic loci in the chromosome or chromosome segment of interest, and wherein the determining the likelihood of aneuploidy comprises obtaining a first probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative allelic analysis of the allelic data, obtaining a second probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative non-allelic analysis of the non-allelic data, and combining the first probability value and the second probability value to produce a combined probability value to determine the likely copy number of the chromosome or chromosome segment of interest,
wherein the quantitative allelic analysis is performed by quantitative allelic maximum likelihood method or het rate method, and wherein the quantitative non-allelic analysis is performed by quantitative non-allelic maximum likelihood method or QMM method and the het rate method is based on analysis of observed allele ratios at each SNP using a joint distribution model, and wherein the QMM method is based on analysis of the number of sequencing reads at each SNP,
wherein the at least one diploid sample is determined to be disomic for the chromosome or chromosome segment of interest by analyzing the genetic data from the parallel analysis, and
wherein the likelihood of aneuploidy is determined by:
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 target sample has the number of copies of the chromosome or chromosome segment of interest that is associated with the ploidy hypothesis, wherein the ploidy probability values are derived from the normalized genetic data,
selecting the ploidy hypothesis with the maximum likelihood as the ploidy hypothesis most likely to be correct; and
outputting the likely ploidy state of the test sample as an indication of the likelihood of aneuploidy.
2. A method for preparing a non-naturally occurring composition of amplified DNA from a test sample useful for determining the likelihood of aneuploidy of a chromosome or chromosome segment of interest in the test sample, comprising:
a. extracting 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;
b. preparing a non-naturally occurring composition of amplified DNA extracted in a. by performing amplification of at least 100 polymorphic loci on the chromosome or chromosome segment of interest in a single reaction from the mixture of fetal cell-free genomic DNA and maternal cell-free genomic DNA; and
c. analyzing the non-naturally occurring composition of amplified DNA produced in b. by performing sequencing to generate genetic data for the chromosome or chromosome segment of interest from each sample in a set of samples comprising the test sample and at least one diploid sample, wherein the genetic data is obtained from a parallel analysis of the samples, and wherein the analyzing comprises:
(i) setting a first bias model using the genetic data for the chromosome or chromosome segment of interest from the at least one diploid sample determined to be disomic for the chromosome or chromosome segment of interest,
(ii) normalizing the genetic data for the chromosome or chromosome segment of interest for the test sample using the first bias model, and
(iii) determining the likelihood of aneuploidy for the chromosome or chromosome segment of interest in the test sample using the normalized data, wherein the normalized data comprise quantitative allelic data from a plurality of polymorphic loci in the chromosome or chromosome segment of interest and quantitative non-allelic data from a plurality of polymorphic and/or non-polymorphic loci in the chromosome or chromosome segment of interest, and wherein the determining the likelihood of aneuploidy comprises obtaining a first probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative allelic analysis of the allelic data, obtaining a second probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative non-allelic analysis of the non-allelic data, and combining the first probability value and the second probability value to produce a combined probability value to determine the likely copy number of the chromosome or chromosome segment of interest,
wherein the at least one diploid sample is determined to be disomic for the chromosome or chromosome segment of interest by analyzing the genetic data from the parallel analysis,
wherein the genetic data comprises an amount of DNA corresponding to each locus in a set of loci wherein the loci are present on the chromosome or chromosome segment of interest, and
wherein the chromosome or chromosome segment of interest in the at least one diploid sample is determined to be disomic by:
creating, for each sample in the set of samples, a plurality of first hypotheses wherein each first hypothesis is associated with a specific copy number for the chromosome or chromosome segment of interest,
determining a first probability value for each first hypothesis, wherein the first probability value indicates the likelihood that the sample has the number of copies of the chromosome or chromosome segment that is associated with the first hypothesis, wherein the first probability values are derived from the genetic data associated with the sample, and
selecting the at least one diploid sample by selecting the at least one sample that matches a disomic copy number hypothesis for the chromosome or chromosome segment of interest,
wherein the at least one diploid sample that is determined to be disomic for the chromosome or chromosome segment of interest is determined by, for each sample in the set of samples,
calculating a proportion of reads that map to the chromosome or chromosome segment of interest;
calculating a z-score for the proportion of reads that map to the chromosome or chromosome segment of interest; and
selecting one or more samples where the absolute value of the z-score is below a threshold value or where the z-score indicates disomy at a level of confidence of at least 90%.
