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FältnamnIndikatorerMetadata
00008981naa a2201117 4500
001oai:lup.lub.lu.se:ff94e0df-eb42-4aa5-a54d-a958094e2bb6
003SwePub
008230329s2020 | |||||||||||000 ||eng|
009oai:prod.swepub.kib.ki.se:143704363
0247 a https://lup.lub.lu.se/record/ff94e0df-eb42-4aa5-a54d-a958094e2bb62 URI
0247 a https://doi.org/10.1038/s41586-020-1970-02 DOI
0247 a http://kipublications.ki.se/Default.aspx?queryparsed=id:1437043632 URI
040 a (SwePub)lud (SwePub)ki
041 a engb eng
042 9 SwePub
072 7a art2 swepub-publicationtype
072 7a ref2 swepub-contenttype
1001 a Calabrese, Claudiau European Bioinformatics Institute4 aut
2451 0a Genomic basis for RNA alterations in cancer
264 c 2020-02-05
264 1b Springer Science and Business Media LLC,c 2020
520 a Transcript 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.
650 7a MEDICIN OCH HÄLSOVETENSKAPx Medicinska och farmaceutiska grundvetenskaperx Medicinsk genetik0 (SwePub)301072 hsv//swe
650 7a MEDICAL AND HEALTH SCIENCESx Basic Medicinex Medical Genetics0 (SwePub)301072 hsv//eng
650 7a NATURVETENSKAPx Biologix Bioinformatik och systembiologi0 (SwePub)106102 hsv//swe
650 7a NATURAL SCIENCESx Biological Sciencesx Bioinformatics and Systems Biology0 (SwePub)106102 hsv//eng
653 a DNA Copy Number Variations
653 a DNA, Neoplasm
653 a Gene Expression Regulation, Neoplastic
653 a Genome, Human
653 a Genomics
653 a Humans
653 a Neoplasms/genetics
653 a RNA/genetics
653 a Transcriptome
7001 a Davidson, Natalie Ru ETH Zürich4 aut
7001 a Demircioğlu, Denizu National University of Singapore4 aut
7001 a Fonseca, Nuno Au European Bioinformatics Institute4 aut
7001 a He, Yaou Peking University4 aut
7001 a Kahles, Andréu ETH Zürich4 aut
7001 a Lehmann, Kjong-Vanu ETH Zürich4 aut
7001 a Liu, Fenglinu Peking University4 aut
7001 a Shiraishi, Yuichiu University of Tokyo4 aut
7001 a Soulette, Cameron Mu University of California, Santa Cruz4 aut
7001 a Urban, Larau European Bioinformatics Institute4 aut
7001 a Greger, Lilianau European Bioinformatics Institute4 aut
7001 a Li, Siliangu Beijing Genomics Institute4 aut
7001 a Liu, Dongbingu Beijing Genomics Institute4 aut
7001 a Perry, Marc Du Ontario Institute for Cancer Research4 aut
7001 a Xiang, Qianu Ontario Institute for Cancer Research4 aut
7001 a Zhang, Fanu Peking University4 aut
7001 a Zhang, Junjunu Ontario Institute for Cancer Research4 aut
7001 a Bailey, Peteru University of Glasgow4 aut
7001 a Erkek, Serapu European Molecular Biology Laboratory Heidelberg4 aut
7001 a Hoadley, Katherine Au University of North Carolina4 aut
7001 a Hou, Yongu Beijing Genomics Institute4 aut
7001 a Huska, Matthew Ru Berlin Institute for Medical Systems Biology4 aut
7001 a Kilpinen, Helenau University College London4 aut
7001 a Korbel, Jan Ou European Molecular Biology Laboratory Heidelberg4 aut
7001 a Marin, Maximillian Gu University of California, Santa Cruz4 aut
7001 a Markowski, Juliau Berlin Institute for Medical Systems Biology4 aut
7001 a Nandi, Tannisthau A*Star, Genome Institute of Singapore (GIS)4 aut
7001 a Pan-Hammarström, Qiangu Karolinska Institutet4 aut
7001 a Pedamallu, Chandra Sekharu Broad Institute4 aut
7001 a Siebert, Reineru University of Ulm,University Hospital of Ulm4 aut
7001 a Stark, Stefan Gu ETH Zürich4 aut
7001 a Su, Hongu Beijing Genomics Institute4 aut
7001 a Tan, Patricku A*Star, Genome Institute of Singapore (GIS)4 aut
7001 a Waszak, Sebastian Mu European Molecular Biology Laboratory Heidelberg4 aut
7001 a Yung, Christinau Ontario Institute for Cancer Research4 aut
7001 a Zhu, Shidau Beijing Genomics Institute4 aut
7001 a Awadalla, Philipu Ontario Institute for Cancer Research4 aut
7001 a Creighton, Chad Ju Baylor College of Medicine4 aut
7001 a Meyerson, Matthewu Broad Institute4 aut
7001 a Ouellette, B F Francisu University of Toronto4 aut
7001 a Wu, Kuiu Beijing Genomics Institute4 aut
7001 a Yang, Huanmingu Beijing Genomics Institute4 aut
7001 a Brazma, Alvisu European Bioinformatics Institute4 aut
7001 a Brooks, Angela Nu University of California, Santa Cruz4 aut
7001 a Göke, Jonathanu A*Star, Genome Institute of Singapore (GIS)4 aut
7001 a Rätsch, Gunnaru ETH Zürich4 aut
7001 a Schwarz, Roland Fu European Bioinformatics Institute4 aut
7001 a Stegle, Oliveru European Bioinformatics Institute4 aut
7001 a Zhang, Zeminu Peking University4 aut
7001 a Borg, Åkeu Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Familjär bröstcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine,Familial Breast Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments4 cre0 (Swepub:lu)onk-abo
7001 a Ringnér, Markusu Lund University,Lunds universitet,Molekylär cellbiologi,Biologiska institutionen,Naturvetenskapliga fakulteten,Molecular Cell Biology,Department of Biology,Faculty of Science4 cre0 (Swepub:lu)thep-mri
7001 a Staaf, Johanu Lund University,Lunds universitet,Avdelningen för translationell cancerforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Forskningsgrupp Lungcancer,Forskargrupper vid Lunds universitet,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,Bröst/lungcancer,Sektion I,Institutionen för kliniska vetenskaper, Lund,Division of Translational Cancer Research,Department of Laboratory Medicine,Faculty of Medicine,Research Group Lung Cancer,Lund University Research Groups,LUCC: Lund University Cancer Centre,Other Strong Research Environments,Breast/lungcancer,Section I,Department of Clinical Sciences, Lund4 cre0 (Swepub:lu)onk-jst
7102 a European Bioinformatics Instituteb ETH Zürich4 org
7102 a PCAWG Transcriptome Core Group
7102 a PCAWG Consortium
7730 t Natured : Springer Science and Business Media LLCg 578:7793, s. 129-136q 578:7793<129-136x 0028-0836x 1476-4687
8564 u http://dx.doi.org/10.1038/s41586-020-1970-0x freey FULLTEXT
8564 u https://www.nature.com/articles/s41586-020-1970-0.pdf
8564 8u https://lup.lub.lu.se/record/ff94e0df-eb42-4aa5-a54d-a958094e2bb6
8564 8u https://doi.org/10.1038/s41586-020-1970-0
8564 8u http://kipublications.ki.se/Default.aspx?queryparsed=id:143704363

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