Yue Jiang1, Yadong Wang, Michael Brudno. 1. Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China. yue.jiang.hit@gmail.com
Abstract
MOTIVATION: The development of high-throughput sequencing technologies has enabled novel methods for detecting structural variants (SVs). Current methods are typically based on depth of coverage or pair-end mapping clusters. However, most of these only report an approximate location for each SV, rather than exact breakpoints. RESULTS: We have developed pair-read informed split mapping (PRISM), a method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types, including arbitrary-sized inversions, deletions and tandem duplications. Comparisons to previous datasets and simulation experiments illustrate PRISM's high sensitivity, while PCR validations of PRISM results, including previously uncharacterized variants, indicate an overall precision of ~90%. AVAILABILITY: PRISM is freely available at http://compbio.cs.toronto.edu/prism.
MOTIVATION: The development of high-throughput sequencing technologies has enabled novel methods for detecting structural variants (SVs). Current methods are typically based on depth of coverage or pair-end mapping clusters. However, most of these only report an approximate location for each SV, rather than exact breakpoints. RESULTS: We have developed pair-read informed split mapping (PRISM), a method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types, including arbitrary-sized inversions, deletions and tandem duplications. Comparisons to previous datasets and simulation experiments illustrate PRISM's high sensitivity, while PCR validations of PRISM results, including previously uncharacterized variants, indicate an overall precision of ~90%. AVAILABILITY: PRISM is freely available at http://compbio.cs.toronto.edu/prism.
Authors: Alexander Y Maslov; Wilber Quispe-Tintaya; Tatyana Gorbacheva; Ryan R White; Jan Vijg Journal: Mutat Res Date: 2015-04-20 Impact factor: 2.433
Authors: Anna Ritz; Ali Bashir; Suzanne Sindi; David Hsu; Iman Hajirasouliha; Benjamin J Raphael Journal: Bioinformatics Date: 2014-10-28 Impact factor: 6.937