System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals

• US 10,227,652 B2
• Filed: 06/20/2016
• Issued: 03/12/2019
• Est. Priority Date: 07/29/2005
• Status: Active Grant

• Current Assignee: Natera Incorporated (Natera)
• Original Assignee: Natera Incorporated (Natera)
• Inventors: Rabinowitz, Matthew, Banjevic, Milena, Demko, Zachary, Johnson, David
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US15/187,555
• Publication Number:
  US 20160298188A1
• Time in Patent Office: 995 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• 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 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 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 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother'"'"'s blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Claims

1. A method for detecting the presence or absence of a chromosomal abnormality in a fetus, the method comprising:

(a) measuring an amount of genetic material at multiple loci on a chromosome or chromosome segment of interest in a sample comprising cell-free DNA derived from the fetus and from the mother of the fetus, wherein the measuring comprises amplifying at least 70 loci in a single reaction and using microarray or sequencing to detect amplified reaction products, and wherein the multiple loci are loci having alleles with 100% penetrance in the population;

(b) determining, on a computer, a probability of the presence and a probability of the absence of a chromosomal abnormality in the fetus by comparing the amounts from step (a) to either (i) a threshold value or (ii) an expected amount for a particular copy number hypothesis;

(c) identifying the presence or absence of a chromosomal abnormality in the fetus by selecting the probability most likely to be true; and

(d) outputting the selected probability as an indication of whether the fetus has a chromosomal abnormality, thereby detecting the presence or absence of a chromosomal abnormality in a fetus.

2. The method of claim 1, wherein the determining is performed by comparing the amount from step (a) to an expected amount, wherein the expected amount is a mean value of genetic material at multiple loci for a reference chromosome or chromosome segment that is present in two copies.

3. The method of claim 1, wherein a microarray is used to measure the amount of genetic material at the multiple loci.

4. The method of claim 1, wherein the amount of genetic material for at least 70 loci is measured by performing a multiplex amplification in a single reaction, and wherein a microarray is used to detect the amplified reaction products.

5. The method of claim 1, wherein the sample comprises cell-free DNA isolated from blood from the mother of the fetus.

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

7. The method of claim 1, wherein the chromosomal abnormality is selected from the group consisting of monosomy, uniparental disomy, trisomy, other aneuploidies, unbalanced translocations, insertions, deletions, and combinations thereof.

8. The method of claim 1, wherein the amount of genetic material for at least 70 loci is measured by performing a multiplex amplification in a single reaction, wherein the method further comprises a PCR amplification using universal amplification sequences, wherein the multiplex amplification reaction and/or the PCR reaction comprise a ligation PCR reaction, and wherein a microarray is used to detect the amplified reaction products.

9. The method of claim 1, wherein the multiple loci on the chromosome or chromosome segment of interest comprise between 32 and 2002 loci.

10. The method of claim 8, wherein the multiple loci on the chromosome or chromosome segment of interest comprise between 70 and 2002 loci.

11. A method for detecting aneuploidy in a fetus, the method comprising:

(a) measuring an amount of genetic material at multiple loci on a chromosome or chromosome segment of interest in a sample comprising cell-free DNA derived from the fetus and from the mother of the fetus, wherein the measuring comprises amplifying at least 70 loci in a single reaction and using microarray or sequencing to detect amplified reaction products, and wherein the amount of genetic material at a particular locus is determined irrespective of an identity of alleles at that locus;

(b) computing, for a particular copy number hypothesis, a difference between a mean of the measured amount of genetic material at the multiple loci and an expected amount, wherein the expected amount is a mean value of genetic material at multiple loci for a reference chromosome or chromosome segment that is present in two copies;

(c) determining, on a computer, a probability of a particular copy number hypothesis by comparing the difference for each particular copy number hypothesis; and

(d) selecting the particular copy number hypothesis with the probability most likely to be true, thereby detecting aneuploidy if the selected hypothesis is an aneuploidy hypothesis.

12. The method of claim 11, wherein the method further comprises using data from a method that makes use of allele calls at a plurality of single nucleotide polymorphic loci to determine the probability of a particular copy number hypothesis.

13. The method of claim 11, wherein a microarray is used to measure the amount of genetic material at the multiple loci and wherein the sample comprises cell-free DNA isolated from blood from the mother of the fetus.

14. The method of claim 11, wherein the chromosome of interest or the chromosome comprising the chromosome segment of interest is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, X chromosome, Y chromosome, and combinations thereof.

15. The method of claim 11, wherein the multiple loci on the chromosome or chromosome segment of interest comprise between 9 and 2002.

16. The method of claim 15, wherein the multiple loci are loci having alleles with 100% penetrance in the population.

17. The method of claim 16, wherein the multiple loci on the chromosome or chromosome segment of interest comprise between 70 and 2002 loci.

18. The method of claim 11, wherein the amount of genetic material for at least 70 loci is measured by performing a multiplex amplification in a single reaction, wherein the method further comprises a PCR amplification using universal amplification sequences, wherein the multiplex amplification reaction and/or the PCR reaction comprise a ligation PCR reaction, and wherein a microarray is used to detect the amplified reaction products.

19. The method of claim 18, wherein the multiplex amplification reaction and the ligation PCR reaction are performed in an Illumina Golden Gate assay.

20. The method of claim 13, wherein the selecting comprises calculating an odds ratio using the probabilities for each copy number hypothesis.