Quantification of aneuploidy in targeted sequencing data using ASCETS

Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number cha...

Full description

Saved in:
Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2021-08, Vol.37 (16), p.2461-2463
Main Authors: Spurr, Liam F, Touat, Mehdi, Taylor, Alison M, Dubuc, Adrian M, Shih, Juliann, Meredith, David M, Pisano, William V, Meyerson, Matthew L, Ligon, Keith L, Cherniack, Andrew D, Li, Yvonne Y, Beroukhim, Rameen
Format: Article
Language:English
Subjects:
Aneuploidy
Applications Notes
Availability
Bioinformatics
Documentation
Genome
Genomic analysis
Genomics
Human health and pathology
Humans
Life Sciences
Sequences
Software
Citations: Items that this one cites
Items that cite this one
Online Access:Request full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203
cites cdi_FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203
container_end_page 2463
container_issue 16
container_start_page 2461
container_title Bioinformatics (Oxford, England)
container_volume 37
creator Spurr, Liam F
Touat, Mehdi
Taylor, Alison M
Dubuc, Adrian M
Shih, Juliann
Meredith, David M
Pisano, William V
Meyerson, Matthew L
Ligon, Keith L
Cherniack, Andrew D
Li, Yvonne Y
Beroukhim, Rameen
description Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. Availability and implementation ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. Supplementary information Supplementary data are available at Bioinformatics online.
doi_str_mv 10.1093/bioinformatics/btaa980
format article
fullrecord <record><control><sourceid>proquest_TOX</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8388019</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><oup_id>10.1093/bioinformatics/btaa980</oup_id><sourcerecordid>2465444953</sourcerecordid><originalsourceid>FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203</originalsourceid><addsrcrecordid>eNqNUU1rGzEQFSUh338hLPSSHtxoViut9lIwxk0ChlCSnoWklRyFteRK2kD-fWTsmCSnnmaQ3nvzZh5Cl4B_Au7ItXLBeRviSman07XKUnYcf0MnQFg7aTjAwb7H5BidpvSMMaaYsiN0TEjdtC3QEzT_M0qfnXW6CAVfBVtJb8b1EFz_WjlfZRmXJpu-SubfaLx2fln1MstqTJt2-jCbPz6co0Mrh2QudvUM_f09f5zdThb3N3ez6WKiKfA86QEIUMIlYwwTg3te94TwtlNS9bzRVildqrWUMMqhY1i1vG6YJZwrqDE5Q7-2uutRrUyvjc9RDmId3UrGVxGkE59_vHsSy_AieFHA0BWBH1uBpy-02-lCbN5wQxkDTl6gYK92w2Ioq6csVi5pMwzlQGFMohijTdN0lBTo9y_Q5zBGX04hCNS83J2yjXu2RekYUorG7h0AFptUxedUxS7VQrz8uPae9h5jAcAWEMb1_4q-AQgitDI</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3128005560</pqid></control><display><type>article</type><title>Quantification of aneuploidy in targeted sequencing data using ASCETS</title><source>Open Access: Oxford University Press Open Journals</source><creator>Spurr, Liam F ; Touat, Mehdi ; Taylor, Alison M ; Dubuc, Adrian M ; Shih, Juliann ; Meredith, David M ; Pisano, William V ; Meyerson, Matthew L ; Ligon, Keith L ; Cherniack, Andrew D ; Li, Yvonne Y ; Beroukhim, Rameen</creator><contributor>Robinson, Peter</contributor><creatorcontrib>Spurr, Liam F ; Touat, Mehdi ; Taylor, Alison M ; Dubuc, Adrian M ; Shih, Juliann ; Meredith, David M ; Pisano, William V ; Meyerson, Matthew L ; Ligon, Keith L ; Cherniack, Andrew D ; Li, Yvonne Y ; Beroukhim, Rameen ; Robinson, Peter</creatorcontrib><description>Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. Availability and implementation ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. Supplementary information Supplementary data are available at Bioinformatics online.</description><identifier>ISSN: 1367-4803</identifier><identifier>EISSN: 1367-4811</identifier><identifier>DOI: 10.1093/bioinformatics/btaa980</identifier><identifier>PMID: 33247715</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Aneuploidy ; Applications Notes ; Availability ; Bioinformatics ; Documentation ; Genome ; Genomic analysis ; Genomics ; Human health and pathology ; Humans ; Life Sciences ; Sequences ; Software</subject><ispartof>Bioinformatics (Oxford, England), 2021-08, Vol.37 (16), p.2461-2463</ispartof><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020</rights><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</rights><rights>The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203</citedby><cites>FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203</cites><orcidid>0000-0001-6465-7739 ; 0000-0002-7054-8624</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388019/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8388019/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,1604,27924,27925,53791,53793</link.rule.ids><linktorsrc>$$Uhttps://dx.doi.org/10.1093/bioinformatics/btaa980$$EView_record_in_Oxford_University_Press$$FView_record_in_$$GOxford_University_Press</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33247715$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04566183$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Robinson, Peter</contributor><creatorcontrib>Spurr, Liam F</creatorcontrib><creatorcontrib>Touat, Mehdi</creatorcontrib><creatorcontrib>Taylor, Alison M</creatorcontrib><creatorcontrib>Dubuc, Adrian M</creatorcontrib><creatorcontrib>Shih, Juliann</creatorcontrib><creatorcontrib>Meredith, David M</creatorcontrib><creatorcontrib>Pisano, William V</creatorcontrib><creatorcontrib>Meyerson, Matthew L</creatorcontrib><creatorcontrib>Ligon, Keith L</creatorcontrib><creatorcontrib>Cherniack, Andrew D</creatorcontrib><creatorcontrib>Li, Yvonne Y</creatorcontrib><creatorcontrib>Beroukhim, Rameen</creatorcontrib><title>Quantification of aneuploidy in targeted sequencing data using ASCETS</title><title>Bioinformatics (Oxford, England)</title><addtitle>Bioinformatics</addtitle><description>Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. Availability and implementation ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. Supplementary information Supplementary data are available at Bioinformatics online.</description><subject>Aneuploidy</subject><subject>Applications Notes</subject><subject>Availability</subject><subject>Bioinformatics</subject><subject>Documentation</subject><subject>Genome</subject><subject>Genomic analysis</subject><subject>Genomics</subject><subject>Human health and pathology</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Sequences</subject><subject>Software</subject><issn>1367-4803</issn><issn>1367-4811</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNqNUU1rGzEQFSUh338hLPSSHtxoViut9lIwxk0ChlCSnoWklRyFteRK2kD-fWTsmCSnnmaQ3nvzZh5Cl4B_Au7ItXLBeRviSman07XKUnYcf0MnQFg7aTjAwb7H5BidpvSMMaaYsiN0TEjdtC3QEzT_M0qfnXW6CAVfBVtJb8b1EFz_WjlfZRmXJpu-SubfaLx2fln1MstqTJt2-jCbPz6co0Mrh2QudvUM_f09f5zdThb3N3ez6WKiKfA86QEIUMIlYwwTg3te94TwtlNS9bzRVildqrWUMMqhY1i1vG6YJZwrqDE5Q7-2uutRrUyvjc9RDmId3UrGVxGkE59_vHsSy_AieFHA0BWBH1uBpy-02-lCbN5wQxkDTl6gYK92w2Ioq6csVi5pMwzlQGFMohijTdN0lBTo9y_Q5zBGX04hCNS83J2yjXu2RekYUorG7h0AFptUxedUxS7VQrz8uPae9h5jAcAWEMb1_4q-AQgitDI</recordid><startdate>20210815</startdate><enddate>20210815</enddate><creator>Spurr, Liam F</creator><creator>Touat, Mehdi</creator><creator>Taylor, Alison M</creator><creator>Dubuc, Adrian M</creator><creator>Shih, Juliann</creator><creator>Meredith, David M</creator><creator>Pisano, William V</creator><creator>Meyerson, Matthew L</creator><creator>Ligon, Keith L</creator><creator>Cherniack, Andrew D</creator><creator>Li, Yvonne Y</creator><creator>Beroukhim, Rameen</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><general>Oxford University Press (OUP)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7TO</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>K9.</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope><scope>1XC</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0001-6465-7739</orcidid><orcidid>https://orcid.org/0000-0002-7054-8624</orcidid></search><sort><creationdate>20210815</creationdate><title>Quantification of aneuploidy in targeted sequencing data using ASCETS</title><author>Spurr, Liam F ; Touat, Mehdi ; Taylor, Alison M ; Dubuc, Adrian M ; Shih, Juliann ; Meredith, David M ; Pisano, William V ; Meyerson, Matthew L ; Ligon, Keith L ; Cherniack, Andrew D ; Li, Yvonne Y ; Beroukhim, Rameen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Aneuploidy</topic><topic>Applications