CopywriteR: DNA copy number detection from off-target sequence data.

Kuilman, Thomas; Velds, Arno; Kemper, Kristel; Ranzani, Marco; Bombardelli, Lorenzo; Hoogstraat, Marlous; Nevedomskaya, Ekaterina; Xu, Guotai; de Ruiter, Julian; Lolkema, Martijn P; Ylstra, Bauke; Jonkers, Jos; Rottenberg, Sven; Wessels, Lodewyk F; Adams, David J; Peeper, Daniel S; Krijgsman, Oscar (2015). CopywriteR: DNA copy number detection from off-target sequence data. Genome biology, 16(49), p. 49. BioMed Central Ltd. 10.1186/s13059-015-0617-1

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Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP) > Institute of Animal Pathology
05 Veterinary Medicine > Department of Infectious Diseases and Pathobiology (DIP)

UniBE Contributor:

Rottenberg, Sven

Subjects:

600 Technology > 630 Agriculture

ISSN:

1465-6906

Publisher:

BioMed Central Ltd.

Language:

English

Submitter:

Barbara Gautschi-Steffen

Date Deposited:

04 Feb 2016 09:04

Last Modified:

26 Jun 2016 02:10

Publisher DOI:

10.1186/s13059-015-0617-1

PubMed ID:

25887352

BORIS DOI:

10.7892/boris.75536

URI:

https://boris.unibe.ch/id/eprint/75536

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