Methods for non-invasive prenatal ploidy calling

• US 10,061,889 B2
• Filed: 12/29/2015
• Issued: 08/28/2018
• 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): Riggs, II, Larry D
• Application Number:
  US14/983,128
• Publication Number:
  US 20160171152A1
• Time in Patent Office: 973 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. An in vitro method for determining a ratio of fetal to maternal DNA and a ploidy state of a set of chromosomes of interest in a mixed sample comprising DNA from a fetus and DNA from the mother of the fetus, the method comprising:

obtaining genotypic data from the mixed sample for a set of single nucleotide polymorphisms (SNPs) on a set of chromosomes comprising at least one chromosome that is expected to be disomic and at least one chromosome whose ploidy state is to be determined, using a genetic measurement platform, by amplifying and measuring at least 500 SNP alleles from the mixed sample which is derived from maternal blood or maternal plasma and comprises free floating fetal and maternal DNA, wherein the amount of DNA measured at each allele at each SNP of the set of SNPs will depend on the number and type of alleles present at that SNP for the mother and the fetus and the overall concentrations of DNA present in the sample from the mother and the fetus;

determining a mathematical characterization of the input/output characteristics of the genetic measurement platform using the measured genetic data from the chromosome expected to be disomic;

creating, on a computer, a set of expected measurements for a possible set of inherited alleles for the set of SNPs for the mixed sample for different ploidy states at different ratios of fetal to maternal DNA in the mixed sample using the mathematical characterization; and

determining on a computer, the ratio of fetal to maternal DNA and the ploidy state of the chromosome of interest in the mixed sample by comparing the genotypic measurements of the mixed sample to the set of expected measurements, wherein the ploidy determination is made with a computed confidence.

2. A method according to claim 1, wherein the fetus has an allele at a SNP of the set of SNPs the mother does not possess.

3. A method according to claim 1, wherein the fetal DNA is not purified away from maternal DNA to obtain the genotypic data.

4. A method according to claim 1, wherein the at least one chromosome that is expected to be disomic is the chromosome whose ploidy state is to be determined.

5. A method according to claim 1, wherein the at least one chromosome that is expected to be disomic is not a chromosome of the set of chromosomes.

6. A method according to claim 1, wherein the computed confidence is calculated using Bayes rule.

7. A method according to claim 1, wherein the comparing is performed by evaluating the likelihood of the measured data for each of the set of models and incorporating priors using Bayes rule.

8. A method according to claim 1, wherein genotypic data generated for the mother is phased, wherein the comparing is performed by evaluating the likelihood of the measured data for each of the set of models using the phased genotypic data of the mother.

9. A method according to claim 1, wherein DNA from the mixed sample is amplified before the genotypic data is generated and wherein the genotypic data is generated using an array platform.

10. A method according to claim 1, wherein DNA from the mixed sample is amplified before the genotypic data is generated and wherein the genotypic data is generated using a high throughput sequencing platform.

11. A method according to claim 1, wherein the comparing is performed by evaluating the likelihood of the measured data for each of the set of models and incorporating probabilities from prior population studies based on maternal age.

12. A method according to claim 1, wherein the set of chromosomes comprises chromosome 13, chromosome 18, chromosome 21, the X chromosome, the Y chromosome, and combinations thereof.

13. A method according to claim 1, wherein the set of chromosomes comprises chromosome 21.

14. A method according to claim 8, wherein the phased genotypic data generated for the mother is analyzed with knowledge regarding haplotype blocks of the phased data.

15. A method according to claim 9, wherein the array platforms is a SNP array.

16. A method according to claim 1, wherein a triploid state is determined for one chromosome of the set of chromosomes.

17. A method according to claim 1, wherein a diploid state is determined for all of the chromosomes of the set of chromosomes.