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 reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yamagata K,Yamanishi A,Kokubu C,Takeda J,Sese Jdoi
10.1093/nar/gkw026subject
Has Abstractpub_date
2016-05-05 00:00:00pages
e78issue
8eissn
0305-1048issn
1362-4962pii
gkw026journal_volume
44pub_type
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