3. The method according to claim 2 , wherein the determining is performed using a quantitative non-allelic method.
4. The method according to claim 2 , wherein the determining is performed using a quantitative allelic method.
5. The method according to claim 1 , wherein the first bias model comprises sample bias.
6. The method according to claim 2 , wherein the method further comprises estimating a fetal fraction and setting a second bias model, wherein the fetal fraction and the second bias model are used to determine the at least one diploid sample and/or to determine the ploidy probability.
7. The method according to claim 6 , wherein determining a first probability value for each first hypothesis comprises:
(a) determining an initial probability of each first hypothesis for each grid point using a uniform hypothesis prior on a 2d grid of fetal fraction and the second bias model;
(b) determining a parameter distribution for each chromosome or chromosome segment of interest based on the initial probability;
(c) determining a composite parameter distribution from the parameter distribution for each chromosome or chromosome segment of interest;
(d) determining a posterior probability of each first hypothesis based on the composite parameter distribution; and
(e) repeating steps (a)-(e) using the posterior probability as a new initial probability for each iteration until convergence is reached.
8. The method according to claim 6 , wherein determining a ploidy probability value for each ploidy hypothesis comprises:
(a) determining an initial probability of each ploidy hypothesis for each grid point using a uniform hypothesis prior on a 2d grid of fetal fraction and the first bias model;
(b) determining a parameter distribution for each chromosome or chromosome segment of interest based on the initial probability;
(c) determining a composite parameter distribution from the parameter distribution for each chromosome or chromosome segment of interest;
(d) determining a posterior probability of each ploidy hypothesis based on the composite parameter distribution; and
(e) repeating steps (a)-(e) using the posterior probability as a new initial probability for each iteration until convergence is reached.
9. The method according claim 2 , further comprising
outputting the selected one or more samples as an indication of the likely presence of aneuploidy.
10. The method according to claim 2 , wherein the at least one diploid sample is determined to be disomic for the chromosome or chromosome segment of interest without using a control chromosome or control chromosome segment that is different than the chromosome or chromosome segment of interest.
11. A method for preparing a non-naturally occurring composition of amplified DNA from a test sample useful for determining the likelihood of aneuploidy for a first chromosome or chromosome segment of interest in a test sample from the test subject, comprising:
a. extracting 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;
b. producing a non-naturally occurring composition of amplified DNA extracted in a. by performing amplification of at least 100 polymorphic loci on the chromosome or chromosome segment of interest in a single reaction from the mixture of fetal cell-free genomic DNA and maternal cell-free genomic DNA and sequence the amplification products;
c. analyzing the non-naturally occurring composition of amplified DNA produced in b. by performing sequencing to generate genetic sequencing data from a parallel analysis of the first chromosome or chromosome segment of interest from cell free DNA from each sample in a set of liquid samples comprising the test sample, wherein the set of liquid samples comprises at least 3 samples, wherein the genetic sequencing data determines an amount of DNA corresponding to each locus in a first set of loci present on the first chromosome or chromosome segment of interest respectively, and wherein the analyzing comprises:
(i) estimating a fetal fraction for each sample in the set of samples,
(ii) selecting a diploid subset of samples from the set of liquid samples, wherein the diploid subset of samples are samples that are initially determined to be disomic for the first chromosome or chromosome segment of interest using an initial bias model, wherein the subset of samples comprises at least 2 samples,
(iii) setting a confirmatory bias model from the genetic data from the first chromosome or chromosome segment of interest from the diploid subset of patients,
(iv) normalizing the genetic data for the test subject using the confirmatory bias model, to give normalized genetic data for the test subject, and
(v) determining, using the normalized data, whether genetic data from the test subject is indicative of an aneuploidy in the first chromosome or chromosome segment of interest, wherein the normalized data comprise quantitative allelic data from a plurality of polymorphic loci in the chromosome or chromosome segment of interest and quantitative non-allelic data from a plurality of polymorphic and/or non-polymorphic loci in the chromosome or chromosome segment of interest, and wherein the determining the likelihood of aneuploidy comprises obtaining a first probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative allelic analysis of the allelic data, obtaining a second probability value indicating the likely copy number of the chromosome or chromosome segment of interest by quantitative non-allelic analysis of the non-allelic data, and combining the first probability value and the second probability value to produce a combined probability value to determine the likely copy number of the chromosome or chromosome segment of interest,
wherein the fetal fraction is used to select the diploid subset of samples and/or to determine whether the genetic data from the test subject is indicative of an aneuploidy, and
wherein the at least one diploid sample that is determined to be disomic for the chromosome or chromosome segment of interest is determined by, for each sample in the set of samples:
calculating a proportion of reads that map to the chromosome or chromosome segment of interest;
calculating a z-score for the proportion of reads that map to the chromosome or chromosome segment of interest; and
selecting one or more samples where the absolute value of the z-score is below a threshold value.
