Methods for non-invasive prenatal ploidy calling

• US 9,163,282 B2
• Filed: 03/08/2013
• Issued: 10/20/2015
• Est. Priority Date: 05/18/2010
• Status: Active Grant

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Rabinowitz, Matthew, Gemelos, George, Banjevic, Milena, Ryan, Allison, Demko, Zachary, Hill, Matthew, Zimmermann, Bernhard, Baner, Johan
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US13/791,397
• Publication Number:
  US 20130178373A1
• Time in Patent Office: 956 Days
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2527/113 Time
• CPC Class Codes: C12Q 2527/143 Concentration of primer or probe
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2537/149 Sequential reactions
• CPC Class Codes: C12Q 2537/159 Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions
• CPC Class Codes: C12Q 2537/161 A competitive reaction step
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/10 Ploidy or copy number detection
• CPC Class Codes: G16B 20/20 : Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/40 : Population genetics; Linkage disequilibrium
• CPC Class Codes: G16B 40/00 : ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

The present disclosure provides methods for determining the ploidy status of a chromosome in a gestating fetus from genotypic data measured from a mixed sample of DNA comprising DNA from both the mother of the fetus and from the fetus, and optionally from genotypic data from the mother and father. The ploidy state is determined by using a joint distribution model to create a plurality of expected allele distributions for different possible fetal ploidy states given the parental genotypic data, and comparing the expected allelic distributions to the pattern of measured allelic distributions measured in the mixed sample, and choosing the ploidy state whose expected allelic distribution pattern most closely matches the observed allelic distribution pattern. The mixed sample of DNA may be preferentially enriched at a plurality of polymorphic loci in a way that minimizes the allelic bias, for example using massively multiplexed targeted PCR.

Claims

1. A method for determining a ploidy status of a chromosome or chromosome segment in a gestating fetus, the method comprising:

measuring the DNA in a sample that comprises maternal DNA from the mother of the fetus and fetal DNA from the fetus at a plurality of at least 10 polymorphic loci on the chromosome or chromosome segment;

determining, on a computer, allele counts at the plurality of polymorphic loci from the DNA measurements made on the sample;

generating, on a computer, a plurality of ploidy hypotheses each specifying a different possible ploidy state of the chromosome or chromosome segment;

generating, on a computer, a joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts at the plurality of polymorphic loci on the chromosome or chromosome segment for each ploidy hypothesis;

determining, on a computer, a relative probability of each of the ploidy hypotheses by comparing (i) the joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts at the plurality of polymorphic loci to (ii) the allele counts measured on the sample at the plurality of polymorphic loci; and

outputting the hypothesis with the greatest probability of being true as an indication of the ploidy state of the fetus.

2. The method of claim 1, wherein the DNA in the sample originates from maternal plasma.

3. The method of claim 1, wherein the method further comprises preferentially enriching the DNA in the sample at a plurality of polymorphic loci prior to the measuring step.

4. The method of claim 3, wherein the preferentially enriching the DNA in the sample at the plurality of polymorphic loci comprises:

obtaining a plurality of pre-circularized probes in which each probe targets one of the polymorphic loci, wherein the 3′ and

5′

end of each probe is designed to hybridize to a region of DNA that is separated from the polymorphic site of the locus by a small number of bases, and wherein the small number is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 to 25, 26 to 30, 31 to 60, or a combination thereof;

hybridizing the pre-circularized probes to DNA from the sample;

filling the gap between the hybridized probe ends using DNA polymerase;

circularizing the pre-circularized probe; and

amplifying the circularized probe.

5. The method of claim 3, wherein the preferentially enriching the DNA at the plurality of polymorphic loci comprises:

obtaining a plurality of ligation-mediated PCR probes in which each PCR probe targets one of the polymorphic loci, wherein the corresponding upstream and downstream PCR probes are designed to hybridize to a region of DNA on one strand of DNA that is separated from the polymorphic site of the locus by a small number of bases, and wherein the small number is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 19, 20, 21 to 25, 26 to 30, 31 to 60, or a combination thereof;

hybridizing the litigation-mediated PCR probes to the DNA from the sample;

filing the gap between the ligation-mediated PCR probe ends using DNA polymerase;

ligating the ligation-mediated PCR probes; and

amplifying the ligated ligation-mediated PCR probes.

6. The method of claim 3, wherein the preferentially enriching the DNA at the plurality of polymorphic loci comprises:

obtaining a plurality of hybrid capture probes that target the polymorphic loci;

hybridizing the hybrid capture probes to the DNA in the sample; and

physically removing some or all of the unhybridized DNA from the sample of DNA.

7. The method of claim 3, wherein the preferentially enriching the DNA at a plurality of polymorphic loci comprises:

obtaining a plurality of inner forward primers in which each primer targets one of the polymorphic loci, wherein the 3′

end of each of the inner forward primers is designed to hybridize to a region of DNA upstream from the polymorphic site of the locus and separated from the polymorphic site by a small number of bases, and wherein the small number is selected from the group consisting of 1, 2, 3, 4, 5, 6 to 10, 11 to 15, 16 to 20, 21 to 25, 26 to 30, and 31 to 60 base pairs;

optionally obtaining a plurality of inner reverse primers in which each primer targets one of the polymorphic loci, wherein the 3′

end of each of the inner reverse primers is designed to hybridize to a region of DNA upstream from the polymorphic site of the locus and separated from the polymorphic site by a small number of bases, and wherein the small number is selected from the group consisting of 1, 2, 3, 4, 5, 6 to 10, 11 to 15, 16 to 20, 21 to 25, 26 to 30, and 31 to 60 base pairs;

hybridizing the inner primers to the DNA; and

amplifying the DNA using the polymerase chain reaction to form amplicons.

