ClinSeK: a targeted variant characterization framework for clinical sequencing

Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients’ samples, an objective substantially different from the standard discovery process, in which every base in every sequenced read must be examined. Fur...

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Main Authors:	Zhou, Wanding, Zhao, Hao, Chong, Zechen, Mark, Routbort J, Eterovic, Agda K, Meric-Bernstam, Funda, Chen, Ken
Format:	Online
Language:	English
Published:	BioMed Central 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410453/

id	pubmed-4410453
recordtype	oai_dc
spelling	pubmed-44104532015-04-28 ClinSeK: a targeted variant characterization framework for clinical sequencing Zhou, Wanding Zhao, Hao Chong, Zechen Mark, Routbort J Eterovic, Agda K Meric-Bernstam, Funda Chen, Ken Method Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients’ samples, an objective substantially different from the standard discovery process, in which every base in every sequenced read must be examined. Further, the approach must be sufficiently robust as to be able to detect multiple and potentially rare variants from heterogeneous samples. To meet this critical objective, we developed a novel variant characterization framework, ClinSeK, which performs targeted analysis of relevant reads from high-throughput sequencing data. ClinSeK is designed for efficient targeted short read alignment and is capable of characterizing a wide spectrum of genetic variants from single nucleotide variation to large-scale genomic rearrangement breakpoints. Applying ClinSeK to over a thousand cancer patients demonstrated substantively better performance, in terms of accuracy, runtime and disk storage, for clinical applications than existing variant discovery tools. ClinSeK is freely available for academic use at http://bioinformatics.mdanderson.org/main/clinsek. BioMed Central 2015-03-31 /pmc/articles/PMC4410453/ /pubmed/25918555 http://dx.doi.org/10.1186/s13073-015-0155-1 Text en © Zhou et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Zhou, Wanding Zhao, Hao Chong, Zechen Mark, Routbort J Eterovic, Agda K Meric-Bernstam, Funda Chen, Ken
spellingShingle	Zhou, Wanding Zhao, Hao Chong, Zechen Mark, Routbort J Eterovic, Agda K Meric-Bernstam, Funda Chen, Ken ClinSeK: a targeted variant characterization framework for clinical sequencing
author_facet	Zhou, Wanding Zhao, Hao Chong, Zechen Mark, Routbort J Eterovic, Agda K Meric-Bernstam, Funda Chen, Ken
author_sort	Zhou, Wanding
title	ClinSeK: a targeted variant characterization framework for clinical sequencing
title_short	ClinSeK: a targeted variant characterization framework for clinical sequencing
title_full	ClinSeK: a targeted variant characterization framework for clinical sequencing
title_fullStr	ClinSeK: a targeted variant characterization framework for clinical sequencing
title_full_unstemmed	ClinSeK: a targeted variant characterization framework for clinical sequencing
title_sort	clinsek: a targeted variant characterization framework for clinical sequencing
description	Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients’ samples, an objective substantially different from the standard discovery process, in which every base in every sequenced read must be examined. Further, the approach must be sufficiently robust as to be able to detect multiple and potentially rare variants from heterogeneous samples. To meet this critical objective, we developed a novel variant characterization framework, ClinSeK, which performs targeted analysis of relevant reads from high-throughput sequencing data. ClinSeK is designed for efficient targeted short read alignment and is capable of characterizing a wide spectrum of genetic variants from single nucleotide variation to large-scale genomic rearrangement breakpoints. Applying ClinSeK to over a thousand cancer patients demonstrated substantively better performance, in terms of accuracy, runtime and disk storage, for clinical applications than existing variant discovery tools. ClinSeK is freely available for academic use at http://bioinformatics.mdanderson.org/main/clinsek.
publisher	BioMed Central
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4410453/
_version_	1613215889155424256

ClinSeK: a targeted variant characterization framework for clinical sequencing

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