Analyzing genome sequencing information to determine likelihood of co-segregating alleles on haplotypes

• US 8,880,456 B2
• Filed: 08/22/2012
• Issued: 11/04/2014
• Est. Priority Date: 08/25/2011
• Status: Active Grant

• Current Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Original Assignee: Complete Genomics Incorporated (BGI Genomics Co., Ltd.)
• Inventors: Kermani, Bahram Ghaffarzadeh, Drmanac, Radoje
• Primary Examiner(s): Holmes, Michael B
• Application Number:
  US13/591,741
• Publication Number:
  US 20130054508A1
• Time in Patent Office: 804 Days
• US Class Current: 706/52
• 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 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 30/20 Sequence assembly

Abstract

Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength.

Claims

1. A method of determining at least part of a genome of an organism from one or more samples, the one or more samples including nucleic acid molecules of the organism, the method comprising:

receiving sequencing information of a plurality of the nucleic acid molecules in the one or more samples;

identifying a plurality of loci of a first chromosome;

computing, with a computer system, a first strength conveying a likelihood that a first allele of a first locus and a second allele of a second locus are on a first 2-allele haplotype of the organism, wherein computing the first strength includes;

determining a first positive contribution to the likelihood based on sequencing information consistent with the first allele and the second allele being on the first 2-allele haplotype;

determining a first negative contribution to the likelihood based on sequencing information inconsistent with the first allele and the second allele being on the first 2-allele haplotype; and

using the first positive and first negative contributions to compute the first strength; and

calculating two haplotypes involving the first locus and the second locus using the first strength.

2. The method of claim 1, wherein using the first positive and first negative contributions to compute the first strength includes inputting the first positive and first negative contributions into a fuzzy logic engine that outputs the first strength.

3. The method of claim 1, wherein calculating two haplotypes involving the first locus and the second locus using the first strength includes confirming and/or correcting a base call at at least one of the first and second locus.

4. The method of claim 3, wherein confirming and/or correcting a base call at at least one of the first and second locus includes determining a nocall to be at one of the first or second loci for one of the two haplotypes.

5. The method of claim 1, wherein determining the first positive contribution includes identifying a number of reads that are correlated and that have the first allele at the first locus and the second allele at the second locus.

6. The method of claim 5, further comprising:

scaling each of the number of reads by a factor that is dependent on a type of correlation for the respective read.

7. The method of claim 6, wherein the types of correlations include at least two of:

two alleles being on a same read, two alleles being on mated pair reads, and two alleles being from a same aliquot of a sample of the organism.

8. The method of claim 1, wherein the two haplotypes are of size N-allele haplotypes, wherein N is greater than two.

9. The method of claim 1, wherein the second locus is a heterozygous loci that has been used to phase haplotypes involving the second locus, and wherein calculating two haplotypes involving the first locus and the second locus using the first strength includes:

using the phased haplotypes and the first strength to calculate whether the first allele of the first locus is on a particular phased haplotype.

10. The method of claim 9, wherein the first locus is not a heterozygous locus.

11. The method of claim 10, wherein non-heterozygous loci include homozygous loci and loci that include a nocall for a base.

12. The method of claim 10, further comprising:

computing a plurality of additional strengths, each conveying a likelihood that the first allele of the first locus and a second allele of an additional locus are on a 2-allele haplotype of the organism, wherein each additional locus is a heterozygous loci that has been used to phase haplotypes.

13. The method of claim 1, wherein the plurality of loci include a plurality of candidate hets, a candidate het being a locus identified as having or potentially having two or more different alleles, and wherein the first locus is a first candidate het and the second locus is a second candidate het.

14. The method of claim 13, further comprising:

computing one or more additional strengths, each conveying a likelihood that the first allele of the first candidate het and a second allele of an additional candidate are on a 2-allele haplotype of the organism.

15. The method of claim 13, wherein the first strength also conveys a likelihood that a third allele of the first candidate het and a fourth allele of the second candidate het are on a second 2-allele haplotype of the organism.

16. The method of claim 15, wherein determining the first positive contribution to the likelihood is also based on sequencing information consistent with the third allele and the fourth allele being on the second 2-allele haplotype, and wherein determining the first negative contribution to the likelihood is also based on sequencing information inconsistent with the third allele and the fourth allele being on the second 2-allele haplotype.

