000153599 001__ 153599
000153599 005__ 20240229123045.0
000153599 0247_ $$2doi$$a10.1038/s41586-020-1970-0
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000153599 0247_ $$2ISSN$$a0028-0836
000153599 0247_ $$2ISSN$$a1476-4687
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000153599 037__ $$aDKFZ-2020-00343
000153599 041__ $$aeng
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000153599 1001_ $$aGroup, PCAWG Transcriptome Core$$b0$$eCollaboration Author
000153599 245__ $$aGenomic basis for RNA alterations in cancer.
000153599 260__ $$aLondon [u.a.]$$bNature Publ. Group52462$$c2020
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000153599 520__ $$aTranscript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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000153599 7001_ $$aCalabrese, Claudia$$b1
000153599 7001_ $$aDavidson, Natalie R$$b2
000153599 7001_ $$aDemircioğlu, Deniz$$b3
000153599 7001_ $$aFonseca, Nuno A$$b4
000153599 7001_ $$aHe, Yao$$b5
000153599 7001_ $$aKahles, André$$b6
000153599 7001_ $$aLehmann, Kjong-Van$$b7
000153599 7001_ $$aLiu, Fenglin$$b8
000153599 7001_ $$aShiraishi, Yuichi$$b9
000153599 7001_ $$aSoulette, Cameron M$$b10
000153599 7001_ $$aUrban, Lara$$b11
000153599 7001_ $$aGreger, Liliana$$b12
000153599 7001_ $$aLi, Siliang$$b13
000153599 7001_ $$aLiu, Dongbing$$b14
000153599 7001_ $$aPerry, Marc D$$b15
000153599 7001_ $$aXiang, Qian$$b16
000153599 7001_ $$aZhang, Fan$$b17
000153599 7001_ $$aZhang, Junjun$$b18
000153599 7001_ $$aBailey, Peter$$b19
000153599 7001_ $$aErkek, Serap$$b20
000153599 7001_ $$aHoadley, Katherine A$$b21
000153599 7001_ $$aHou, Yong$$b22
000153599 7001_ $$aHuska, Matthew R$$b23
000153599 7001_ $$aKilpinen, Helena$$b24
000153599 7001_ $$aKorbel, Jan O$$b25
000153599 7001_ $$aMarin, Maximillian G$$b26
000153599 7001_ $$aMarkowski, Julia$$b27
000153599 7001_ $$aNandi, Tannistha$$b28
000153599 7001_ $$aPan-Hammarström, Qiang$$b29
000153599 7001_ $$aPedamallu, Chandra Sekhar$$b30
000153599 7001_ $$aSiebert, Reiner$$b31
000153599 7001_ $$aStark, Stefan G$$b32
000153599 7001_ $$aSu, Hong$$b33
000153599 7001_ $$aTan, Patrick$$b34
000153599 7001_ $$aWaszak, Sebastian M$$b35
000153599 7001_ $$aYung, Christina$$b36
000153599 7001_ $$aZhu, Shida$$b37
000153599 7001_ $$aAwadalla, Philip$$b38
000153599 7001_ $$aCreighton, Chad J$$b39
000153599 7001_ $$aMeyerson, Matthew$$b40
000153599 7001_ $$aOuellette, B F Francis$$b41
000153599 7001_ $$aWu, Kui$$b42
000153599 7001_ $$aYang, Huanming$$b43
000153599 7001_ $$aGroup, PCAWG Transcriptome Working$$b44$$eCollaboration Author
000153599 7001_ $$aBrazma, Alvis$$b45
000153599 7001_ $$aBrooks, Angela N$$b46
000153599 7001_ $$aGöke, Jonathan$$b47
000153599 7001_ $$aRätsch, Gunnar$$b48
000153599 7001_ $$0P:(DE-HGF)0$$aSchwarz, Roland F$$b49
000153599 7001_ $$0P:(DE-He78)9aabcfee1a1fc9202398a45a63f0b1e3$$aStegle, Oliver$$b50$$eLast author
000153599 7001_ $$aZhang, Zemin$$b51
000153599 7001_ $$aConsortium, PCAWG$$b52$$eCollaboration Author
000153599 7001_ $$aCalabrese, Claudia$$b53
000153599 7001_ $$aDavidson, Natalie R$$b54
000153599 7001_ $$aDemircioğlu, Deniz$$b55
000153599 7001_ $$aFonseca, Nuno A$$b56
000153599 7001_ $$aHe, Yao$$b57
000153599 7001_ $$aKahles, André$$b58
000153599 7001_ $$aLehmann, Kjong-Van$$b59
