Genomic basis for RNA alterations in cancer
PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Claudia Calabrese, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter J. Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan‐Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina K. Yung, Shida Zhu, Philip Awadalla, Chad J. Creighton, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, PCAWG Transcriptome Working Group, Nuno A. Fonseca, André Kahles, Kjong-Van Lehmann, Lara Urban, Cameron M. Soulette, Yuichi Shiraishi, Fenglin Liu, Yao He, Deniz Demircioğlu, Natalie R. Davidson, Claudia Calabrese, Junjun Zhang, Marc D. Perry, Qian Xiang, Liliana Greger, Siliang Li, Dongbing Liu, Stefan G. Stark, Fan Zhang, Samirkumar B. Amin, Peter J. Bailey, Aurélien Chateigner, Isidro Cortés-Ciriano, Brian Craft, Serap Erkek, Milana Frenkel‐Morgenstern, Mary J. Goldman, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Ekta Khurana, Helena Kilpinen, Jan O. Korbel, Fabien C. Lamaze, David K. Chang, Xiaobo Li, Xinyue Li, Xingmin Liu, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Morten M. Nielsen, Akinyemi I. Ojesina, Qiang Pan‐Hammarström
Abstract
Abstract Transcript alterations often result from somatic changes in cancer genomes 1 . Various forms of RNA alterations have been described in cancer, including overexpression 2 , altered splicing 3 and gene fusions 4 ; 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.