CopywriteR: DNA copy number detection from off-target sequence data
Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we...
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| Veröffentlicht in: | Genome Biology 2015-02, Vol.16 (1), p.49, Article 49 |
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| creator | Kuilman, Thomas Velds, Arno Kemper, Kristel Ranzani, Marco Bombardelli, Lorenzo Hoogstraat, Marlous Nevedomskaya, Ekaterina Xu, Guotai de Ruiter, Julian Lolkema, Martijn P Ylstra, Bauke Jonkers, Jos Rottenberg, Sven Wessels, Lodewyk F Adams, David J Peeper, Daniel S Krijgsman, Oscar |
| description | Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools. |
| doi_str_mv | 10.1186/s13059-015-0617-1 |
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Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.</description><identifier>ISSN: 1465-6906</identifier><identifier>ISSN: 1474-7596</identifier><identifier>EISSN: 1474-760X</identifier><identifier>EISSN: 1465-6906</identifier><identifier>EISSN: 1465-6914</identifier><identifier>DOI: 10.1186/s13059-015-0617-1</identifier><identifier>PMID: 25887352</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Algorithms ; Analysis ; Archives & records ; Bioinformatics ; Cancer ; Chromatin ; Consortia ; Copy number ; Deoxyribonucleic acid ; Disease ; DNA ; DNA Copy Number Variations - genetics ; Exome - genetics ; Exons ; Exons - genetics ; Gene expression ; Genes ; Genome, Human ; Genomes ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoprecipitation ; Instrument industry ; Melanoma ; Method ; Methods ; Mutation ; Nucleotide sequence ; Principal components analysis ; Sequence Analysis, DNA ; Technology application</subject><ispartof>Genome Biology, 2015-02, Vol.16 (1), p.49, Article 49</ispartof><rights>COPYRIGHT 2015 BioMed Central Ltd.</rights><rights>2015. This work is licensed under http://creativecommons.org/licenses/by/4.0 (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Kuilman et al.; licensee BioMed Central. 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c562t-579e9f6d38b93ece3299005904c4de6c0c9e571daeb3f714955c81eea6efd093</citedby><cites>FETCH-LOGICAL-c562t-579e9f6d38b93ece3299005904c4de6c0c9e571daeb3f714955c81eea6efd093</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396974/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396974/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25887352$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kuilman, Thomas</creatorcontrib><creatorcontrib>Velds, Arno</creatorcontrib><creatorcontrib>Kemper, Kristel</creatorcontrib><creatorcontrib>Ranzani, Marco</creatorcontrib><creatorcontrib>Bombardelli, Lorenzo</creatorcontrib><creatorcontrib>Hoogstraat, Marlous</creatorcontrib><creatorcontrib>Nevedomskaya, Ekaterina</creatorcontrib><creatorcontrib>Xu, Guotai</creatorcontrib><creatorcontrib>de Ruiter, Julian</creatorcontrib><creatorcontrib>Lolkema, Martijn P</creatorcontrib><creatorcontrib>Ylstra, Bauke</creatorcontrib><creatorcontrib>Jonkers, Jos</creatorcontrib><creatorcontrib>Rottenberg, Sven</creatorcontrib><creatorcontrib>Wessels, Lodewyk F</creatorcontrib><creatorcontrib>Adams, David J</creatorcontrib><creatorcontrib>Peeper, Daniel S</creatorcontrib><creatorcontrib>Krijgsman, Oscar</creatorcontrib><title>CopywriteR: DNA copy number detection from off-target sequence data</title><title>Genome Biology</title><addtitle>Genome Biol</addtitle><description>Current methods for detection of copy number variants (CNV) and aberrations (CNA) from targeted sequencing data are based on the depth of coverage of captured exons. 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CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.