000153599 7001_ $$aLiu, Fenglin$$b60
000153599 7001_ $$aShiraishi, Yuichi$$b61
000153599 7001_ $$aSoulette, Cameron M$$b62
000153599 7001_ $$aUrban, Lara$$b63
000153599 7001_ $$aFonseca, Nuno A$$b64
000153599 7001_ $$aKahles, André$$b65
000153599 7001_ $$aLehmann, Kjong-Van$$b66
000153599 7001_ $$aUrban, Lara$$b67
000153599 7001_ $$aSoulette, Cameron M$$b68
000153599 7001_ $$aShiraishi, Yuichi$$b69
000153599 7001_ $$aLiu, Fenglin$$b70
000153599 7001_ $$aHe, Yao$$b71
000153599 7001_ $$aDemircioğlu, Deniz$$b72
000153599 7001_ $$aDavidson, Natalie R$$b73
000153599 7001_ $$aCalabrese, Claudia$$b74
000153599 7001_ $$aZhang, Junjun$$b75
000153599 7001_ $$aPerry, Marc D$$b76
000153599 7001_ $$aXiang, Qian$$b77
000153599 7001_ $$aGreger, Liliana$$b78
000153599 7001_ $$aLi, Siliang$$b79
000153599 7001_ $$aLiu, Dongbing$$b80
000153599 7001_ $$aStark, Stefan G$$b81
000153599 7001_ $$aZhang, Fan$$b82
000153599 7001_ $$aAmin, Samirkumar B$$b83
000153599 7001_ $$aBailey, Peter$$b84
000153599 7001_ $$aChateigner, Aurélien$$b85
000153599 7001_ $$aCortés-Ciriano, Isidro$$b86
000153599 7001_ $$aCraft, Brian$$b87
000153599 7001_ $$aErkek, Serap$$b88
000153599 7001_ $$aFrenkel-Morgenstern, Milana$$b89
000153599 7001_ $$aGoldman, Mary$$b90
000153599 7001_ $$aHoadley, Katherine A$$b91
000153599 7001_ $$aHou, Yong$$b92
000153599 7001_ $$aHuska, Matthew R$$b93
000153599 7001_ $$aKhurana, Ekta$$b94
000153599 7001_ $$aKilpinen, Helena$$b95
000153599 7001_ $$aKorbel, Jan O$$b96
000153599 7001_ $$aLamaze, Fabien C$$b97
000153599 7001_ $$aLi, Chang$$b98
000153599 7001_ $$aLi, Xiaobo$$b99
000153599 7001_ $$aLi, Xinyue$$b100
000153599 7001_ $$aLiu, Xingmin$$b101
000153599 7001_ $$aMarin, Maximillian G$$b102
000153599 7001_ $$aMarkowski, Julia$$b103
000153599 7001_ $$aNandi, Tannistha$$b104
000153599 7001_ $$aNielsen, Morten M$$b105
000153599 7001_ $$aOjesina, Akinyemi I$$b106
000153599 7001_ $$aPan-Hammarström, Qiang$$b107
000153599 7001_ $$aPark, Peter J$$b108
000153599 7001_ $$aPedamallu, Chandra Sekhar$$b109
000153599 7001_ $$aPedersen, Jakob S$$b110
000153599 7001_ $$aSiebert, Reiner$$b111
000153599 7001_ $$aSu, Hong$$b112
000153599 7001_ $$aTan, Patrick$$b113
000153599 7001_ $$aTeh, Bin Tean$$b114
000153599 7001_ $$aWang, Jian$$b115
000153599 7001_ $$aWaszak, Sebastian M$$b116
000153599 7001_ $$aXiong, Heng$$b117
000153599 7001_ $$aYakneen, Sergei$$b118
000153599 7001_ $$aYe, Chen$$b119
000153599 7001_ $$aYung, Christina$$b120
000153599 7001_ $$aZhang, Xiuqing$$b121
000153599 7001_ $$aZheng, Liangtao$$b122
000153599 7001_ $$aZhu, Jingchun$$b123
000153599 7001_ $$aZhu, Shida$$b124
000153599 7001_ $$aAwadalla, Philip$$b125
000153599 7001_ $$aCreighton, Chad J$$b126
000153599 7001_ $$aMeyerson, Matthew$$b127
000153599 7001_ $$aOuellette, B F Francis$$b128
000153599 7001_ $$aWu, Kui$$b129
000153599 7001_ $$aYang, Huanming$$b130
000153599 7001_ $$aGöke, Jonathan$$b131
000153599 7001_ $$aSchwarz, Roland F$$b132
000153599 7001_ $$0P:(DE-He78)9aabcfee1a1fc9202398a45a63f0b1e3$$aStegle, Oliver$$b133$$eLast author
000153599 7001_ $$aZhang, Zemin$$b134
000153599 7001_ $$aBrazma, Alvis$$b135
000153599 7001_ $$aRätsch, Gunnar$$b136
000153599 7001_ $$aBrooks, Angela N$$b137
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