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dc.contributor.authorZhang, Yiqun
dc.contributor.authorChen, Fengju
dc.contributor.authorHe, Yao
dc.contributor.authorFujita, Masashi
dc.contributor.authorNakagawa, Hidewaki
dc.contributor.authorZhang, Zemin
dc.contributor.authorAmin, Samirkumar B.
dc.contributor.authorAwadalla, Philip
dc.contributor.authorBailey, Peter J.
dc.contributor.authorBrazma, Alvis
dc.contributor.authorBrooks, Angela N.
dc.contributor.authorCalabrese, Claudia
dc.contributor.authorChateigner, Aurélien
dc.contributor.authorCortés-Ciriano, Isidro
dc.contributor.authorCraft, Brian
dc.contributor.authorCraft, David
dc.contributor.authorCreighton, Chad J.
dc.contributor.authorDavidson, Natalie R.
dc.contributor.authorDemircioğlu, Deniz
dc.contributor.authorErkek, Serap
dc.contributor.authorFonseca, Nuno A.
dc.contributor.authorFrenkel-Morgenstern, Milana
dc.contributor.authorGoldman, Mary J.
dc.contributor.authorGreger, Liliana
dc.contributor.authorGöke, Jonathan
dc.contributor.authorHoadley, Katherine A.
dc.contributor.authorHou, Yong
dc.contributor.authorHuska, Matthew R.
dc.contributor.authorKahles, Andre
dc.contributor.authorKhurana, Ekta
dc.contributor.authorKilpinen, Helena
dc.contributor.authorKorbel, Jan O.
dc.contributor.authorLamaze, Fabien C.
dc.contributor.authorLehmann, Kjong-Van
dc.contributor.authorLi, Chang
dc.contributor.authorLi, Siliang
dc.contributor.authorLi, Xiaobo
dc.contributor.authorLi, Xinyue
dc.contributor.authorLiu, Dongbing
dc.contributor.authorLiu, Fenglin
dc.contributor.authorLiu, Xingmin
dc.contributor.authorMarin, Maximillian G.
dc.contributor.authorMarkowski, Julia
dc.contributor.authorMeyerson, Matthew
dc.contributor.authorNandi, Tannistha
dc.contributor.authorNielsen, Morten Muhlig
dc.contributor.authorOjesina, Akinyemi I.
dc.contributor.authorOuellette, B. F. Francis
dc.contributor.authorPan-Hammarström, Qiang
dc.contributor.authorPark, Peter J.
dc.contributor.authorPedamallu, Chandra Sekhar
dc.contributor.authorPedersen, Jakob Skou
dc.contributor.authorPerry, Marc D.
dc.contributor.authorRätsch, Gunnar
dc.contributor.authorSchwarz, Roland F.
dc.contributor.authorShiraishi, Yuichi
dc.contributor.authorSiebert, Reiner
dc.contributor.authorSoulette, Cameron M.
dc.contributor.authorStark, Stefan G.
dc.contributor.authorStegle, Oliver
dc.contributor.authorSu, Hong
dc.contributor.authorTan, Patrick
dc.contributor.authorTeh, Bin Tean
dc.contributor.authorUrban, Lara
dc.contributor.authorWang, Jian
dc.contributor.authorWaszak, Sebastian M.
dc.contributor.authorWu, Kui
dc.contributor.authorXiang, Qian
dc.contributor.authorXiong, Heng
dc.contributor.authorYakneen, Sergei
dc.contributor.authorYang, Huanming
dc.contributor.authorYe, Chen
dc.contributor.authorYung, Christina K.
dc.contributor.authorZhang, Fan
dc.contributor.authorZhang, Junjun
dc.contributor.authorZhang, Xiuqing
dc.contributor.authorZheng, Liangtao
dc.contributor.authorZhu, Jingchun
dc.contributor.authorZhu, Shida
dc.contributor.authorAkdemir, Kadir C.
dc.contributor.authorAlvarez, Eva G.
dc.contributor.authorBaez-Ortega, Adrian
dc.contributor.authorBeroukhim, Rameen
dc.contributor.authorBoutros, Paul C.
dc.contributor.authorBowtell, David D. L.
dc.contributor.authorBrors, Benedikt
dc.contributor.authorBurns, Kathleen H.
dc.contributor.authorCampbell, Peter J.
dc.contributor.authorChan, Kin
dc.contributor.authorChen, Ken
dc.contributor.authorDueso-Barroso, Ana
dc.contributor.authorDunford, Andrew J.
dc.contributor.authorEdwards, Paul A.
