Identifying tumorigenic non-coding mutations through altered cis-regulation

Summary: Identification of non-coding mutations driving tumorigenesis requires alternative approaches to coding mutations. Enriched associations between mutated regulatory elements and altered cis-regulation in tumors are a promising approach to stratify candidate non-coding driver mutations. Here w...

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Autores principales:	Zhongshan Cheng, Michael Vermeulen, Micheal Rollins-Green, Tomas Babak, Brian DeVeale
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Bioinformatics Sequence analysis Cancer Genomics RNAseq Science (General) Q1-390
Acceso en línea:	https://doaj.org/article/6395de5f28e04b289848e10d87506912
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spelling	oai:doaj.org-article:6395de5f28e04b289848e10d875069122021-11-10T04:41:26ZIdentifying tumorigenic non-coding mutations through altered cis-regulation2666-166710.1016/j.xpro.2021.100934https://doaj.org/article/6395de5f28e04b289848e10d875069122021-12-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2666166721006407https://doaj.org/toc/2666-1667Summary: Identification of non-coding mutations driving tumorigenesis requires alternative approaches to coding mutations. Enriched associations between mutated regulatory elements and altered cis-regulation in tumors are a promising approach to stratify candidate non-coding driver mutations. Here we provide a bioinformatics pipeline to mine data from the Cancer Genomic Commons (GDC) for such associations. The pipeline integrates RNA and whole-genome sequencing with genotyping data to reveal putative non-coding driver mutations by cancer type.For complete information on the generation and use of this protocol, please refer to Cheng et al. (2021).Zhongshan ChengMichael VermeulenMicheal Rollins-GreenTomas BabakBrian DeVealeElsevierarticleBioinformaticsSequence analysisCancerGenomicsRNAseqScience (General)Q1-390ENSTAR Protocols, Vol 2, Iss 4, Pp 100934- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Bioinformatics Sequence analysis Cancer Genomics RNAseq Science (General) Q1-390
spellingShingle	Bioinformatics Sequence analysis Cancer Genomics RNAseq Science (General) Q1-390 Zhongshan Cheng Michael Vermeulen Micheal Rollins-Green Tomas Babak Brian DeVeale Identifying tumorigenic non-coding mutations through altered cis-regulation
description	Summary: Identification of non-coding mutations driving tumorigenesis requires alternative approaches to coding mutations. Enriched associations between mutated regulatory elements and altered cis-regulation in tumors are a promising approach to stratify candidate non-coding driver mutations. Here we provide a bioinformatics pipeline to mine data from the Cancer Genomic Commons (GDC) for such associations. The pipeline integrates RNA and whole-genome sequencing with genotyping data to reveal putative non-coding driver mutations by cancer type.For complete information on the generation and use of this protocol, please refer to Cheng et al. (2021).
format	article
author	Zhongshan Cheng Michael Vermeulen Micheal Rollins-Green Tomas Babak Brian DeVeale
author_facet	Zhongshan Cheng Michael Vermeulen Micheal Rollins-Green Tomas Babak Brian DeVeale
author_sort	Zhongshan Cheng
title	Identifying tumorigenic non-coding mutations through altered cis-regulation
title_short	Identifying tumorigenic non-coding mutations through altered cis-regulation
title_full	Identifying tumorigenic non-coding mutations through altered cis-regulation
title_fullStr	Identifying tumorigenic non-coding mutations through altered cis-regulation
title_full_unstemmed	Identifying tumorigenic non-coding mutations through altered cis-regulation
title_sort	identifying tumorigenic non-coding mutations through altered cis-regulation
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/6395de5f28e04b289848e10d87506912
work_keys_str_mv	AT zhongshancheng identifyingtumorigenicnoncodingmutationsthroughalteredcisregulation AT michaelvermeulen identifyingtumorigenicnoncodingmutationsthroughalteredcisregulation AT michealrollinsgreen identifyingtumorigenicnoncodingmutationsthroughalteredcisregulation AT tomasbabak identifyingtumorigenicnoncodingmutationsthroughalteredcisregulation AT briandeveale identifyingtumorigenicnoncodingmutationsthroughalteredcisregulation
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Identifying tumorigenic non-coding mutations through altered cis-regulation

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