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@ARTICLE{Group:153599,
author = {C. Calabrese and N. R. Davidson and D. Demircioğlu and N.
A. Fonseca and Y. He and A. Kahles and K.-V. Lehmann and F.
Liu and Y. Shiraishi and C. M. Soulette and L. Urban and L.
Greger and S. Li and D. Liu and M. D. Perry and Q. Xiang and
F. Zhang and J. Zhang and P. Bailey and S. Erkek and K. A.
Hoadley and Y. Hou and M. R. Huska and H. Kilpinen and J. O.
Korbel and M. G. Marin and J. Markowski and T. Nandi and Q.
Pan-Hammarström and C. S. Pedamallu and R. Siebert and S.
G. Stark and H. Su and P. Tan and S. M. Waszak and C. Yung
and S. Zhu and P. Awadalla and C. J. Creighton and M.
Meyerson and B. F. F. Ouellette and K. Wu and H. Yang and A.
Brazma and A. N. Brooks and J. Göke and G. Rätsch and R.
F. Schwarz$^*$ and O. Stegle$^*$ and Z. Zhang and C.
Calabrese and N. R. Davidson and D. Demircioğlu and N. A.
Fonseca and Y. He and A. Kahles and K.-V. Lehmann and F. Liu
and Y. Shiraishi and C. M. Soulette and L. Urban and N. A.
Fonseca and A. Kahles and K.-V. Lehmann and L. Urban and C.
M. Soulette and Y. Shiraishi and F. Liu and Y. He and D.
Demircioğlu and N. R. Davidson and C. Calabrese and J.
Zhang and M. D. Perry and Q. Xiang and L. Greger and S. Li
and D. Liu and S. G. Stark and F. Zhang and S. B. Amin and
P. Bailey and A. Chateigner and I. Cortés-Ciriano and B.
Craft and S. Erkek and M. Frenkel-Morgenstern and M. Goldman
and K. A. Hoadley and Y. Hou and M. R. Huska and E. Khurana
and H. Kilpinen and J. O. Korbel and F. C. Lamaze and C. Li
and X. Li and X. Li and X. Liu and M. G. Marin and J.
Markowski and T. Nandi and M. M. Nielsen and A. I. Ojesina
and Q. Pan-Hammarström and P. J. Park and C. S. Pedamallu
and J. S. Pedersen and R. Siebert and H. Su and P. Tan and
B. T. Teh and J. Wang and S. M. Waszak and H. Xiong and S.
Yakneen and C. Ye and C. Yung and X. Zhang and L. Zheng and
J. Zhu and S. Zhu and P. Awadalla and C. J. Creighton and M.
Meyerson and B. F. F. Ouellette and K. Wu and H. Yang and J.
Göke and R. F. Schwarz and O. Stegle$^*$ and Z. Zhang and
A. Brazma and G. Rätsch and A. N. Brooks},
collaboration = {P. T. C. Group and P. T. W. Group and P. Consortium},
title = {{G}enomic basis for {RNA} alterations in cancer.},
journal = {Nature},
volume = {578},
number = {7793},
issn = {1476-4687},
address = {London [u.a.]},
publisher = {Nature Publ. Group52462},
reportid = {DKFZ-2020-00343},
pages = {129 - 136},
year = {2020},
abstract = {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.},
cin = {B080 / B240 / B370 / B330 / HD01 / B060 / B360 / BE01 /
B062 / B066 / B063 / W190 / B260 / W610 / B087},
ddc = {500},
cid = {I:(DE-He78)B080-20160331 / I:(DE-He78)B240-20160331 /
I:(DE-He78)B370-20160331 / I:(DE-He78)B330-20160331 /
I:(DE-He78)HD01-20160331 / I:(DE-He78)B060-20160331 /
I:(DE-He78)B360-20160331 / I:(DE-He78)BE01-20160331 /
I:(DE-He78)B062-20160331 / I:(DE-He78)B066-20160331 /
I:(DE-He78)B063-20160331 / I:(DE-He78)W190-20160331 /
I:(DE-He78)B260-20160331 / I:(DE-He78)W610-20160331 /
I:(DE-He78)B087-20160331},
pnm = {312 - Functional and structural genomics (POF3-312)},
pid = {G:(DE-HGF)POF3-312},
typ = {PUB:(DE-HGF)16},
pubmed = {pmid:32025019},
doi = {10.1038/s41586-020-1970-0},
url = {https://inrepo02.dkfz.de/record/153599},
}
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