COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

ABSTRACT: An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reac

SUBMITTER: Yamagata K 

PROVIDER: S-EPMC4856976 | biostudies-literature | 2016 May

REPOSITORIES: biostudies-literature