Universität zu Köln

Crispatzu, Giuliano, Kulkarni, Pranav, Toliat, Mohammad R., Nuernberg, Peter, Herling, Marco, Herling, Carmen D. and Frommolt, Peter ORCID: 0000-0002-1966-8014 (2017). Semi-automated cancer genome analysis using high-performance computing. Hum. Mutat., 38 (10). S. 1325 - 1336. HOBOKEN: WILEY. ISSN 1098-1004

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Abstract

Next-generation sequencing (NGS) has turned from a new and experimental technology into a standard procedure for cancer genome studies and clinical investigation. While a multitude of software packages for cancer genome data analysis have been made available, these need to be combined into efficient analytical workflows that cover multiple aspects relevant to a clinical environment and that deliver handy results within a reasonable time frame. Here, we introduce Quick-NGS Cancer as a new suite of bioinformatics pipelines that is focused on cancer genomics and significantly reduces the analytical hurdles that still limit a broader applicability of NGS technology, particularly to clinically driven research. QuickNGS Cancer allows a highly efficient analysis of a broad variety of NGS data types, specifically considering cancer-specific issues, such as biases introduced by tumor impurity and aneuploidy or the assessment of genomic variations regarding their biomedical relevance. It delivers highly reproducible analysis results ready for interpretation within only a few days after sequencing, as shown by a reanalysis of 140 tumor/normal pairs from The Cancer Genome Atlas (TCGA) in which QuickNGS Cancer detected a significant number of mutations calling pipeline. Finally, QuickNGS Cancer obtained several unexpected mutations in leukemias that could be confirmed by Sanger sequencing.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Crispatzu, Giuliano UNSPECIFIED UNSPECIFIED UNSPECIFIED Kulkarni, Pranav UNSPECIFIED UNSPECIFIED UNSPECIFIED Toliat, Mohammad R. UNSPECIFIED UNSPECIFIED UNSPECIFIED Nuernberg, Peter UNSPECIFIED UNSPECIFIED UNSPECIFIED Herling, Marco UNSPECIFIED UNSPECIFIED UNSPECIFIED Herling, Carmen D. UNSPECIFIED UNSPECIFIED UNSPECIFIED Frommolt, Peter UNSPECIFIED orcid.org/0000-0002-1966-8014 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-215494
DOI:	10.1002/humu.23275
Journal or Publication Title:	Hum. Mutat.
Volume:	38
Number:	10
Page Range:	S. 1325 - 1336
Date:	2017
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1098-1004
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language SOMATIC POINT MUTATIONS; DISCOVERY; FRAMEWORK; LANDSCAPE; PLATFORM; GALAXY Multiple languages Genetics & Heredity Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/21549