
@article {80107,
	title = {Analyses of non-coding somatic drivers in 2,658~cancer whole genomes.},
	journal = {Nature},
	volume = {578},
	year = {2020},
	month = {2020 02},
	pages = {102-111},
	abstract = {<p>The discovery of drivers of cancer has traditionally focused on protein-coding genes. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658\&nbsp;genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers, raise doubts about others and identify novel candidates, including point mutations in the 5{\textquoteright} region of TP53, in the 3{\textquoteright} untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although\&nbsp;point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.</p>
},
	keywords = {Databases, Genetic, DNA Breaks, Gene Expression Regulation, Neoplastic, Genome, Human, Genome-Wide Association Study, Humans, INDEL Mutation, Mutation, Neoplasms},
	issn = {1476-4687},
	doi = {10.1038/s41586-020-1965-x},
	author = {Rheinbay, Esther and Nielsen, Morten Muhlig and Abascal, Federico and Wala, Jeremiah A and Shapira, Ofer and Tiao, Grace and Hornsh{\o}j, Henrik and Hess, Julian M and Juul, Randi Istrup and Lin, Ziao and Feuerbach, Lars and Sabarinathan, Radhakrishnan and Madsen, Tobias and Kim, Jaegil and Mularoni, Loris and Shuai, Shimin and Lanz{\'o}s, Andr{\'e}s and Herrmann, Carl and Maruvka, Yosef E and Shen, Ciyue and Amin, Samirkumar B and Bandopadhayay, Pratiti and Bertl, Johanna and Boroevich, Keith A and Busanovich, John and Carlevaro-Fita, Joana and Chakravarty, Dimple and Chan, Calvin Wing Yiu and Craft, David and Dhingra, Priyanka and Diamanti, Klev and Fonseca, Nuno A and Gonzalez-Perez, Abel and Guo, Qianyun and Hamilton, Mark P and Haradhvala, Nicholas J and Hong, Chen and Isaev, Keren and Johnson, Todd A and Juul, Malene and Kahles, Andre and Kahraman, Abdullah and Kim, Youngwook and Komorowski, Jan and Kumar, Kiran and Kumar, Sushant and Lee, Donghoon and Lehmann, Kjong-Van and Li, Yilong and Liu, Eric Minwei and Lochovsky, Lucas and Park, Keunchil and Pich, Oriol and Roberts, Nicola D and Saksena, Gordon and Schumacher, Steven E and Sidiropoulos, Nikos and Sieverling, Lina and Sinnott-Armstrong, Nasa and Stewart, Chip and Tamborero, David and Tubio, Jose M C and Umer, Husen M and Uusk{\"u}la-Reimand, Liis and Wadelius, Claes and Wadi, Lina and Yao, Xiaotong and Zhang, Cheng-Zhong and Zhang, Jing and Haber, James E and Hobolth, Asger and Imielinski, Marcin and Kellis, Manolis and Lawrence, Michael S and von Mering, Christian and Nakagawa, Hidewaki and Raphael, Benjamin J and Rubin, Mark A and Sander, Chris and Stein, Lincoln D and Stuart, Joshua M and Tsunoda, Tatsuhiko and Wheeler, David A and Johnson, Rory and Reimand, J{\"u}ri and Gerstein, Mark and Khurana, Ekta and Campbell, Peter J and Lopez-Bigas, Nuria and Weischenfeldt, Joachim and Beroukhim, Rameen and Martincorena, I{\~n}igo and Pedersen, Jakob Skou and Getz, Gad}
}
@article {87674,
	title = {Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.},
	journal = {Commun Biol},
	volume = {3},
	year = {2020},
	month = {2020 02 05},
	pages = {56},
	abstract = {<p>Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive tumorigenesis, and whether such functions could be conserved during evolution. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we introduce the Cancer LncRNA Census (CLC), a compilation of 122 GENCODE lncRNAs with causal roles in cancer phenotypes. In contrast to existing databases, CLC requires strong functional or genetic evidence. CLC genes are enriched amongst driver genes predicted from somatic mutations, and display characteristic genomic features. Strikingly, CLC genes are enriched for driver mutations from unbiased, genome-wide transposon-mutagenesis screens in mice. We identified 10 tumour-causing mutations in orthologues of 8 lncRNAs, including LINC-PINT and NEAT1, but not MALAT1. Thus CLC represents a dataset of high-confidence cancer lncRNAs. Mutagenesis maps are a novel means for identifying deeply-conserved roles of lncRNAs in tumorigenesis.</p>
},
	issn = {2399-3642},
	doi = {10.1038/s42003-019-0741-7},
	author = {Carlevaro-Fita, Joana and Lanz{\'o}s, Andr{\'e}s and Feuerbach, Lars and Hong, Chen and Mas-Ponte, David and Pedersen, Jakob Skou and Johnson, Rory}
}
