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dc.contributor.authorAlioto, Tyler S.
dc.contributor.authorBuchhalter, Ivo
dc.contributor.authorDerdak, Sophia
dc.contributor.authorHutter, Barbara
dc.contributor.authorEldridge, Matthew D.
dc.contributor.authorHovig, Eivind
dc.contributor.authorHeisler, Lawrence E.
dc.contributor.authorBeck, Timothy A.
dc.contributor.authorSimpson, Jared T.
dc.contributor.authorTonon, Laurie
dc.contributor.authorSertier, Anne-Sophie
dc.contributor.authorPatch, Ann-Marie
dc.contributor.authorJaeger, Natalie
dc.contributor.authorGinsbach, Philip
dc.contributor.authorDrews, Ruben
dc.contributor.authorParamasivam, Nagarajan
dc.contributor.authorKabbe, Rolf
dc.contributor.authorChotewutmontri, Sasithorn
dc.contributor.authorDiessl, Nicolle
dc.contributor.authorPreviti, Christopher
dc.contributor.authorSchmidt, Sabine
dc.contributor.authorBrors, Benedikt
dc.contributor.authorFeuerbach, Lars
dc.contributor.authorHeinold, Michael
dc.contributor.authorGroebner, Susanne
dc.contributor.authorKorshunov, Andrey
dc.contributor.authorTarpey, Patrick S.
dc.contributor.authorButler, Adam P.
dc.contributor.authorHinton, Jonathan
dc.contributor.authorJones, David
dc.contributor.authorMenzies, Andrew
dc.contributor.authorRaine, Keiran
dc.contributor.authorShepherd, Rebecca
dc.contributor.authorStebbings, Lucy
dc.contributor.authorTeague, Jon W.
dc.contributor.authorRibeca, Paolo
dc.contributor.authorGiner, Francesc Castro
dc.contributor.authorBeltran, Sergi
dc.contributor.authorRaineri, Emanuele
dc.contributor.authorDabad, Marc
dc.contributor.authorHeath, Simon C.
dc.contributor.authorGut, Marta
dc.contributor.authorDenroche, Robert E.
dc.contributor.authorHarding, Nicholas J.
dc.contributor.authorYamaguchi, Takafumi N.
dc.contributor.authorFujimoto, Akihiro
dc.contributor.authorNakagawa, Hidewaki
dc.contributor.authorQuesada, Ctor
dc.contributor.authorValdes-Mas, Rafael
dc.contributor.authorNakken, Sigve
dc.contributor.authorVodak, Daniel
dc.contributor.authorBower, Lawrence
dc.contributor.authorLynch, Andrew G.
dc.contributor.authorAnderson, Charlotte L.
dc.contributor.authorWaddell, Nicola
dc.contributor.authorPearson, John V.
dc.contributor.authorGrimmond, Sean M.
dc.contributor.authorPeto, Myron
dc.contributor.authorSpellman, Paul
dc.contributor.authorHe, Minghui
dc.contributor.authorKandoth, Cyriac
dc.contributor.authorLee, Semin
dc.contributor.authorZhang, John
dc.contributor.authorLetourneau, Louis
dc.contributor.authorMa, Singer
dc.contributor.authorSeth, Sahil
dc.contributor.authorTorrents, David
dc.contributor.authorXi, Liu
dc.contributor.authorWheeler, David A.
dc.contributor.authorLopez-Otin, Carlos
dc.contributor.authorCampo, Elias
dc.contributor.authorCampbell, Peter J.
dc.contributor.authorBoutros, Paul C.
dc.contributor.authorPuente, Xose S.
dc.contributor.authorGerhard, Daniela S.
dc.contributor.authorPfister, Stefan M.
dc.contributor.authorMcPherson, John D.
dc.contributor.authorHudson, Thomas J.
dc.contributor.authorSchlesner, Matthias
dc.contributor.authorLichter, Peter
dc.contributor.authorEils, Roland
dc.contributor.authorJones, David T. W.
dc.contributor.authorGut, Ivo G.
dc.date.accessioned2017-08-14T11:30:10Z
dc.date.available2017-08-14T11:30:10Z
dc.date.issued2015-12-09
dc.identifier250729379
dc.identifierd2a2726e-8a42-46f2-967a-6c3765653d4e
dc.identifier000367579200001
dc.identifier84949564442
dc.identifier.citationAlioto , T S , Buchhalter , I , Derdak , S , Hutter , B , Eldridge , M D , Hovig , E , Heisler , L E , Beck , T A , Simpson , J T , Tonon , L , Sertier , A-S , Patch , A-M , Jaeger , N , Ginsbach , P , Drews , R , Paramasivam , N , Kabbe , R , Chotewutmontri , S , Diessl , N , Previti , C , Schmidt , S , Brors , B , Feuerbach , L , Heinold , M , Groebner , S , Korshunov , A , Tarpey , P S , Butler , A P , Hinton , J , Jones , D , Menzies , A , Raine , K , Shepherd , R , Stebbings , L , Teague , J W , Ribeca , P , Giner , F C , Beltran , S , Raineri , E , Dabad , M , Heath , S C , Gut , M , Denroche , R E , Harding , N J , Yamaguchi , T N , Fujimoto , A , Nakagawa , H , Quesada , C , Valdes-Mas , R , Nakken , S , Vodak , D , Bower , L , Lynch , A G , Anderson , C L , Waddell , N , Pearson , J V , Grimmond , S M , Peto , M , Spellman , P , He , M , Kandoth , C , Lee , S , Zhang , J , Letourneau , L , Ma , S , Seth , S , Torrents , D , Xi , L , Wheeler , D A , Lopez-Otin , C , Campo , E , Campbell , P J , Boutros , P C , Puente , X S , Gerhard , D S , Pfister , S M , McPherson , J D , Hudson , T J , Schlesner , M , Lichter , P , Eils , R , Jones , D T W & Gut , I G 2015 , ' A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing ' , Nature Communications , vol. 6 , 10001 . https://doi.org/10.1038/ncomms10001en
dc.identifier.issn2041-1723
dc.identifier.otherORCID: /0000-0002-7876-7338/work/35946871
dc.identifier.urihttps://hdl.handle.net/10023/11442
dc.descriptionSequence data for this study have been deposited in the European Genome-phenome Archive (EGA) under the accession number EGAS00001001539.en
dc.description.abstractAs whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to similar to 100 x shows benefits, as long as the tumour: control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.
dc.format.extent13
dc.format.extent1386406
dc.language.isoeng
dc.relation.ispartofNature Communicationsen
dc.subjectCancer geneticsen
dc.subjectDNA sequencingen
dc.subjectGenome informaticsen
dc.subjectMutationen
dc.subjectRC0254 Neoplasms. Tumors. Oncology (including Cancer)en
dc.subjectQH426 Geneticsen
dc.subjectDASen
dc.subjectSDG 3 - Good Health and Well-beingen
dc.subject.lccRC0254en
dc.subject.lccQH426en
dc.titleA comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencingen
dc.typeJournal articleen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.contributor.institutionUniversity of St Andrews. Statisticsen
dc.identifier.doi10.1038/ncomms10001
dc.description.statusPeer revieweden
dc.identifier.urlhttps://www.nature.com/articles/ncomms10001#supplementary-informationen


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