Notes</topic><topic>Availability</topic><topic>Bioinformatics</topic><topic>Documentation</topic><topic>Genome</topic><topic>Genomic analysis</topic><topic>Genomics</topic><topic>Human health and pathology</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Sequences</topic><topic>Software</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Spurr, Liam F</creatorcontrib><creatorcontrib>Touat, Mehdi</creatorcontrib><creatorcontrib>Taylor, Alison M</creatorcontrib><creatorcontrib>Dubuc, Adrian M</creatorcontrib><creatorcontrib>Shih, Juliann</creatorcontrib><creatorcontrib>Meredith, David M</creatorcontrib><creatorcontrib>Pisano, William V</creatorcontrib><creatorcontrib>Meyerson, Matthew L</creatorcontrib><creatorcontrib>Ligon, Keith L</creatorcontrib><creatorcontrib>Cherniack, Andrew D</creatorcontrib><creatorcontrib>Li, Yvonne Y</creatorcontrib><creatorcontrib>Beroukhim, Rameen</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics &amp; Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical &amp; Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology &amp; Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>ProQuest Health &amp; Medical Complete (Alumni)</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts – Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics (Oxford, England)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Spurr, Liam F</au><au>Touat, Mehdi</au><au>Taylor, Alison M</au><au>Dubuc, Adrian M</au><au>Shih, Juliann</au><au>Meredith, David M</au><au>Pisano, William V</au><au>Meyerson, Matthew L</au><au>Ligon, Keith L</au><au>Cherniack, Andrew D</au><au>Li, Yvonne Y</au><au>Beroukhim, Rameen</au><au>Robinson, Peter</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantification of aneuploidy in targeted sequencing data using ASCETS</atitle><jtitle>Bioinformatics (Oxford, England)</jtitle><addtitle>Bioinformatics</addtitle><date>2021-08-15</date><risdate>2021</risdate><volume>37</volume><issue>16</issue><spage>2461</spage><epage>2463</epage><pages>2461-2463</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><abstract>Abstract Summary The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data. Availability and implementation ASCETS is implemented in R and is freely available to non-commercial users on GitHub: https://github.com/beroukhim-lab/ascets, along with detailed documentation. Supplementary information Supplementary data are available at Bioinformatics online.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33247715</pmid><doi>10.1093/bioinformatics/btaa980</doi><tpages>3</tpages><orcidid>https://orcid.org/0000-0001-6465-7739</orcidid><orcidid>https://orcid.org/0000-0002-7054-8624</orcidid><oa>free_for_read</oa></addata></record>
fulltext fulltext_linktorsrc
identifier ISSN: 1367-4803
ispartof Bioinformatics (Oxford, England), 2021-08, Vol.37 (16), p.2461-2463
issn 1367-4803
1367-4811
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_8388019
source Open Access: Oxford University Press Open Journals
subjects Aneuploidy
Applications Notes
Availability
Bioinformatics
Documentation
Genome
Genomic analysis
Genomics
Human health and pathology
Humans
Life Sciences
Sequences
Software
title Quantification of aneuploidy in targeted sequencing data using ASCETS
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-29T23%3A19%3A43IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_TOX&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Quantification%20of%20aneuploidy%20in%20targeted%20sequencing%20data%20using%20ASCETS&rft.jtitle=Bioinformatics%20(Oxford,%20England)&rft.au=Spurr,%20Liam%20F&rft.date=2021-08-15&rft.volume=37&rft.issue=16&rft.spage=2461&rft.epage=2463&rft.pages=2461-2463&rft.issn=1367-4803&rft.eissn=1367-4811&rft_id=info:doi/10.1093/bioinformatics/btaa980&rft_dat=%3Cproquest_TOX%3E2465444953%3C/proquest_TOX%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c518t-d1131538a66603e0d82d33879babd84cfbbcd84ff536581960b78246f388b1203%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=3128005560&rft_id=info:pmid/33247715&rft_oup_id=10.1093/bioinformatics/btaa980&rfr_iscdi=true