download0 view241
twitter facebook

공공누리This item is licensed Korea Open Government License

Title
Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination
Author(s)
김준호김상우맹주헌손현주이정호이준학임재석
Publication Year
2016-06-22
Abstract
Motivation: Advances in sequencing technologies have remarkably lowered the detection limit of somatic variants to a low frequency. However, calling mutations at this range is still confounded by many factors including environmental contamination. Vector contamination is a continuously occurring issue and is especially problematic since vector inserts are hardly distinguishable from the sample sequences. Such inserts, which may harbor polymorphisms and engineered functional mutations, can result in calling false variants at corresponding sites. Numerous vector-screening methods have been developed, but none could handle contamination from inserts because they are focusing on vector backbone sequences alone.Results: We developed a novel method—Vecuum—that identifies vector-originated reads and re- sultant false variants. Since vector inserts are generally constructed from intron-less cDNAs, Vecuum identifies vector-originated reads by inspecting the clipping patterns at exon junctions. False variant calls are further detected based on the biased distribution of mutant alleles to vector- originated reads. Tests on simulated and spike-in experimental data validated that Vecuum could detect 93% of vector contaminants and could remove up to 87% of variant-like false calls with 100% precision. Application to public sequence datasets demonstrated the utility of Vecuum in de- tecting false variants resulting from various types of external contamination.
Keyword
vector contamination; low frequency mutation; genomics
Journal Title
 Bioinformatics
Citation Volume
32
ISSN
1367-4803
Files in This Item:
There are no files associated with this item.
Appears in Collections:
7. KISTI 연구성과 > 학술지 발표논문
URI
https://repository.kisti.re.kr/handle/10580/14527
http://www.ndsl.kr/ndsl/search/detail/article/articleSearchResultDetail.do?cn=NART77234517
Export
RIS (EndNote)
XLS (Excel)
XML

Browse