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IDENTIFYING REARRANGEMENTS IN A SEQUENCED GENOME

  • US 20120197533A1
  • Filed: 01/28/2011
  • Published: 08/02/2012
  • Est. Priority Date: 10/11/2010
  • Status: Abandoned Application
First Claim
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1. A method of determining whether a junction exists between a sample genome and a reference genome, the sample genome being of an organism providing a biological sample, the method comprising:

  • receiving results of paired-end sequencing of a plurality of fragments from the biological sample, the results including mate pairs of fragments and mappings of the mate pairs to the reference genome, wherein a mate pair includes a first arm read for a first end of a fragment and a corresponding arm read of an opposite end of the fragment;

    identifying a junction region in the sample genome based on the mappings of the mate pairs to the reference genome, the junction region including;

    a first edge portion including a first edge of the junction region;

    a second edge portion including a second edge of the junction region, the first edge opposite the second edge; and

    a potential junction between the first edge and the second edge;

    identifying a first set of first arm reads, each at least partially mapping to the first edge portion or having a non-negligible probability to at least partially map to the first edge portion based on a mapped location of the respective corresponding arm read; and

    comparing the sequences of the first arm reads of the first set to each other to determine whether a junction exists in the junction region.

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