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US 11,081,209 B2Granted
Methods for genome assembly and haplotype phasing
AssigneeThe Regents of the University of California
InventorsRichard E. Green, Jr., Liana F. Lareau
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Abstract
The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure further provides methods for haplotype phasing and meta-genomics assemblies.
Claims28
A method, comprising:
- contacting a sample to a stabilizing agent, said sample comprising a nucleic acid molecule complexed to at least one nucleic acid binding protein;
- cleaving the nucleic acid into a plurality of segments comprising at least a first segment and a second segment;
- attaching the first segment and the second segment at a junction;
- obtaining at least some sequence on each side of the junction to generate a first read pair;
- mapping the first read pair to a set of contigs;
- and
- determining, from the set of contigs, a presence of a structural variant or loss of heterozygosity in the sample.
4 more elements
A method, comprising:
- contacting a sample to a stabilizing agent, said sample comprising a nucleic acid molecule complexed to at least one nucleic acid binding protein;
- cleaving the nucleic acid into a plurality of segments comprising at least a first segment and a second segment;
- attaching the first segment and the second segment at a junction;
- obtaining at least some sequence on each side of the junction to generate a first read pair;
- mapping the first read pair to a set of contigs;
- and
- assigning a variant in the set of contigs to a phase.
4 more elements
A method, comprising:
- contacting a sample to a stabilizing agent, said sample comprising a nucleic acid molecule complexed to at least one nucleic acid binding protein;
- cleaving the nucleic acid into a plurality of segments comprising at least a first segment and a second segment;
- attaching the first segment and the second segment at a junction;
- obtaining at least some sequence on each side of the junction to generate a first read pair;
- mapping the first read pair to a set of contigs;
- determining, from the set of contigs, a presence of a variant in the set of contigs;
- and
- (i) identifying a disease stage, a prognosis, or a course of treatment for the sample;
- (ii) selecting a drug based on the presence of the variant;
- or (iii) identifying a drug efficacy for the sample.
7 more elements
Dependencies are inferred from the claim text.