CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA
We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood samp...
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| Veröffentlicht in: | Genome Biology 2017-03, Vol.18 (1), p.53-53, Article 53 |
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| creator | Kang, Shuli Li, Qingjiao Chen, Quan Zhou, Yonggang Park, Stacy Lee, Gina Grimes, Brandon Krysan, Kostyantyn Yu, Min Wang, Wei Alber, Frank Sun, Fengzhu Dubinett, Steven M Li, Wenyuan Zhou, Xianghong Jasmine |
| description | We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios. CancerLocator also achieves promising results on patient plasma samples with low DNA methylation sequencing coverage. |
| doi_str_mv | 10.1186/s13059-017-1191-5 |
| format | Article |
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CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios. CancerLocator also achieves promising results on patient plasma samples with low DNA methylation sequencing coverage.</description><identifier>ISSN: 1474-760X</identifier><identifier>ISSN: 1474-7596</identifier><identifier>EISSN: 1474-760X</identifier><identifier>DOI: 10.1186/s13059-017-1191-5</identifier><identifier>PMID: 28335812</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Algorithms ; Bioinformatics ; Biomarkers ; blood sampling ; Breast cancer ; Cancer ; Cancer cells ; Cancer diagnosis ; Computer Simulation ; CpG Islands ; Deoxyribonucleic acid ; Diagnosis ; DNA ; DNA Methylation ; DNA sequencing ; DNA, Neoplasm - blood ; DNA, Neoplasm - genetics ; Epigenesis, Genetic ; Epigenomics - methods ; Gene expression ; Genes ; Genomes ; Genomics ; Humans ; Medical diagnosis ; Medical screening ; Method ; Methods ; Methylation ; Models, Statistical ; neoplasms ; Neoplasms - diagnosis ; Neoplasms - genetics ; Pancreatic cancer ; Patients ; prediction ; Reproducibility of Results ; Tumors ; Workflow</subject><ispartof>Genome Biology, 2017-03, Vol.18 (1), p.53-53, Article 53</ispartof><rights>COPYRIGHT 2017 BioMed Central Ltd.</rights><rights>2017. 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>The Author(s). 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c528t-afd3e55a23f88b0b58badeb1c1e57817fcb22bdaa98303ae57d16820320daa313</citedby><cites>FETCH-LOGICAL-c528t-afd3e55a23f88b0b58badeb1c1e57817fcb22bdaa98303ae57d16820320daa313</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/PMC5364586/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364586/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28335812$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kang, Shuli</creatorcontrib><creatorcontrib>Li, Qingjiao</creatorcontrib><creatorcontrib>Chen, Quan</creatorcontrib><creatorcontrib>Zhou, Yonggang</creatorcontrib><creatorcontrib>Park, Stacy</creatorcontrib><creatorcontrib>Lee, Gina</creatorcontrib><creatorcontrib>Grimes, Brandon</creatorcontrib><creatorcontrib>Krysan, Kostyantyn</creatorcontrib><creatorcontrib>Yu, Min</creatorcontrib><creatorcontrib>Wang, Wei</creatorcontrib><creatorcontrib>Alber, Frank</creatorcontrib><creatorcontrib>Sun, Fengzhu</creatorcontrib><creatorcontrib>Dubinett, Steven M</creatorcontrib><creatorcontrib>Li, Wenyuan</creatorcontrib><creatorcontrib>Zhou, Xianghong Jasmine</creatorcontrib><title>CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA</title><title>Genome Biology</title><addtitle>Genome Biol</addtitle><description>We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios. CancerLocator also achieves promising results on patient plasma samples with low DNA methylation sequencing coverage.</description><subject>Algorithms</subject><subject>Bioinformatics</subject><subject>Biomarkers</subject><subject>blood sampling</subject><subject>Breast cancer</subject><subject>Cancer</subject><subject>Cancer cells</subject><subject>Cancer diagnosis</subject><subject>Computer Simulation</subject><subject>CpG Islands</subject><subject>Deoxyribonucleic acid</subject><subject>Diagnosis</subject><subject>DNA</subject><subject>DNA Methylation</subject><subject>DNA sequencing</subject><subject>DNA, Neoplasm - blood</subject><subject>DNA, Neoplasm - genetics</subject><subject>Epigenesis, Genetic</subject><subject>Epigenomics - methods</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Humans</subject><subject>Medical diagnosis</subject><subject>Medical screening</subject><subject>Method</subject><subject>Methods</subject><subject>Methylation</subject><subject>Models, Statistical</subject><subject>neoplasms</subject><subject>Neoplasms - diagnosis</subject><subject>Neoplasms - genetics</subject><subject>Pancreatic cancer</subject><subject>Patients</subject><subject>prediction</subject><subject>Reproducibility of