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US 12,725,678 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.
Claims40
A method comprising:
- (a) contacting a sample with a stabilizing agent, wherein the sample comprises a nucleic acid molecule complexed to at least one nucleic acid binding protein;
- (b) cleaving the nucleic acid molecule into a plurality of segments comprising at least a first segment and a second segment;
- (c) attaching the first segment to the second segment, thereby forming a junction;
- (d) obtaining at least some sequence on each side of the junction to generate a first read pair;
- (e) aligning the first read pair to a reference genome;
- (f) identifying a variant in the first read pair relative to the reference genome;
- and
- (g) assigning the variant in the first read pair to a phase.
5 more elements
A method comprising:
- (a) contacting a sample with a stabilizing agent, wherein the sample comprises a nucleic acid molecule complexed to at least one nucleic acid binding protein;
- (b) cleaving the nucleic acid molecule into a plurality of segments comprising at least a first segment and a second segment;
- (c) attaching the first segment to the second segment, thereby forming a junction;
- (d) obtaining at least some sequence on each side of the junction to generate a first read pair;
- (e) aligning the first read pair to a reference genome;
- and
- (f) determining the presence of a structural variant or loss of heterozygosity in the sample based on the aligning.
4 more elements
A method comprising:
- (a) contacting a sample with a stabilizing agent, wherein the sample comprises a nucleic acid molecule complexed to at least one nucleic acid binding protein, and wherein the sample is from a subject;
- (b) cleaving the nucleic acid molecule into a plurality of segments comprising at least a first segment and a second segment;
- (c) attaching the first segment to the second segment, thereby forming a junction;
- (d) obtaining at least some sequence on each side of the junction to generate a first read pair;
- (e) aligning the first read pair to a reference genome;
- (f) determining a presence of a variant in the first read pair based on the aligning;
- and
- (g) based on the presence of the variant:
- (i) identifying a disease stage of the subject,
- (ii) identifying a prognosis of the subject;
- (iii) identifying a course of treatment for the subject;
- (iv) selecting a drug for the subject;
- or
- (v) identifying a drug efficacy in the subject.
11 more elements
Dependencies are inferred from the claim text.