12. The method according to claim 11 , wherein the set of samples comprises at least 40 samples and the diploid subset of samples comprises at least 10 diploid samples.
13. The method according to claim 11 , wherein the selecting is performed by a method comprising, for each sample in the set of samples,
creating a plurality of first hypotheses considering the fetal fraction estimate and the initial bias model, wherein each first hypothesis is associated with a specific copy number for the chromosome or chromosome segment of interest in a genome of a target sample,
determining a first probability value for each first hypothesis, wherein the first probability value indicates the likelihood that the genome of the target cell has the number of copies of the chromosome or chromosome segment that is associated with the first hypothesis, wherein the first probability values are derived from the genetic data associated with that sample, and
selecting the subset of samples from those samples that match a disomic copy number hypothesis for the chromosome or chromosome segment of interest.
14. The method according to claim 11 , wherein the determining whether the normalized data is indicative of aneuploidy is performed by, for each sample in the set of samples,
creating a plurality of second hypotheses wherein each second hypothesis is associated with a specific copy number for the chromosome or chromosome segment in the genome of the test sample,
determining a second probability value for each second hypothesis, wherein the second probability value indicates the likelihood that the genome of the target sample has the number of copies of the chromosome or chromosome segment that is associated with the second hypothesis, wherein the second probability values are derived from the normalized genetic data,
selecting the second hypothesis with the maximum likelihood as the second hypothesis most likely to be correct; and
outputting the ploidy state of the test sample as an indication of the likelihood of aneuploidy.
15. The method according to claim 14 , wherein the first hypothesis, the second hypothesis, or both the first and second hypothesis provide an expected distribution of quantitative data for each of the first, second, and third sets of loci.
16. The method according to claim 14 , wherein the plurality of first hypotheses, the plurality of second hypotheses, or both the first and second hypothesis comprise estimates of sample parameters for each sample of the set of samples at a given ploidy state.
17. The method according to claim 14 , wherein the genetic data comprises quantitative allelic data from a plurality of polymorphic loci in the set of loci, and wherein each of the first hypotheses specifies an expected distribution of quantitative allelic data at the plurality of polymorphic loci, and wherein the first probability values are determined by calculating, for each of the first hypotheses, the fit between the expected genetic data and the obtained genetic data.
18. The method according to claim 17 , wherein the genetic data comprises quantitative non-allelic data from the plurality of polymorphic loci in the set of loci, and wherein each of the second hypotheses specifies an expected mean value of quantitative non-allelic data at the plurality of polymorphic loci, and wherein the second probability values are determined by calculating, for each of the second hypotheses, the fit between the expected genetic data and the obtained genetic data.
19. The method according to claim 18 , wherein the first probability values and the second probability values for hypotheses that are indicative of aneuploidy are separately combined for each of the first chromosome or chromosome segments of interest for the test sample, to determine whether aneuploidy is likely present in the first chromosome or chromosome segment of interest for the test sample.
20. The method according to claim 17 , wherein the method is performed by analyzing a second chromosome or chromosome segment of interest and a third chromosome or chromosome of interest in the parallel analysis, wherein the diploid samples are identified by a method comprising comparing genetic data from the first, second, and third chromosome or chromosome segments of interest for each sample of the set of samples.
21. The method according to claim 11 , wherein the sample is blood, or a fraction thereof, from the mother of the fetus and the method is performed by analyzing in the parallel analysis chromosomes 13, 18, and 21, or chromosome segments thereof.
22. The method according to claim 11 , wherein the first chromosome or chromosome segment of interest is selected from the group consisting of one or more of chromosome 22q11.2, chromosome 1p36, chromosome 15q11-q13, chromosome 4p16.3, chromosome Sp15.2, chromosome 17p13.3, chromosome 22q13.3, chromosome 2q37, chromosome 3q29, chromosome 9q34, chromosome 17q21.31, and the terminus of a chromosome.
23. The method according to claim 11 , wherein the test sample is blood, or a fraction thereof and wherein at least a portion of the genetic data is generated from circulating tumor DNA.
24. The method according claim 11 , further comprising
outputting the selected one or more samples as an indication of the likely presence of aneuploidy.