8. The method of claim 7, further comprising:

obtaining a plurality of outer forward primers in which each primer targets one of the polymorphic loci, wherein each of the outer forward primers is designed to hybridize to the region of DNA upstream from the corresponding inner forward primer;

optionally obtaining a plurality of outer reverse primers in which each primer targets one of the polymorphic loci, wherein each of the outer reverse primers is designed to hybridize to the region of DNA immediately downstream from the corresponding inner reverse primer;

hybridizing the first primers to the DNA; and

amplifying the DNA using the polymerase chain reaction.

9. The method of claim 7, further comprising:

obtaining a plurality of outer reverse primers in which each primer targets one of the polymorphic loci, wherein each of the outer reverse primers is designed to hybridize to the region of DNA immediately downstream from the corresponding inner reverse primer;

optionally obtaining a plurality of outer forward primers in which each primer targets one of the polymorphic loci, wherein each of the outer forward primers is designed to hybridize to the region of DNA upstream from the corresponding inner forward primer;

hybridizing the first primers to the DNA; and

amplifying the DNA using the polymerase chain reaction.

10. The method of claim 7, further comprising:

appending universal adapters to the DNA in the sample; and

amplifying the DNA in the sample using the polymerase chain reaction.

11. The method of claim 7, wherein the amplifying the DNA is done in one or a plurality of individual reaction volumes, wherein each individual reaction volume contains more than 500 different forward and reverse primer pairs.

12. The method of claim 7, further comprises dividing the first sample into a plurality of portions, and wherein the DNA in each portion is preferentially enriched at a subset of the plurality of polymorphic loci.

13. The method of claim 7, wherein the inner primers are selected by identifying primer pairs likely to form undesired primer duplexes and removing from the plurality of primers at least one of the pair of primers identified as being likely to form undesired primer duplexes.

14. The method of claim 1, further comprising obtaining genotypic data at the plurality of polymorphic loci from one or both parents of the fetus.

15. The method of claim 14, wherein the building the joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts at the plurality of polymorphic loci on the chromosome or chromosome segment is done using the obtained genetic data from the one or both parents.

16. The method of claim 14, wherein the sample is isolated from maternal plasma, and wherein the obtaining genotypic data from the mother is done by estimating the maternal genotypic data from the DNA measurements made on the sample.

17. The method of claim 3, wherein the preferential enrichment results in an average degree of allelic bias between the sample after preferential enrichment and the sample prior to preferential enrichment of no more than a factor of 1.2.

18. The method of claim 1, wherein the plurality of polymorphic loci are single nucleotide polymorphisms.

19. The method of claim 1, wherein the step of measuring the DNA in the sample is done by sequencing.

20. The method of claim 1, wherein the measurements of the DNA in the sample at the plurality of polymorphic loci are used to determine whether or not the fetus has inherited one or a plurality of disease linked haplotypes.

21. The method of claim 1, wherein the step of building the joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts is done by using data about the probability of chromosomes crossing over at different locations in the chromosome or chromosome segment to model dependence between polymorphic alleles on the chromosome or chromosome segment.

22. The method of claim 1, wherein both the step of building the joint distribution model for the expected allele counts and for the expected linkage between the expected allele counts and the step of determining the relative probability of each hypothesis are done using a method that does not require the use of a reference chromosome.

23. The method of claim 1, wherein the step of determining the relative probability of each hypothesis makes use of an estimated fraction of fetal DNA in the sample.

24. The method of claim 1, wherein determining the ploidy state of the fetus further comprises:

combining (i) the relative probabilities of each of the ploidy hypotheses determined using the joint distribution model and the allele counts measured on the sample with (ii) relative probabilities of each of the ploidy hypotheses that are calculated using one or more statistical techniques selected from the group consisting of a read count analysis, comparing heterozygosity rates, a statistic that is only available when parental genetic information is used, the probability of normalized genotype signals for certain parent contexts, a statistic that is calculated using an estimated fetal fraction of the sample, and combinations thereof.

25. The method of claim 1, wherein a confidence estimate is calculated for the outputted ploidy state.

26. The method of claim 25, wherein the confidence exceeds 99% for chromosomes 13, chromosome 18, and chromosome 21.

27. The method of claim 1, wherein the allele counts measured on the sample comprise quantitative measurements of the number of independent observations of each allele at each polymorphic locus, and wherein the expected allele counts comprise expected quantitative measurements of the number of independent observations of each allele at each polymorphic locus.

28. The method of claim 1, wherein determining the relative probability of each of the ploidy hypotheses does not involve calculating the ratio of the alleles counts measured on the sample at a polymorphic locus.

29. The method of claim 1, further comprising obtaining phased genotypic data at the plurality of polymorphic loci from one or both parents of the fetus.

30. The method of claim 1, further comprising:

obtaining phased genotypic data at the plurality of polymorphic loci from one or both parents of the fetus; and

using the phased genotypic data from the one or both parents to determine the expected linkage between the expected allele counts at the plurality of polymorphic loci in the joint distribution model.