RISK CALCULATION FOR EVALUATION OF FETAL ANEUPLOIDY

• US 20160002729A1
• Filed: 09/14/2015
• Published: 01/07/2016
• Est. Priority Date: 01/25/2011
• Status: Active Grant

• Current Assignee: Roche Molecular Systems Inc (Roche Holding AG)
• Original Assignee: Ariosa Diagnostics Incorporated (Roche Holding AG)
• Inventors: Oliphant, Arnold, Sparks, Andrew, Wang, Eric, Struble, Craig
• Granted Patent: US 10,718,019 B2
• Time in Patent Office: 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 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• 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 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The present invention provides processes for determining accurate risk probabilities for fetal aneuploidies. Specifically, the invention provides non-invasive evaluation of genomic variations through chromosome-selective sequencing and non-host fraction data analysis of maternal samples.

Claims

1. A method to calculate a risk that a first fetal chromosome in a maternal sample comprising maternal and fetal nucleic acids is aneuploid, comprising:

designing sequence-specific oligonucleotide probes directed to a plurality of non-polymorphic loci on each of at least a first and second chromosome;

designing sequence-specific oligonucleotide probes directed to a plurality of polymorphic loci on at least a third chromosome;

amplifying the plurality of non-polymorphic and polymorphic loci using the sequence-specific oligonucleotide probes;

determining a number of each non-polymorphic locus on the at least first and second chromosomes;

determining a number of alleles at each polymorphic locus on the at least third chromosome;

estimating a chromosome frequency for the at least first and second chromosomes based on the number of non-polymorphic loci on the at least the first and second chromosomes;

calculating a fetal nucleic acid proportion in the maternal sample based on the number of alleles at the polymorphic loci;

determining whether the fetal nucleic acid proportion in the maternal sample is adequate to reliably perform analysis;

calculating a value of likelihood that the first fetal chromosome is disomic using the fetal nucleic acid proportion to adjust the estimated chromosome frequency of the first and second chromosomes;

calculating a value of likelihood that the first fetal chromosome is aneuploid using the fetal nucleic acid proportion to adjust the estimated chromosome frequency of the first and second chromosomes; and

calculating the risk of a fetal aneuploidy of the first fetal chromosome by comparing the values of likelihood to a first mathematic model assuming a disomic first fetal chromosome and a second mathematic model assuming an aneuploid first fetal chromosome.

2. The method of claim 1, wherein the calculated risk is an odds ratio comparing the first mathematic model assuming a disomic first fetal chromosome and a second mathematic model assuming a trisomic first fetal chromosome.

3. The method of claim 1, wherein the fetal nucleic acid proportion is determined using the frequency of alleles on two or more chromosomes in the maternal sample.

4. The method of claim 1, wherein the fetal aneuploidy is a result of one or no copies of a chromosome or part of a chromosome.

5. The method of claim 1, wherein the fetal aneuploidy is a result of three or more copies of a chromosome or part of a chromosome.

6. The method of claim 1, wherein the maternal sample is maternal plasma or serum.

7. The method of claim 1, further comprising a step of adjusting the calculated risk using extrinsic information on prior risk.

8. The method of claim 1, further comprising a step of adjusting the calculated risk using information on prior risk associated with maternal age or gestational age.

9. The method of claim 1, further comprising the step of identifying a set of non-polymorphic loci best able to discriminate trisomy samples from normal samples.

10. A method to calculate a risk that a first fetal chromosome in a maternal sample comprising maternal and fetal nucleic acids is aneuploid, comprising:

designing sequence-specific oligonucleotide probes directed to a plurality of non-polymorphic loci on each of at least a first and second chromosome;

designing sequence-specific oligonucleotide probes directed to a plurality of polymorphic loci on at least a third chromosome;

amplifying the plurality of non-polymorphic and polymorphic loci using the sequence-specific oligonucleotide probes;

determining a number of each non-polymorphic locus on the at least first and second chromosomes;

determining a number of alleles at each polymorphic locus on the at least third chromosome;

estimating a chromosome frequency for the at least first and second chromosomes based on the number of the non-polymorphic loci on the at least the first and second chromosomes;

calculating a fetal nucleic acid proportion in the maternal sample based on the number of alleles at the polymorphic loci;

determining whether the fetal nucleic acid proportion in the maternal sample is adequate to reliably perform analysis;

calculating a value of likelihood that the first fetal chromosome is disomic;

calculating a value of likelihood that the first fetal chromosome is aneuploid using the fetal nucleic acid proportion in the maternal sample to adjust the estimated chromosome frequency of the first and second chromosomes;

calculating the risk of a fetal aneuploidy of the first fetal chromosome by comparing the values of likelihood to a first mathematic model assuming a disomic first fetal chromosome and a second mathematic model assuming an aneuploid first fetal chromosome; and

adjusting the calculated risk using extrinsic information on prior risk.

11. The method of claim 10, wherein the calculated risk is an odds ratio comparing the first mathematic model assuming a disomic first fetal chromosome and a second mathematic model assuming a trisomic first fetal chromosome.

12. The method of claim 10, wherein the fetal nucleic acid proportion is determined using the frequency of alleles on two or more chromosomes in the maternal sample.

13. The method of claim 10, wherein the fetal aneuploidy is a result of one or no copies of a chromosome or part of a chromosome.

14. The method of claim 10, wherein the fetal aneuploidy is a result of three or more copies of a chromosome or part of a chromosome.

15. The method of claim 10, wherein the maternal sample is maternal plasma or serum.

16. The method of claim 10, further comprising a step of adjusting the calculated risk using extrinsic information on prior risk.

17. The method of claim 10, further comprising a step of adjusting the calculated risk using information on prior risk associated with maternal age or gestational age.

18. The method of claim 10, further comprising the step of identifying a set of non-polymorphic loci best able to discriminate trisomy samples from normal samples.

19. A method to calculate a risk that a first fetal chromosome in a maternal sample comprising maternal and fetal nucleic acids is triploid, comprising:

designing sequence-specific oligonucleotide probes directed to a plurality of non-polymorphic loci on each of at least a first and second chromosome;

identifying a set of non-polymorphic loci best able to discriminate trisomy samples from normal samples;

designing sequence-specific oligonucleotide probes directed to a plurality of polymorphic loci on at least a third chromosome;

amplifying a plurality of non-polymorphic loci using the identified non-polymorphic loci best able to discriminate trisomy samples from normal samples and amplifying a plurality of polymorphic loci using the sequence-specific oligonucleotide probes;

determining a number of each non-polymorphic locus on the at least first and second chromosomes;

determining a number of alleles at each polymorphic locus on the at least third chromosome;

estimating a chromosome frequency for the at least first and second chromosomes based on the number of non-polymorphic loci on the at least the first and second chromosomes;

calculating a fetal nucleic acid proportion in the maternal sample based on the number of alleles at the polymorphic loci;

determining whether the fetal nucleic acid proportion in the maternal sample is adequate to reliably perform analysis;

calculating a value of likelihood that the first fetal chromosome is disomic using the fetal nucleic acid proportion to adjust the estimated chromosome frequency of the first and second chromosomes;

calculating a value of likelihood that the first fetal chromosome is triploid using the fetal nucleic acid proportion to adjust the estimated chromosome frequency of the first and second chromosomes; and

calculating the risk of a fetal trisomy of the first fetal chromosome by comparing the values of likelihood to a first mathematic model assuming a disomic first fetal chromosome and a second mathematic model assuming an triploid first fetal chromosome.

20. The method of claim 19, wherein the fetal nucleic acid proportion is determined using the frequency of alleles on two or more chromosomes in the maternal sample.