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Bambam: parallel comparative analysis of high-throughput sequencing data

  • US 10,249,384 B2
  • Filed: 05/27/2016
  • Issued: 04/02/2019
  • Est. Priority Date: 05/25/2010
  • Status: Active Grant
First Claim
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1. A computer implemented method of displaying genomic variants between a tumor tissue and a matched normal tissue comprising:

  • receiving a reference genome or portion thereof, a first genetic sequence string object including first sub-strings from the tumor tissue and aligned to the reference genome or portion thereof, and a second genetic sequence string object including second sub-strings from the matched normal tissue and aligned to the reference genome or portion thereof;

    generating at least one differential sequence object, each generated through incremental synchronized reading of the first sub-strings from the first genetic sequence string object and the second sub-strings from the second genetic sequence string object using a known position of at least one of a plurality of sub-strings corresponding to the known position to produce local alignment between the first sub-strings and the second sub-strings, the known position determined based on the reference genome or portion thereof, the incremental synchronized reading keeping sequence data read from the first genetic sequence string object and the second genetic sequence string object at common genomic locations across the reference genome or portion thereof during the generating;

    instantiating, via a browser computer, the at least one differential sequence object stored in a computer memory, the at least one differential sequence object representing a difference between a localized alignment of multiple sequence reads of a tumor genome sequence of the tumor tissue and a matched normal genome sequence of the matched normal tissues;

    identifying, via the browser computer, at least one genomic variant between the tumor tissue and the matched normal tissue based on the at least one differential sequence object at a genomic position corresponding to the localized alignment;

    generating, via the browser computer, a browser image including a representation of the at least one genomic variant with respect to a reference genome sequence;

    displaying, via the browser computer, on a display, the browser image; and

    allowing, via the browser computer, displaying of genomic regions associated with the at least one genomic variant relative to the reference genome sequence.

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