SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression

Abstract Whole genome sequencing (WGS) has enabled the discovery of genomic structural variants (SVs), including those targeting intergenic and intronic non-coding regions that eluded previous exome focused strategies. However, the field currently lacks an automated tool that analyzes SV candidates...

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Main Authors:	Abdallah M. Eteleeb, David A. Quigley, Shuang G. Zhao, Duy Pham, Rendong Yang, Scott M. Dehm, Jingqin Luo, Felix Y. Feng, Ha X. Dang, Christopher A. Maher
Format:	article
Language:	EN
Published:	Nature Portfolio 2020
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/028d671856044b26a0873e62b77eaea6
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spelling	oai:doaj.org-article:028d671856044b26a0873e62b77eaea62021-12-02T18:51:06ZSV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression10.1038/s41598-020-71168-72045-2322https://doaj.org/article/028d671856044b26a0873e62b77eaea62020-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-71168-7https://doaj.org/toc/2045-2322Abstract Whole genome sequencing (WGS) has enabled the discovery of genomic structural variants (SVs), including those targeting intergenic and intronic non-coding regions that eluded previous exome focused strategies. However, the field currently lacks an automated tool that analyzes SV candidates to identify recurrent SVs and their targeted sites (hotspot regions), visualizes these genomic events within the context of various functional elements, and evaluates their potential effect on gene expression. To address this, we developed SV-HotSpot, an automated tool that integrates SV candidates, copy number alterations, gene expression, and genome annotations (e.g. gene and regulatory elements) to discover, annotate, and visualize recurrent SVs and their targeted hotspot regions that may affect gene expression. We applied SV-HotSpot to WGS and matched transcriptome data from metastatic castration resistant prostate cancer patients and rediscovered recurrent SVs targeting coding and non-coding functional elements known to promote prostate cancer progression and metastasis. SV-HotSpot provides a valuable resource to integrate SVs, gene expression, and genome annotations for discovering biologically relevant SVs altering coding and non-coding genome. SV-HotSpot is available at https://github.com/ChrisMaherLab/SV-HotSpot .Abdallah M. EteleebDavid A. QuigleyShuang G. ZhaoDuy PhamRendong YangScott M. DehmJingqin LuoFelix Y. FengHa X. DangChristopher A. MaherNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-10 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Abdallah M. Eteleeb David A. Quigley Shuang G. Zhao Duy Pham Rendong Yang Scott M. Dehm Jingqin Luo Felix Y. Feng Ha X. Dang Christopher A. Maher SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
description	Abstract Whole genome sequencing (WGS) has enabled the discovery of genomic structural variants (SVs), including those targeting intergenic and intronic non-coding regions that eluded previous exome focused strategies. However, the field currently lacks an automated tool that analyzes SV candidates to identify recurrent SVs and their targeted sites (hotspot regions), visualizes these genomic events within the context of various functional elements, and evaluates their potential effect on gene expression. To address this, we developed SV-HotSpot, an automated tool that integrates SV candidates, copy number alterations, gene expression, and genome annotations (e.g. gene and regulatory elements) to discover, annotate, and visualize recurrent SVs and their targeted hotspot regions that may affect gene expression. We applied SV-HotSpot to WGS and matched transcriptome data from metastatic castration resistant prostate cancer patients and rediscovered recurrent SVs targeting coding and non-coding functional elements known to promote prostate cancer progression and metastasis. SV-HotSpot provides a valuable resource to integrate SVs, gene expression, and genome annotations for discovering biologically relevant SVs altering coding and non-coding genome. SV-HotSpot is available at https://github.com/ChrisMaherLab/SV-HotSpot .
format	article
author	Abdallah M. Eteleeb David A. Quigley Shuang G. Zhao Duy Pham Rendong Yang Scott M. Dehm Jingqin Luo Felix Y. Feng Ha X. Dang Christopher A. Maher
author_facet	Abdallah M. Eteleeb David A. Quigley Shuang G. Zhao Duy Pham Rendong Yang Scott M. Dehm Jingqin Luo Felix Y. Feng Ha X. Dang Christopher A. Maher
author_sort	Abdallah M. Eteleeb
title	SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
title_short	SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
title_full	SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
title_fullStr	SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
title_full_unstemmed	SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression
title_sort	sv-hotspot: detection and visualization of hotspots targeted by structural variants associated with gene expression
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/028d671856044b26a0873e62b77eaea6
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SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression

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