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dc.contributor.authorJiao, Wei
dc.contributor.authorKarlic, Rosa
dc.contributor.authorCuppen, Edwin
dc.contributor.authorDanyi, Alexandra
dc.contributor.authorde Ridder, Jeroen
dc.contributor.authorvan Herpen, Carla
dc.contributor.authorLolkema, Martijn P.
dc.contributor.authorSteeghs, Neeltje
dc.contributor.authorMorris, Quaid
dc.contributor.authorAl-Shahrour, Fatima
dc.contributor.authorAtwal, Gurnit
dc.contributor.authorBailey, Peter J.
dc.contributor.authorBiankin, Andrew V.
dc.contributor.authorBoutros, Paul C.
dc.contributor.authorCampbell, Peter J.
dc.contributor.authorChang, David K.
dc.contributor.authorCooke, Susanna L.
dc.contributor.authorDeshpande, Vikram
dc.contributor.authorFaltas, Bishoy M.
dc.contributor.authorFaquin, William C.
dc.contributor.authorGarraway, Levi
dc.contributor.authorGetz, Gad
dc.contributor.authorGrimmond, Sean M.
dc.contributor.authorHaider, Syed
dc.contributor.authorHoadley, Katherine A.
dc.contributor.authorKaiser, Vera B.
dc.contributor.authorKarlić, Rosa
dc.contributor.authorKato, Mamoru
dc.contributor.authorKübler, Kirsten
dc.contributor.authorLazar, Alexander J.
dc.contributor.authorLi, Constance H.
dc.contributor.authorLouis, David N.
dc.contributor.authorMargolin, Adam
dc.contributor.authorMartin, Sancha
dc.contributor.authorNahal-Bose, Hardeep K.
dc.contributor.authorNielsen, G. Petur
dc.contributor.authorNik-Zainal, Serena
dc.contributor.authorOmberg, Larsson
dc.contributor.authorP’ng, Christine
dc.contributor.authorPerry, Marc D.
dc.contributor.authorPolak, Paz
dc.contributor.authorRheinbay, Esther
dc.contributor.authorRubin, Mark A.
dc.contributor.authorSemple, Colin A.
dc.contributor.authorSgroi, Dennis C.
dc.contributor.authorShibata, Tatsuhiro
dc.contributor.authorSiebert, Reiner
dc.contributor.authorSmith, Jaclyn
dc.contributor.authorStein, Lincoln D.
dc.contributor.authorStobbe, Miranda D.
dc.contributor.authorSun, Ren X.
dc.contributor.authorThai, Kevin
dc.contributor.authorWright, Derek W.
dc.contributor.authorWu, Chin-Lee
dc.contributor.authorYuan, Ke
dc.contributor.authorZhang, Junjun
dc.date.accessioned2021-02-04T16:24:25Z
dc.date.available2021-02-04T16:24:25Z
dc.date.issued2020-02-05
dc.date.submitted2017-11-27
dc.identifier.others41467-019-13825-8
dc.identifier.other13825
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/317145
dc.description.abstractAbstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here,as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
dc.languageen
dc.publisherNature Publishing Group UK
dc.rightsAttribution 4.0 International (CC BY 4.0)en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectArticle
dc.subject/631/208/69
dc.subject/692/699/67/1680
dc.subject/45
dc.subject/45/23
dc.subject/139
dc.subject/119
dc.subjectarticle
dc.titleA deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
dc.typeArticle
dc.date.updated2021-02-04T16:24:25Z
prism.issueIdentifier1
prism.publicationNameNature Communications
prism.volume11
dc.identifier.doi10.17863/CAM.64256
dcterms.dateAccepted2019-11-26
rioxxterms.versionofrecord10.1038/s41467-019-13825-8
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidAtwal, Gurnit [0000-0003-2817-3117]
dc.contributor.orcidPolak, Paz [0000-0002-2153-4488]
dc.contributor.orcidKarlic, Rosa [0000-0002-1291-2897]
dc.contributor.orcidde Ridder, Jeroen [0000-0002-0828-3477]
dc.contributor.orcidLolkema, Martijn P. [0000-0003-0466-2928]
dc.contributor.orcidGetz, Gad [0000-0002-0936-0753]
dc.contributor.orcidMorris, Quaid [0000-0002-2760-6999]
dc.identifier.eissn2041-1723


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)