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공공누리This item is licensed Korea Open Government License

dc.contributor.author
김준호
dc.contributor.author
김상우
dc.contributor.author
맹주헌
dc.contributor.author
손현주
dc.contributor.author
이정호
dc.contributor.author
이준학
dc.contributor.author
임재석
dc.date.accessioned
2019-08-28T07:41:55Z
dc.date.available
2019-08-28T07:41:55Z
dc.date.issued
2016-06-22
dc.identifier.issn
1367-4803
dc.identifier.uri
https://repository.kisti.re.kr/handle/10580/14527
dc.identifier.uri
http://www.ndsl.kr/ndsl/search/detail/article/articleSearchResultDetail.do?cn=NART77234517
dc.description.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.
dc.language
eng
dc.relation.ispartofseries
 Bioinformatics
dc.title
Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination
dc.citation.endPage
3080
dc.citation.number
20
dc.citation.startPage
3072
dc.citation.volume
32
dc.subject.keyword
vector contamination
dc.subject.keyword
low frequency mutation
dc.subject.keyword
genomics
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