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Methods and systems for detecting sequence variants

  • US 9,904,763 B2
  • Filed: 06/29/2016
  • Issued: 02/27/2018
  • Est. Priority Date: 08/21/2013
  • Status: Active Grant
First Claim
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1. A method of identifying variations in sequence data, the method comprising:

  • using at least one computer hardware processor to perform;

    receiving a plurality of nucleotide sequence reads from a genomic sample, wherein at least one sequence read comprises a mutation and at least a portion of a structural variation;

    representing, in at least one non-transitory computer-readable storage medium connected to the computer hardware processor, a reference sequence and a plurality of known variations from the reference sequence as a reference graph, wherein the reference graph is an assembled construct represented as a directed graph stored in the at least one non-transitory computer-readable storage medium, the reference graph comprising a first node representing a conserved portion of the reference sequence, the first node connected by directed edges to a second node and a third node, the second node representing a first alternative sequence and the third node representing a second alternative sequence, the second alternative sequence comprising a sequence matching the structural variation;

    mapping, using the computer hardware processor, the at least one sequence read to the reference graph, the mapping comprising determining a location on the reference graph for which a score for the at least one sequence read is maximized, wherein the determined location of the mapped at least one sequence read spans the first node and the third node; and

    identifying the mutation within the mapped at least one sequence read with respect to the conserved portion of the reference sequence represented by the first node.

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