dc.contributor.authorEstivill, Xavier
dc.contributor.authorEtemadmoghadam, Dariush
dc.contributor.authorFeuerbach, Lars
dc.contributor.authorFink, J. Lynn
dc.contributor.authorGarsed, Dale W.
dc.contributor.authorGerstein, Mark
dc.contributor.authorGordenin, Dmitry A.
dc.contributor.authorHaan, David
dc.contributor.authorHaber, James E.
dc.contributor.authorHess, Julian M.
dc.contributor.authorHutter, Barbara
dc.contributor.authorImielinski, Marcin
dc.contributor.authorJones, David T. W.
dc.contributor.authorJu, Young Seok
dc.contributor.authorKazanov, Marat D.
dc.contributor.authorKlimczak, Leszek J.
dc.contributor.authorKoh, Youngil
dc.contributor.authorKumar, Kiran
dc.contributor.authorLee, Eunjung Alice
dc.contributor.authorLee, Jake June-Koo
dc.contributor.authorLi, Yilong
dc.contributor.authorLynch, Andy G.
dc.contributor.authorMacintyre, Geoff
dc.contributor.authorMarkowetz, Florian
dc.contributor.authorMartincorena, Iñigo
dc.contributor.authorMartinez-Fundichely, Alexander
dc.contributor.authorMiyano, Satoru
dc.contributor.authorNavarro, Fabio C. P.
dc.contributor.authorOssowski, Stephan
dc.contributor.authorPearson, John V.
dc.contributor.authorPuiggròs, Montserrat
dc.contributor.authorRippe, Karsten
dc.contributor.authorRoberts, Nicola D.
dc.contributor.authorRoberts, Steven A.
dc.contributor.authorRodriguez-Martin, Bernardo
dc.contributor.authorSchumacher, Steven E.
dc.contributor.authorScully, Ralph
dc.contributor.authorShackleton, Mark
dc.contributor.authorSidiropoulos, Nikos
dc.contributor.authorSieverling, Lina
dc.contributor.authorStewart, Chip
dc.contributor.authorTorrents, David
dc.contributor.authorTubio, Jose M. C.
dc.contributor.authorVillasante, Izar
dc.contributor.authorWaddell, Nicola
dc.contributor.authorWala, Jeremiah A.
dc.contributor.authorWeischenfeldt, Joachim
dc.contributor.authorYang, Lixing
dc.contributor.authorYao, Xiaotong
dc.contributor.authorYoon, Sung-Soo
dc.contributor.authorZamora, Jorge
dc.contributor.authorZhang, Cheng-Zhong
dc.date.accessioned2021-02-04T16:23:58Z
dc.date.available2021-02-04T16:23:58Z
dc.date.issued2020-02-05
dc.date.submitted2017-12-22
dc.identifier.others41467-019-13885-w
dc.identifier.other13885
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/317142
dc.description.abstractAbstract: The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing data and RNA sequencing from a common set of 1220 cancer cases, we report hundreds of genes for which the presence within 100 kb of an SV breakpoint associates with altered expression. For the majority of these genes, expression increases rather than decreases with corresponding breakpoint events. Up-regulated cancer-associated genes impacted by this phenomenon include TERT, MDM2, CDK4, ERBB2, CD274, PDCD1LG2, and IGF2. TERT-associated breakpoints involve ~3% of cases, most frequently in liver biliary, melanoma, sarcoma, stomach, and kidney cancers. SVs associated with up-regulation of PD1 and PDL1 genes involve ~1% of non-amplified cases. For many genes, SVs are significantly associated with increased numbers or greater proximity of enhancer regulatory elements near the gene. DNA methylation near the promoter is often increased with nearby SV breakpoint, which may involve inactivation of repressor elements.
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/631/67/69
dc.subject/631/208/199
dc.subject/45/23
dc.subject/45/91
dc.subjectarticle
dc.titleHigh-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis -regulatory alterations
dc.typeArticle
dc.date.updated2021-02-04T16:23:57Z
prism.issueIdentifier1
prism.publicationNameNature Communications
prism.volume11
dc.identifier.doi10.17863/CAM.64253
dcterms.dateAccepted2019-12-04
rioxxterms.versionofrecord10.1038/s41467-019-13885-w
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.contributor.orcidFonseca, Nuno A. [0000-0003-4832-578X]
dc.contributor.orcidFujita, Masashi [0000-0002-1457-6233]
dc.contributor.orcidBrazma, Alvis [0000-0001-5988-7409]
dc.contributor.orcidCreighton, Chad J. [0000-0002-6090-703X]
dc.identifier.eissn2041-1723
pubs.funder-project-idU.S. Department of Health & Human Services | National Institutes of Health (NIH) (CA125123)
pubs.funder-project-idCancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas) (RP120713)


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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)