</description><subject>Algorithms</subject><subject>Analysis</subject><subject>Archives & records</subject><subject>Bioinformatics</subject><subject>Cancer</subject><subject>Chromatin</subject><subject>Consortia</subject><subject>Copy number</subject><subject>Deoxyribonucleic acid</subject><subject>Disease</subject><subject>DNA</subject><subject>DNA Copy Number Variations - genetics</subject><subject>Exome - genetics</subject><subject>Exons</subject><subject>Exons - genetics</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genome, Human</subject><subject>Genomes</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Humans</subject><subject>Immunoprecipitation</subject><subject>Instrument industry</subject><subject>Melanoma</subject><subject>Method</subject><subject>Methods</subject><subject>Mutation</subject><subject>Nucleotide sequence</subject><subject>Principal components analysis</subject><subject>Sequence Analysis, DNA</subject><subject>Technology application</subject><issn>1465-6906</issn><issn>1474-7596</issn><issn>1474-760X</issn><issn>1465-6906</issn><issn>1465-6914</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>KPI</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNpVkUtPGzEUha2qqDzaH9BNNVJXXZj67TELpCgtFIGgqlh0Zzme63RQZhxsDy3_HkehiMgL-9rnHH3WQegjJceUtuprppxIgwmVmCiqMX2DDqjQAmtFfr_dnJXEyhC1jw5zviOEGsHUO7TPZNtqLtkBms_j-vFv6gv8Omm-Xc8aX-dmnIYFpKaDAr70cWxCikMTQ8DFpSWUJsP9BKOHpnPFvUd7wa0yfHjej9Dt2ffb-Q98dXN-MZ9dYS8VK1hqAyaojrcLw8EDZ8aQyk-EFx0oT7wBqWnnYMGDpsJI6VsK4BSEjhh-hE63setpMUDnYSzJrew69YNLjza63u6-jP0fu4wPVnCjjBY14PNzQIoVPxd7F6c0VmTLGNFScc1YVR1vVUu3AtuPIdYwX1cHQ-_jCKGv9zMpqDRciA3Xlx1D1RT4V5Zuytle_rzY1dKt1qeYc4Lwgk-J3XRqt53a2qnddGpp9Xx6_e8Xx_8S-RNGa5wa</recordid><startdate>20150227</startdate><enddate>20150227</enddate><creator>Kuilman, Thomas</creator><creator>Velds, Arno</creator><creator>Kemper, Kristel</creator><creator>Ranzani, Marco</creator><creator>Bombardelli, Lorenzo</creator><creator>Hoogstraat, Marlous</creator><creator>Nevedomskaya, Ekaterina</creator><creator>Xu, Guotai</creator><creator>de Ruiter, Julian</creator><creator>Lolkema, Martijn P</creator><creator>Ylstra, Bauke</creator><creator>Jonkers, Jos</creator><creator>Rottenberg, Sven</creator><creator>Wessels, Lodewyk F</creator><creator>Adams, David J</creator><creator>Peeper, Daniel S</creator><creator>Krijgsman, Oscar</creator><general>BioMed Central Ltd</general><general>BioMed Central</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>KPI</scope><scope>IAO</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>5PM</scope></search><sort><creationdate>20150227</creationdate><title>CopywriteR: DNA copy number detection from off-target sequence data</title><author>Kuilman, Thomas ; Velds, Arno ; Kemper, Kristel ; Ranzani, Marco ; Bombardelli, Lorenzo ; Hoogstraat, Marlous ; Nevedomskaya, Ekaterina ; Xu, Guotai ; de Ruiter, Julian ; Lolkema, Martijn P ; Ylstra, Bauke ; Jonkers, Jos ; Rottenberg, Sven ; Wessels, Lodewyk F ; Adams, David J ; Peeper, Daniel S ; Krijgsman, Oscar</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c562t-579e9f6d38b93ece3299005904c4de6c0c9e571daeb3f714955c81eea6efd093</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Algorithms</topic><topic>Analysis</topic><topic>Archives & records</topic><topic>Bioinformatics</topic><topic>Cancer</topic><topic>Chromatin</topic><topic>Consortia</topic><topic>Copy number</topic><topic>Deoxyribonucleic acid</topic><topic>Disease</topic><topic>DNA</topic><topic>DNA Copy Number Variations - 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Accurate CNA determination is complicated by uneven genomic distribution and non-uniform capture efficiency of targeted exons. Here we present CopywriteR, which eludes these problems by exploiting 'off-target' sequence reads. CopywriteR allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. CopywriteR outperforms existing methods and constitutes a widely applicable alternative to available tools.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25887352</pmid><doi>10.1186/s13059-015-0617-1</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Analysis Archives & records Bioinformatics Cancer Chromatin Consortia Copy number Deoxyribonucleic acid Disease DNA DNA Copy Number Variations - genetics Exome - genetics Exons Exons - genetics Gene expression Genes Genome, Human Genomes High-Throughput Nucleotide Sequencing Humans Immunoprecipitation Instrument industry Melanoma Method Methods Mutation Nucleotide sequence Principal components analysis Sequence Analysis, DNA Technology application |
| title | CopywriteR: DNA copy number detection from off-target sequence data |
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