Universität zu Köln

Abdallah, Ali T., Fischer, Matthias, Nuernberg, Peter, Nothnagel, Michael ORCID: 0000-0001-8305-7114 and Frommolt, Peter ORCID: 0000-0002-1966-8014 (2015). CoNCoS: Copy number estimation in cancer with controlled support. J. Bioinform. Comput. Biol., 13 (5). LONDON: IMPERIAL COLLEGE PRESS. ISSN 1757-6334

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Abstract

Somatic copy number (CN) alterations are major drivers of tumorigenesis and growth. Although next-generation sequencing (NGS) technologies enable a deep genomic analysis of cancers, the analysis of the data remains subject to biases and multiple sources of error, including varying local read coverage. The currently existing algorithms for NGS-based detection of CN abberations do not incorporate information on the local coverage quality. We have developed a new algorithm, copy number estimation with controlled support (CoNCoS) that increases the accuracy of CN estimation in paired tumor/normal exome sequencing data sets by assessing and optimizing the support for a site-specific CN estimate. We show by simulations and in a benchmarking study against single nucleotide polymorphism (SNP) microarray data that our approach outperforms the commonly used methods CNAnorm and VarScan2. Our algorithm is suitable to increase the accuracy of somatic CN analysis by a support-optimized estimation approach.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Abdallah, Ali T. UNSPECIFIED UNSPECIFIED UNSPECIFIED Fischer, Matthias UNSPECIFIED UNSPECIFIED UNSPECIFIED Nuernberg, Peter UNSPECIFIED UNSPECIFIED UNSPECIFIED Nothnagel, Michael UNSPECIFIED orcid.org/0000-0001-8305-7114 UNSPECIFIED Frommolt, Peter UNSPECIFIED orcid.org/0000-0002-1966-8014 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-390175
DOI:	10.1142/S0219720015500274
Journal or Publication Title:	J. Bioinform. Comput. Biol.
Volume:	13
Number:	5
Date:	2015
Publisher:	IMPERIAL COLLEGE PRESS
Place of Publication:	LONDON
ISSN:	1757-6334
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Faculty of Mathematics and Natural Sciences > Department of Biology > Institute for Genetics
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language Biochemical Research Methods; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/39017