Methods for non-invasive prenatal ploidy calling

• US 10,522,242 B2
• Filed: 11/03/2016
• Issued: 12/31/2019
• Est. Priority Date: 09/30/2009
• Status: Active Grant

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Rabinowitz, Matthew, Ryan, Allison, Gemelos, George, Banjevic, Milena, Demko, Zachary
• Primary Examiner(s): Sims, Jason M
• Application Number:
  US15/343,003
• Publication Number:
  US 20170076038A1
• Time in Patent Office: 1,153 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2537/16 Assays for determining copy number or wherein the copy number is of special importance
• CPC Class Codes: C12Q 2537/165 Mathematical modelling, e.g. logarithm, ratio
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G06N 7/01 Probabilistic graphical models, e.g. probabilistic networks
• 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 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Disclosed herein are methods for determining the copy number of a chromosome in a fetus in the context of non-invasive prenatal diagnosis. In an embodiment, the measured genetic data from a sample of genetic material that contains both fetal DNA and maternal DNA is analyzed, along with the genetic data from the biological parents of the fetus, and the copy number of the chromosome of interest is determined. In an embodiment, the maternal serum is measured using a single-nucleotide polymorphism (SNP) microarray, along with parental genomic data, and the determination of the chromosome copy number is used to make clinical decisions pertaining to the fetus.

Claims

1. A method for determining the number of copies of a chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:

measuring genetic data at a plurality of polymorphic loci on at least one chromosome that is expected to be disomic in both the mother and the fetus and a plurality of polymorphic loci on at least chromosome or chromosome segment of interest, which comprises amplifying at least 500 polymorphic loci from a mixed sample comprising DNA derived from the fetus and DNA derived from the mother, wherein the mixed sample is prepared from a maternal blood or plasma sample that comprises free floating fetal and maternal DNA;

determining a ratio of DNA derived from the fetus to DNA derived from the mother from the measured genetic data at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus;

creating hypotheses specifying the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus;

determining, on a computer, the probability of each of the hypotheses using the measured genetic data for the chromosome or chromosome segment of interest and the ratio of DNA derived from the fetus to DNA derived from the mother; and

selecting the hypothesis with the greatest probability, thereby determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus.

2. The method of claim 1, further comprising obtaining measured genetic data at the plurality of polymorphic loci on the chromosome or chromosome segment of interest from genetic material from the mother and/or father of the fetus, wherein the probability of each of the hypotheses is determined using the measured genetic data of the mother and/or father for the chromosome or chromosome segment of interest, the measured genetic data of the mixed sample for the chromosome or chromosome segment of interest, and the ratio of DNA derived from the fetus to DNA derived from the mother.

3. The method of claim 1, wherein the method comprises measuring genetic data at (i) a plurality of single nucleotide polymorphisms (SNPs) from the chromosome or chromosome segment of interest and (ii) a plurality of SNPs from at least one chromosome or chromosome segment that is expected to be disomic in the fetus.

4. The method of claim 3, wherein the method comprises:

measuring the amount of each allele at each of the SNPs from genetic material from the mother to obtain genotypic data for the mother;

using the genotypic data of the mother to determine parental contexts for each of the SNPs;

grouping the genotypic measurements of the mixed sample into the parental contexts;

using the grouped genotypic measurements from the at least one chromosome that is expected to be disomic to determine a platform response;

using the grouped genotypic measurements from the at least one chromosome that is expected to be disomic to determine a ratio of DNA derived from the fetus to DNA derived from the mother;

using the determined platform response and the determined ratio to calculate expected SNP measurements for the set of SNPs in at least one parental context under each hypothesis; and

calculating the probability that each of the hypotheses is true from the platform response, the determined ratio, the grouped genotypic measurements of the mixed sample, and the expected SNP measurements for the at least one parental context.

5. The method of claim 1, comprising:

estimating expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is euploid;

estimating expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is aneuploid using the ratio of DNA derived from the fetus to DNA derived from the mother in the mixed sample;

calculating (i) a data fit between the measured genetic data and the expected data for the euploid case and (ii) a data fit between the measured genetic data and the expected data for the aneuploid case; and

selecting the case for which the data fit is best, thereby determining whether the chromosome or chromosome segment of interest in the fetus is euploid or aneuploid.

6. The method of claim 5, further comprising obtaining measured genetic data at the plurality of polymorphic loci from genetic material from the mother and/or father of the fetus for the chromosome or chromosome segment of interest, wherein the expected data for the aneuploidy case is determined using the measured genetic data of the mother and/or father, the measured genetic data for the chromosome or chromosome segment of interest of the mixed sample, and the ratio of DNA derived from the fetus to DNA derived from the mother.

7. The method of claim 1, further comprising aggregating the measured data on the chromosome or chromosome segment of interest before determining the number of copies of the chromosome or chromosome segment of interest.

8. The method of claim 7, wherein determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus comprises comparing an aggregated value for the chromosome or chromosome segment of interest to the aggregated value for one or more chromosomes expected to be disomic.

9. The method of claim 1, wherein determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus comprises comparing a mean value for the measured data for the chromosome or chromosome segment of interest to a mean value for the measured data for one or more other chromosomes.

10. The method of claim 1, comprising calculating a maximum likelihood estimate of the ratio of DNA derived from the fetus to DNA derived from the mother, thereby determining the ratio of DNA derived from the fetus to DNA derived from the mother.

