2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2014
Abstrakt

Yue Jiang, Yadong Wang, Michael Brudno. PRISM: pair-read informed split-read mapping for base-pair level detection ofinsertion, deletion and structural variants. Bioinformatics, 28(20):2576-2583. 2012.

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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.