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Items: 1 to 20 of 103

1.

The evolutionary history of 2,658 cancers.

Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD; PCAWG Evolution & Heterogeneity Working Group, Spellman PT, Wedge DC, Van Loo P; PCAWG Consortium.

Nature. 2020 Feb;578(7793):122-128. doi: 10.1038/s41586-019-1907-7. Epub 2020 Feb 6.

2.

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.

Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar A; PCAWG Evolution and Heterogeneity Working Group, Morris Q; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):731. doi: 10.1038/s41467-020-14352-7.

3.

Pan-cancer analysis of whole genomes.

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.

Nature. 2020 Feb;578(7793):82-93. doi: 10.1038/s41586-020-1969-6. Epub 2020 Feb 5.

4.

Divergent mutational processes distinguish hypoxic and normoxic tumours.

Bhandari V, Li CH, Bristow RG, Boutros PC; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):737. doi: 10.1038/s41467-019-14052-x.

5.

Patterns of somatic structural variation in human cancer genomes.

Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Campbell PJ; PCAWG Consortium.

Nature. 2020 Feb;578(7793):112-121. doi: 10.1038/s41586-019-1913-9. Epub 2020 Feb 5.

6.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing.

Cortés-Ciriano I, Lee JJ, Xi R, Jain D, Jung YL, Yang L, Gordenin D, Klimczak LJ, Zhang CZ, Pellman DS; PCAWG Structural Variation Working Group, Park PJ; PCAWG Consortium.

Nat Genet. 2020 Mar;52(3):331-341. doi: 10.1038/s41588-019-0576-7. Epub 2020 Feb 5.

7.

Combined burden and functional impact tests for cancer driver discovery using DriverPower.

Shuai S; PCAWG Drivers and Functional Interpretation Working Group, Gallinger S, Stein L; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):734. doi: 10.1038/s41467-019-13929-1.

8.

Genomic basis for RNA alterations in cancer.

PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium.

Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5.

9.

The repertoire of mutational signatures in human cancer.

Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V; PCAWG Mutational Signatures Working Group, Getz G, Rozen SG, Stratton MR; PCAWG Consortium.

Nature. 2020 Feb;578(7793):94-101. doi: 10.1038/s41586-020-1943-3. Epub 2020 Feb 5.

10.

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Structural Variation Working Group, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G; PCAWG Consortium.

Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5.

11.

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):728. doi: 10.1038/s41467-019-13825-8.

12.

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.

Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA; PCAWG Structural Variation Working Group; PCAWG Consortium.

Nat Genet. 2020 Mar;52(3):294-305. doi: 10.1038/s41588-019-0564-y. Epub 2020 Feb 5.

13.

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort.

Waszak SM, Northcott PA, Buchhalter I, Robinson GW, Sutter C, Groebner S, Grund KB, Brugières L, Jones DTW, Pajtler KW, Morrissy AS, Kool M, Sturm D, Chavez L, Ernst A, Brabetz S, Hain M, Zichner T, Segura-Wang M, Weischenfeldt J, Rausch T, Mardin BR, Zhou X, Baciu C, Lawerenz C, Chan JA, Varlet P, Guerrini-Rousseau L, Fults DW, Grajkowska W, Hauser P, Jabado N, Ra YS, Zitterbart K, Shringarpure SS, De La Vega FM, Bustamante CD, Ng HK, Perry A, MacDonald TJ, Hernáiz Driever P, Bendel AE, Bowers DC, McCowage G, Chintagumpala MM, Cohn R, Hassall T, Fleischhack G, Eggen T, Wesenberg F, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Kjaerheim K, Monoranu CM, Archer TC, Duke E, Pomeroy SL, Shelagh R, Frank S, Sumerauer D, Scheurlen W, Ryzhova MV, Milde T, Kratz CP, Samuel D, Zhang J, Solomon DA, Marra M, Eils R, Bartram CR, von Hoff K, Rutkowski S, Ramaswamy V, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Malkin D, Gajjar A, Korbel JO, Pfister SM.

Lancet Oncol. 2018 Jun;19(6):785-798. doi: 10.1016/S1470-2045(18)30242-0. Epub 2018 May 9.

14.

Pathway and network analysis of more than 2500 whole cancer genomes.

Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group, Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0.

15.

Genomic footprints of activated telomere maintenance mechanisms in cancer.

Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M; PCAWG-Structural Variation Working Group, Brors B, Rippe K, Jones DTW, Feuerbach L; PCAWG Consortium.

Nat Commun. 2020 Feb 5;11(1):733. doi: 10.1038/s41467-019-13824-9.

16.

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A.

BMC Bioinformatics. 2014 Sep 19;15:308. doi: 10.1186/1471-2105-15-308.

17.

Identification of coding and non-coding mutational hotspots in cancer genomes.

Piraino SW, Furney SJ.

BMC Genomics. 2017 Jan 5;18(1):17. doi: 10.1186/s12864-016-3420-9.

18.

Estimating growth patterns and driver effects in tumor evolution from individual samples.

Salichos L, Meyerson W, Warrell J, Gerstein M.

Nat Commun. 2020 Feb 5;11(1):732. doi: 10.1038/s41467-020-14407-9.

19.

Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations.

Poulos RC, Wong YT, Ryan R, Pang H, Wong JWH.

PLoS Genet. 2018 Nov 9;14(11):e1007779. doi: 10.1371/journal.pgen.1007779. eCollection 2018 Nov.

20.

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.

Temko D, Van Gool IC, Rayner E, Glaire M, Makino S, Brown M, Chegwidden L, Palles C, Depreeuw J, Beggs A, Stathopoulou C, Mason J, Baker AM, Williams M, Cerundolo V, Rei M, Taylor JC, Schuh A, Ahmed A, Amant F, Lambrechts D, Smit VT, Bosse T, Graham TA, Church DN, Tomlinson I.

J Pathol. 2018 Jul;245(3):283-296. doi: 10.1002/path.5081. Epub 2018 Apr 30.

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