11. The method of claim 1, wherein determining the ratio of DNA derived from the fetus to DNA derived from the mother comprises:

obtaining measured genetic data from the mixed sample by measuring the quantity of each allele at a plurality of polymorphic loci on at least one chromosome that is expected to be disomic in both the mother and the fetus;

estimating expected allele measurements in the mixed sample at the plurality of polymorphic loci on the at least one chromosome for possible ratios of DNA derived from the fetus to DNA derived from the mother;

calculating a relative probability of each of the possible ratios using the model and the measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus from the mixed sample; and

selecting the possible ratio with the greatest probability, thereby determining the ratio of DNA derived from the fetus to DNA derived from the mother.

12. The method of claim 11, further comprising

obtaining measured genetic data from the mother by measuring the quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus in genetic material from the mother;

optionally obtaining measured genetic data from the father of the fetus by measuring the quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus in genetic material from the father; and

determining the ratio of DNA derived from the fetus to DNA derived from the mother given the measured genetic data of the mixed sample for the at least one chromosome that is expected to be disomic in both the mother and the fetus, the measured genetic data of mother for the at least one chromosome that is expected to be disomic in both the mother and the fetus.

13. The method of claim 11, wherein the polymorphic loci comprise SNPs.

14. The method of claim 1, wherein the ratio of DNA derived from the fetus to DNA derived from the mother is determined by measuring the amount of an allele at one or more polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus in which the fetus has the allele and the mother does not have the allele.

15. The method of claim 1, wherein the ratio of DNA derived from the fetus to DNA derived from the mother in the mixed sample is determined by:

identifying one or more polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at the polymorphic locus; and

using the amount of the second allele in the mixed sample for each of the identified polymorphic loci to determine the ratio of DNA derived from the fetus to DNA derived from the mother.

16. The method of claim 1, wherein the ratio of DNA derived from the fetus to DNA derived from the mother is determined by:

identifying one or more polymorphic loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at the polymorphic locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at the polymorphic locus; and

using the amount of the second allele in the mixed sample for each of the identified polymorphic loci to determine the ratio of DNA derived from the fetus to DNA derived from the mother.

17. The method of claim 1, wherein the method further comprises measuring the difference in methylation between one or more maternal and fetal alleles.

18. The method of claim 1, further comprising:

determining the likelihood that the fetal genome contains three copies of a chromosome or chromosome segment of interest using the ratio of DNA derived from the fetus to DNA derived from the mother.

19. The method of claim 1, wherein a confidence is computed for the determination of the number of copies of the chromosome or chromosome segment of interest in the genome of the target individual.

20. The method of claim 1, wherein the ratio of DNA derived from the fetus to DNA derived from the mother is determined for individual chromosomes.

21. The method of claim 1, wherein the step of measuring genetic data is performed by measuring genetic material using a technique selected from the group consisting of padlock probes, circularizing probes, genotyping microarrays, SNP genotyping assays, chip based microarrays, bead based microarrays, other SNP microarrays, other genotyping methods, Sanger DNA sequencing, pyrosequencing, high throughput sequencing, reversible dye terminator sequencing, sequencing by ligation, sequencing by hybridization, other methods of DNA sequencing, other high throughput genotyping platforms, fluorescent in situ hybridization (FISH), comparative genomic hybridization (CGH), array CGH, and combinations thereof.

22. The method of claim 1 wherein the chromosome of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, the X chromosome, the Y chromosome, and combinations thereof.

24. The method of claim 1, wherein determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus is used to determine whether the fetus has three copies of chromosome 21, three copies of chromosome 18, three copies of chromosome 13, two copies of chromosome X and one copy of chromosome Y, or one copy of chromosome X and no copies of chromosome Y.

23. A method for determining the number of copies of a chromosome or chromosome segment of interest in the genome of a gestating fetus, the method comprising:

obtaining a plurality primers to a locus (i) that is known to be polymorphic in the human population and (i) that is likely to be informative based on the rate of SNP heterozygosity in the human population for the locus;

wherein an informative polymorphic loci is a SNP locus on at least one chromosome that is expected to be disomic in both the mother and the fetus where the mother is homozygous for a first allele at that locus, and the father is (i) heterozygous for the first allele and a second allele or (ii) homozygous for a second allele at that locus;

amplifying at least 500 SNPs from DNA in a mixed sample comprising DNA derived from the fetus and DNA derived from the mother by using the plurality of primers to obtain amplified products comprising the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic, wherein the mixed sample is prepared from a maternal blood or plasma sample that comprises free floating fetal and maternal DNA;

measuring an amount of the amplified products to obtain a measured quantity of each allele at the plurality of polymorphic loci on the at least one chromosome that is expected to be disomic;

determining a ratio of DNA derived from the fetus to DNA derived from the mother using (i) the measured quantity of the second allele or (ii) the measured quantity of the first and second alleles for each of the polymorphic loci on the at least one chromosome that is expected to be disomic;

measuring genetic data at a plurality of loci on a chromosome or chromosome segment of interest in the mixed sample;

creating one or more hypotheses specifying the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus;

determining, on a computer, the probability of each of the hypotheses using the measured genetic data for the chromosome or chromosome segment of interest and the ratio of DNA derived from the fetus to DNA derived from the mother; and

selecting the hypothesis with the greatest probability, thereby determining the number of copies of the chromosome or chromosome segment of interest in the genome of the fetus.

25. The method of claim 23, wherein the plurality of primers comprises 1000 primers.

26. The method of claim 25, wherein the measuring steps are performed using high throughput sequencing.