Methods for non-invasive prenatal ploidy calling

Patent metadata

Field	Value
Publication number	US-9228234-B2
Application number	US-201314080656-A
Country	US
Kind code	B2
Filing date	Nov 14, 2013
Priority date	Sep 30, 2009
Publication date	Jan 5, 2016
Grant date	Jan 5, 2016

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.

First claim

What is claimed is:

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 loci on at least one chromosome that is expected to be disomic in both the mother and the fetus in a mixed sample of DNA comprising fetal DNA and maternal DNA;
determining a ratio of fetal to maternal DNA in the mixed sample from the measured genetic data at the plurality of loci on the at least one chromosome that is expected to be disomic in both the mother and the fetus;
measuring genetic data at a plurality of loci on a chromosome or chromosome segment of interest in the mixed sample of DNA;
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 fetal to maternal DNA; 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 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 fetal to maternal DNA.

3. The method of claim 1 , wherein the method comprises measuring genetic data at (i) a plurality of 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 and optionally from genetic material from the father of the fetus to obtain genotypic data for the mother and optionally for the father;
using the genotypic data of the mother and optionally the genotypic data of the father 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 fetal to maternal DNA in the mixed sample;
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, on a computer, 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, on a computer, expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is euploid;
estimating, on a computer, expected data for the mixed sample for the case where the chromosome or chromosome segment of interest is aneuploid using the ratio of fetal to maternal DNA in the mixed sample;
calculating, on a computer, (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 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 fetal to maternal DNA.

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 fetal to maternal DNA in the mixed sample, thereby determining the ratio of fetal to maternal DNA in the mixed sample.

11. The method of claim 1 , wherein determining the ratio of fetal to maternal DNA in the mixed sample 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, on a computer, expected allele measurements in the mixed sample at the plurality of polymorphic loci on the at least one chromosome for possible ratios of fetal to maternal DNA;
calculating, on a computer, 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 fetal to maternal DNA in the mixed sample.

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, on a computer, the ratio of fetal to maternal DNA in the mixed sample 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, and optionally the measured genetic data of the father for the at least one chromosome that is expected to be dis

Assignees

• Natera Inc

Inventors

• Rabinowitz Matthew
• Ryan Allison
• Gemelos George
• Banjevic Milena
• Demko Zachary

Classifications

• G06N7/01

  Probabilistic graphical models, e.g. probabilistic networks · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q2600/16

  Primer sets for multiplex assays · CPC title

• G16B20/00

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title