17. The method of claim 13, wherein the first strength also conveys a likelihood that a third allele of the first candidate het and a fourth allele of the fourth candidate het are on a second 2-allele haplotype of the organism, wherein computing the first strength includes:

determining a second positive contribution to the likelihood based on sequencing information consistent with the third allele and the fourth allele being on the second 2-allele haplotype,

wherein determining the first negative contribution to the likelihood is also based on sequencing information inconsistent with the third allele and the fourth allele being on the second 2-allele haplotype; and

using the first positive contribution, the second positive contribution, and the first negative contribution to compute the first strength.

18. The method of claim 17, further comprising:

computing a second strength conveying a likelihood that the first allele of the first candidate het and the fourth allele of the second candidate het are on the first 2-allele haplotype and that the third allele of the first candidate het and the second allele of the second candidate het are on the second 2-allele haplotype, wherein computing the first strength includes;

determining a third positive contribution to the likelihood based on sequencing information consistent with the first allele and the fourth allele being on the first 2-allele haplotype;

determining a fourth positive contribution to the likelihood based on sequencing information consistent with the third allele and the second allele being on the second 2-allele haplotype;

determining a second negative contribution to the likelihood based on sequencing information inconsistent with the first allele and the fourth allele being on the first 2-allele haplotype and with the third allele and the second allele being on the second 2-allele haplotype; and

using the third positive contribution, the fourth positive contribution, and the second negative contribution to compute the second strength; and

calculating the two haplotypes involving the first candidate het and the second candidate het using the first strength and the second strength.

19. The method of claim 18, wherein calculating the two haplotypes involving the first candidate het and the second candidate het using the first strength and the second strength includes:

comparing the first strength and the second strength;

selecting an optimal strength based on the comparison; and

determining the first and second 2-allele haplotypes as having the alleles corresponding to the optimal strength.

20. The method of claim 19, wherein the strength with the higher value is selected as the optimal strength.

21. The method of claim 1, wherein the organism has two parents, the method further comprising:

calculating two haplotypes for a plurality of regions of the first chromosome based on the sequencing information;

obtaining genomic information about the parents;

for each region;

determining a heterozygous locus of the organism where the genomic information about the parents indicates a particular allele at the heterozygous locus is from a particular parent;

associating each haplotype of the region with a respective parent based on the particular allele at the heterozygous locus being from a particular parent;

combining the haplotypes associated with the first parent on a first copy of the chromosome; and

combining the haplotypes associated with the second parent on a second copy of the chromosome.

22. The method of claim 21, wherein obtaining genomic information about the parents includes obtaining genotyping information for over 100,000 loci for at least one parent.

23. The method of claim 21, wherein obtaining genomic information about the parents includes obtaining genotyping information for over 300,000 loci for at least one parent.

24. The method of claim 21, wherein obtaining genomic information about the parents includes obtaining genotyping information for over one million loci for at least one parent.

25. A computer program product comprising a tangible computer readable medium storing a plurality of instructions for controlling a processor to perform an operation for determining at least part of a genome of an organism from one or more samples, the one or more samples including nucleic acid molecules of the organism, the instructions comprising:

receiving sequencing information of a plurality of the nucleic acid molecules in the one or more samples;

identifying a plurality of loci of a first chromosome;

computing a first strength conveying a likelihood that a first allele of a first locus and a second allele of a second locus are on a first 2-allele haplotype of the organism, wherein computing the first strength includes;

determining a first positive contribution to the likelihood based on sequencing information consistent with the first allele and the second allele being on the first 2-allele haplotype;

determining a first negative contribution to the likelihood based on sequencing information inconsistent with the first allele and the second allele being on the first 2-allele haplotype; and

using the first positive and first negative contributions to compute the first strength; and

calculating two haplotypes involving the first locus and the second locus using the first strength.

26. A system for determining at least part of a genome of an organism from one or more samples, the one or more samples including nucleic acid molecules of the organism, the system comprising:

an input for receiving sequencing information of a plurality of the nucleic acid molecules in the one or more samples; and

one or more processors configured to;

identify a plurality of loci of a first chromosome;

compute a first strength conveying a likelihood that a first allele of a first locus and a second allele of a second locus are on a first 2-allele haplotype of the organism, wherein computing the first strength includes;

determining a first positive contribution to the likelihood based on sequencing information consistent with the first allele and the second allele being on the first 2-allele haplotype;

determining a first negative contribution to the likelihood based on sequencing information inconsistent with the first allele and the second allele being on the first 2-allele haplotype; and

using the first positive and first negative contributions to compute the first strength; and

calculate two haplotypes involving the first locus and the second locus using the first strength.