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Bambam: parallel comparative analysis of high-throughput sequencing data

  • US 9,824,181 B2
  • Filed: 05/27/2016
  • Issued: 11/21/2017
  • Est. Priority Date: 05/25/2010
  • Status: Active Grant
First Claim
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1. A parallel genomic comparative analysis system comprising:

  • a memory; and

    an sequence analysis engine coupled with the memory and configured to;

    identify a genomic position within a reference genome;

    access a first file storing tumor sequence data including short reads associated with a tumor tissue;

    access a second file storing match normal sequence data short reads associated with a matched normal tissue;

    store in the memory a tumor dataset having tumor short read sequences from the first file where the tumor short read sequences overlap the genomic position;

    store in the memory a matched normal dataset having matched normal short read sequences from the second file and that overlap the genomic position;

    select a tumor genotype and a matched normal genotype that maximize a joint probability as a function of the tumor short read sequences and the match normal short read sequences at the genomic position, wherein the joint probability depends on one of a probability calculated as a multinomial operating as a function of the matched normal genotype or as a probability calculated as a multinomial operating as a function of the tumor genotype; and

    store a difference between the tumor genotype and the matched normal genotype in a device memory.

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