Dec 21, 2013

SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations

PloS One
Steven N HartJean-Pierre Kocher

Abstract

Structural variation (SV) represents a significant, yet poorly understood contribution to an individual's genetic makeup. Advanced next-generation sequencing technologies are widely used to discover such variations, but there is no single detection tool that is considered a community standard. In an attempt to fulfil this need, we developed an algorithm, SoftSearch, for discovering structural variant breakpoints in Illumina paired-end next-generation sequencing data. SoftSearch combines multiple strategies for detecting SV including split-read, discordant read-pair, and unmated pairs. Co-localized split-reads and discordant read pairs are used to refine the breakpoints. We developed and validated SoftSearch using real and synthetic datasets. SoftSearch's key features are 1) not requiring secondary (or exhaustive primary) alignment, 2) portability into established sequencing workflows, and 3) is applicable to any DNA-sequencing experiment (e.g. whole genome, exome, custom capture, etc.). SoftSearch identifies breakpoints from a small number of soft-clipped bases from split reads and a few discordant read-pairs which on their own would not be sufficient to make an SV call. We show that SoftSearch can identify more true SVs by com...Continue Reading

  • References20
  • Citations13

References

  • References20
  • Citations13

Citations

Mentioned in this Paper

BRCA2 Protein
Crest Syndrome
Genome
Gene Deletion Abnormality
Hereditary Breast and Ovarian Cancer Syndrome
Bikinia le-testui
Computer Programs and Programming
Genomics
Sequencing
Massively-Parallel Sequencing

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