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

• US 9,430,611 B2
• Filed: 11/27/2013
• Issued: 08/30/2016
• Est. Priority Date: 11/26/2005
• 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:
  US14/092,457
• Publication Number:
  US 20140087385A1
• Time in Patent Office: 1,007 Days
• US Class Current: 1/1
• 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. An ex vivo method for determining a number of copies of a chromosome or chromosome segment in the genome of a fetus, the method comprising:

hybridizing polymerase chain reaction (PCR) probes to a plurality of at least 100 polymorphic loci on the chromosome or chromosome segment in a sample comprising DNA from the fetus and DNA from the mother of the fetus;

generating amplified products by PCR;

measuring an amount of the amplified products to obtain genetic data at the plurality of polymorphic loci on the chromosome or chromosome segment;

generating a set of one or more hypotheses specifying the number of copies of the chromosome or chromosome segment present in the genome of the fetus;

calculating a likelihood for each of the hypotheses based on a beta binomial distribution of expected and observed genetic data at the plurality of polymorphic loci; and

outputting the hypothesis with the highest probability based on Bayesian estimation, as an indication of the number of copies of the chromosome or chromosome segment in the genome of the fetus.

2. The method of claim 1, wherein a confidence is computed for the determination of the number of copies of the chromosome or chromosome segment in the fetus'"'"'s genome.

3. The method of claim 2, wherein the confidence is at least 99%.

4. The method of claim 1, wherein the probability of each of the hypotheses is determined using data about the probability of chromosomes crossing over at different locations in the chromosome or chromosome segment.

5. The method of claim 4, wherein the number of possible crossovers is 0, 1, or 2.

6. The method of claim 1, wherein the sample includes a substance selected from the group consisting of the fetus'"'"'s bulk diploid tissue, one or more diploid cells from the fetus, one or more haploid cells from the fetus, cell-free DNA from the fetus, cell-free DNA from the fetus found in maternal blood, cells from the fetus found in maternal blood, genetic material known to have originated from the fetus, and combinations thereof.

7. The method of claim 6, wherein the PCR probes are hybridized to cell-free DNA from the fetus found in maternal blood.

8. The method of claim 6, wherein the PCR probes are hybridized to genetic material from one or more fetal cells found in maternal blood.

9. The method of claim 6, wherein the PCR probes are hybridized to DNA from a single cell.

10. The method of claim 9, wherein the cell is a fetal cell.

11. The method of claim 1, wherein the chromosome is selected from the group consisting of chromosome 13, chromosome 18, chromosome 21, the X chromosome, the Y chromosome, and combinations thereof.

12. The method of claim 1, wherein determining the number of copies of the chromosome or chromosome segment is used determine whether the fetus has three copies of chromosome 21, three copies of chromosome 18, three copies of chromosome 13, two copies of chromosome X and one copy of chromosome Y, or one copy of chromosome X and no copies of chromosome Y.

14. The method of claim 1, further comprising normalizing the obtained genetic data for the chromosome or chromosome segment and the obtained genetic data for the one or more reference chromosomes or chromosome segments for differences in amplification and/or measurement efficiency between different polymorphic loci, chromosome segments, or chromosomes.

15. The method of claim 1, wherein the PCR is either accompanied by or preceded by a ligation reaction or ligation of PCR probes at one or more polymorphic loci.

13. An ex vivo method for determining a number of copies of a chromosome or chromosome segment, the method comprising:

hybridizing PCR probes to a plurality of at least 100 polymorphic loci on the chromosome or chromosome segment in the fetus in a sample comprising maternal DNA and fetal DNA;

generating amplified products by PCR;

measuring an amount of the amplified products to obtain genetic data at the plurality of polymorphic loci on the chromosome or chromosome segment;

generating a set of one or more hypotheses specifying the number of copies of the chromosome or chromosome segment present in the genome of the fetus;

calculating, on a computer, the data fit between the obtained genetic data comprising the amount of the amplified products at each locus and expected genetic data for the hypothesis comprising the expected amount of one or more of the alleles, based on a beta binomial distribution of expected and observed genetic data at the plurality of polymorphic loci; and

outputting the hypothesis with the highest probability based on Bayesian estimation, as an indication of the number of copies of the chromosome or chromosome segment in the genome of the fetus.