Methods for non-invasive prenatal ploidy calling

• US 10,061,890 B2
• Filed: 08/22/2016
• 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:
  US15/243,915
• Publication Number:
  US 20160357904A1
• Time in Patent Office: 736 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 risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:

performing a multiplex amplification to amplify at least 100 non-polymorphic loci per chromosome targeted and at least 100 SNP loci of free floating maternal and fetal DNA in a maternal blood, plasma, or serum sample using a plurality of probes to obtain amplified products;

performing microarray analysis to measure the genetic data at a plurality of amplified SNP loci on at least one chromosome that is expected to be disomic in both the mother of the fetus and the fetus;

performing microarray analysis to measure the genetic data at a plurality of amplified non-polymorphic loci;

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

determining the probability of each of the hypotheses of the number of copies of the at least one chromosome or chromosome segment of interest using the measured genetic data from the plurality of amplified SNP loci and the measured genetic data from the plurality of amplified non-polymorphic loci; and

determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest using the determined probabilities of each of the hypotheses.

2. The method of claim 1, further comprising determining a bias of a technique used to measure the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic, and using the bias to statistically correct the measured genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic.

3. The method of claim 1, wherein a maximum likelihood estimate is used to determine the risk of aneuploidy of the at least one chromosome or chromosome segment of interest.

4. The method of claim 3, wherein the maximum likelihood estimate is performed using a gradient descent method.

5. The method of claim 3, wherein the maximum likelihood estimate is performed using a Newton-Raphson optimization method.

6. The method of claim 1, wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy.

7. The method of claim 1, wherein the multiplex amplification is performed in a single amplification reaction before measuring the genetic data of the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome expected to be disomic and before measuring the genetic data of the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome or chromosome segment of interest.

8. The method of claim 1, wherein measuring the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic, and measuring the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome or chromosome segment of interest, are performed in the same reaction using the same measuring technique.

9. The method of claim 1, wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performance of the method.

10. The method of claim 1, further comprising aggregating the measured genetic data from the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome or chromosome segment of interest to determine an aggregated value, and using the aggregated value to determine the risk of aneuploidy of the at least one chromosome or chromosome segment of interest.

11. The method of claim 1, wherein determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest comprises comparing a mean value for the measured genetic data from the plurality of amplified SNP loci and amplified non-polymorphic loci on each of the at least one chromosome or chromosome segment of interest to a mean value for the measured genetic data from the plurality of amplified SNP loci and amplified non-polymorphic loci on one or more of the at least one chromosome that is expected to be disomic.

12. The method of claim 1, wherein at least one of the at least one chromosome or chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, chromosome X, chromosome Y, and combinations thereof.

13. The method of claim 1, further comprising determining a bias of a technique used to measure the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome or chromosome segment of interest, and using the bias to statistically correct the measured genetic data of the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome or chromosome segment of interest before the genetic data is used for determining the probability of each of the one or more hypotheses.

14. A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:

performing a multiplex amplification to amplify at least 100 non-polymorphic loci per chromosome targeted and at least 100 SNP loci from DNA from a maternal blood, serum, or plasma sample comprising free floating maternal and fetal DNA, in a single amplification reaction;

performing microarray analysis to measure in the same reaction the genetic data at a plurality of amplified SNP loci and amplified non-polymorphic loci on at least one chromosome that is expected to be disomic and at least one chromosome or chromosome segment of interest in both the mother of the fetus and the fetus;

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

determining the probability of each of the hypotheses of the number of copies of the at least one chromosome or chromosome segment of interest using the measured genetic data from the plurality of amplified SNP loci and amplified non-polymorphic loci; and

determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest using the determined probabilities of each of the hypotheses.

15. The method of claim 14, wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performing the amplifying.

16. The method of claim 14, wherein a maximum likelihood estimate is used to determine the risk of aneuploidy of the at least one chromosome or chromosome segment of interest.

17. The method of claim 16, further comprising determining a bias of a technique used to measure the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic, and using the bias to statistically correct the measured genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic and wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy.

18. The method of claim 14, further comprising determining a bias of a technique used to measure the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic, and using the bias to statistically correct the measured genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the at least one chromosome that is expected to be disomic, and wherein prior probabilities of aneuploidy given maternal age and/or gestational age of the mother are used in determining the risk of aneuploidy.

19. A method for determining the risk of aneuploidy of at least one chromosome or chromosome segment of interest in the genome of a fetus, the method comprising:

performing a multiplex amplification to amplify at least 100 non-polymorphic loci per chromosome targeted and at least 100 SNP loci from DNA from a maternal blood, serum, or plasma sample comprising free floating maternal and fetal DNA, in a single amplification reaction;

performing microarray analysis to measure in the same reaction the genetic data at a plurality of amplified SNP loci and amplified non-polymorphic loci on at least one chromosome that is expected to be disomic and at least one chromosome or chromosome segment of interest in both the mother of the fetus and the fetus, wherein the fetal DNA in the sample is not preferentially enriched over the maternal DNA before performing the amplifying or the measuring;

performing microarray analysis to measure the amount of amplified SNP loci and amplified non-polymorphic loci;

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

determining the probability of each of the hypotheses of the number of copies of the at least one chromosome or chromosome segment of interest using the measured genetic data from the plurality of amplified SNP loci and amplified non-polymorphic loci; and

determining the risk of aneuploidy of the at least one chromosome or chromosome segment of interest using the determined probabilities of each of the hypotheses.

20. The method of claim 19, further comprising determining a bias of a technique used to measure the genetic data at the plurality of amplified SNP loci and amplified non-polymorphic loci on the chromosome or chromosome segment of interest, and using the bias to statistically correct the measured genetic data at the chromosome or chromosome segment of interest.