Results</subject><subject>Tumors</subject><subject>Workflow</subject><issn>1474-760X</issn><issn>1474-7596</issn><issn>1474-760X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>KPI</sourceid><sourceid>BENPR</sourceid><recordid>eNqFkk9v1DAQxSNERcvCB-CCLHGBg1uPHScOB6TV8q_qCjiAxM1ynEnqKmsvdrJqvz3ebqkKF04evXke6T39iuIFsFMAVZ0lEEw2lEFNARqg8lFxAmVd0rpiPx8_mI-LpyldMQZNyasnxTFXQkgF_KS4XhlvMa6DNVOIb4kPnjq_M8ntkNjbHemcGXxILhHjOzK5lGakoachusF5so3YOTu54MmcnB_IBqfLm9HcKtsYejdiIqEnFseR9hGRvP-yfFYc9WZM-PzuXRQ_Pn74vvpM118_na-Wa2olVxM1fSdQSsNFr1TLWqla02ELFlDWCuretpy3nTGNEkyYLHZQKc4EZ1kUIBbFu8Pd7dxusLPop2hGvY1uY-KNDsbpvzfeXeoh7LQUVSlVlQ-8vjsQw68Z06Q3Lu2jGI9hTpozxiSvG1b-1woqd17JhtXZ-uof61WYo89NaM6ZYqysSpVdbw6uwYyonbfBT3g9DWZOSV98O9fLimUE6hr2QeHgtTGkFLG_zwhM73HRB1x0xkXvcckJF8XLh-Xc__jDh_gNYoy8nA</recordid><startdate>20170324</startdate><enddate>20170324</enddate><creator>Kang, Shuli</creator><creator>Li, Qingjiao</creator><creator>Chen, Quan</creator><creator>Zhou, Yonggang</creator><creator>Park, Stacy</creator><creator>Lee, Gina</creator><creator>Grimes, Brandon</creator><creator>Krysan, Kostyantyn</creator><creator>Yu, Min</creator><creator>Wang, Wei</creator><creator>Alber, Frank</creator><creator>Sun, Fengzhu</creator><creator>Dubinett, Steven M</creator><creator>Li, Wenyuan</creator><creator>Zhou, Xianghong Jasmine</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>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>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20170324</creationdate><title>CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA</title><author>Kang, Shuli ; Li, Qingjiao ; Chen, Quan ; Zhou, Yonggang ; Park, Stacy ; Lee, Gina ; Grimes, Brandon ; Krysan, Kostyantyn ; Yu, Min ; Wang, Wei ; Alber, Frank ; Sun, Fengzhu ; Dubinett, Steven M ; Li, Wenyuan ; Zhou, Xianghong Jasmine</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c528t-afd3e55a23f88b0b58badeb1c1e57817fcb22bdaa98303ae57d16820320daa313</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Algorithms</topic><topic>Bioinformatics</topic><topic>Biomarkers</topic><topic>blood sampling</topic><topic>Breast cancer</topic><topic>Cancer</topic><topic>Cancer cells</topic><topic>Cancer diagnosis</topic><topic>Computer Simulation</topic><topic>CpG Islands</topic><topic>Deoxyribonucleic acid</topic><topic>Diagnosis</topic><topic>DNA</topic><topic>DNA Methylation</topic><topic>DNA sequencing</topic><topic>DNA, Neoplasm - blood</topic><topic>DNA, Neoplasm - genetics</topic><topic>Epigenesis, Genetic</topic><topic>Epigenomics - methods</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Humans</topic><topic>Medical diagnosis</topic><topic>Medical screening</topic><topic>Method</topic><topic>Methods</topic><topic>Methylation</topic><topic>Models, Statistical</topic><topic>neoplasms</topic><topic>Neoplasms - diagnosis</topic><topic>Neoplasms - genetics</topic><topic>Pancreatic cancer</topic><topic>Patients</topic><topic>prediction</topic><topic>Reproducibility of Results</topic><topic>Tumors</topic><topic>Workflow</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kang, Shuli</creatorcontrib><creatorcontrib>Li, Qingjiao</creatorcontrib><creatorcontrib>Chen, Quan</creatorcontrib><creatorcontrib>Zhou, Yonggang</creatorcontrib><creatorcontrib>Park, Stacy</creatorcontrib><creatorcontrib>Lee, Gina</creatorcontrib><creatorcontrib>Grimes, Brandon</creatorcontrib><creatorcontrib>Krysan, Kostyantyn</creatorcontrib><creatorcontrib>Yu, Min</creatorcontrib><creatorcontrib>Wang, Wei</creatorcontrib><creatorcontrib>Alber, Frank</creatorcontrib><creatorcontrib>Sun, Fengzhu</creatorcontrib><creatorcontrib>Dubinett, Steven M</creatorcontrib><creatorcontrib>Li, Wenyuan</creatorcontrib><creatorcontrib>Zhou, Xianghong Jasmine</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Global Issues</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - 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CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios. CancerLocator also achieves promising results on patient plasma samples with low DNA methylation sequencing coverage.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>28335812</pmid><doi>10.1186/s13059-017-1191-5</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Algorithms Bioinformatics Biomarkers blood sampling Breast cancer Cancer Cancer cells Cancer diagnosis Computer Simulation CpG Islands Deoxyribonucleic acid Diagnosis DNA DNA Methylation DNA sequencing DNA, Neoplasm - blood DNA, Neoplasm - genetics Epigenesis, Genetic Epigenomics - methods Gene expression Genes Genomes Genomics Humans Medical diagnosis Medical screening Method Methods Methylation Models, Statistical neoplasms Neoplasms - diagnosis Neoplasms - genetics Pancreatic cancer Patients prediction Reproducibility of Results Tumors Workflow |
| title | CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA |
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