Universität zu Köln

Lu, Xin, Thomas, Roman K. and Peifer, Martin ORCID: 0000-0002-5243-5503 (2014). CGARS: cancer genome analysis by rank sums. Bioinformatics, 30 (9). S. 1295 - 1297. OXFORD: OXFORD UNIV PRESS. ISSN 1460-2059

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Abstract

Motivation: Cancer genomes are characterized by the accumulation of point mutations and structural alterations such as copy-number alterations and genomic rearrangements. Among structural changes, systematic analyses of copy-number alterations have provided deeper insight into the architecture of cancer genomes and had led to new potential treatment opportunities. During the course of cancer genome evolution, selection mechanisms are leading to a non-random pattern of mutational events contributing to fitness benefits of the cancer cells. We therefore developed a new method to dissect random from non-random patterns in copy-number data and thereby to assess significantly enriched somatic copy-number aberrations across a set of tumor specimens or cell lines. In contrast to existing approaches, the method is invariant to any strictly monotonous transformation of the input data which results to an insensitivity of differences in tumor purity, array saturation effects and copy-number baseline levels. Results: We applied our approach to recently published datasets of small-cell lung cancer and squamous cell lung cancer and validated its performance by comparing the results to an orthogonal approach. In addition, we found a new deletion peak containing the HLA-A gene in squamous cell lung cancer.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Lu, Xin UNSPECIFIED UNSPECIFIED UNSPECIFIED Thomas, Roman K. UNSPECIFIED UNSPECIFIED UNSPECIFIED Peifer, Martin UNSPECIFIED orcid.org/0000-0002-5243-5503 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-438874
DOI:	10.1093/bioinformatics/btu011
Journal or Publication Title:	Bioinformatics
Volume:	30
Number:	9
Page Range:	S. 1295 - 1297
Date:	2014
Publisher:	OXFORD UNIV PRESS
Place of Publication:	OXFORD
ISSN:	1460-2059
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language CELL LUNG-CANCER; TARGETS Multiple languages Biochemical Research Methods; Biotechnology & Applied Microbiology; Computer Science, Interdisciplinary Applications; Mathematical & Computational Biology; Statistics & Probability Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/43887