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MOBILE GENOMES & DISEASE

'We investigate the impact of mobile DNA on disease, and the genetic mechanisms that make cancers transmissible'


2017


Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

Sebastian M. Waszak, Grace Tiao, Bin Zhu, Tobias Rausch, Francesc Muyas, Bernardo Rodriguez-Martin, Raquel Rabionet, Sergei Yakneen, Georgia Escaramis, Yilong Li, Natalie Saini, Steven A. Roberts, German M. Demidov, Esa Pitkanen, Olivier Delaneau, Jose M. Heredia-Genestar, Joachim Weischenfeldt, Suyash S. Shringarpure, Jieming Chen, Hidewaki Nakagawa, Ludmil B. Alexandrov, Oliver Drechsel, L. Jonathan Dursi, Ayellet V. Segre, Erik Garrison, Serap Erkek, Nina Habermann, Lara Urban, Ekta Khurana, Andy Cafferkey, Shuto Hayashi, Seiya Imoto, Lauri A. Aaltonen, Eva G. Alvarez, Adrian Baez-Ortega, Matthew Bailey, Mattia Bosio, Alicia L. Bruzos, Ivo Buchhalter, Carlos D. Bustamante, Claudia Calabrese, Anthony DiBiase, Mark Gerstein, Aliaksei Z. Holik, Xing Hua, Kuan-lin Huang, Ivica Letunic, Leszek J. Klimczak, Roelof Koster, Sushant Kumar, Mike McLellan, Jay Mashl, Lisa Mirabello, Steven Newhouse, Aparna Prasad, Gunnar Raetsch, Matthias Schlesner, Roland Schwarz, Pramod Sharma, Tal Shmaya, Nikos Sidiropoulos, Lei Song, Hana Susak, Tomas Tanskanen, Marta Tojo, David C. Wedge, Mark Wright, Ying Wu, Kai Ye, Venkata D. Yellapantula, Jorge Zamora, Atul J. Butte, Gad Getz, Jared Simpson, Li Ding, Tomas Marques-Bonet, Arcadi Navarro, Alvis Brazma, Peter Campbell, Stephen J. Chanock, Nilanjan Chatterjee, Oliver Stegle, Reiner Siebert, Stephan Ossowski, Olivier Harismendy, Dmitry A. Gordenin, Jose M. C. Tubio, Francisco M. De La Vega, Douglas F. Easton, Xavier Estivill, Jan Korbel, PCAWG Germline Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net

bioRxiv posted November 1, 2017

doi: https://doi.org/10.1101/208330


Selective and mechanistic sources of recurrent rearrangements across the cancer genome

Jeremiah Anthony Wala, Shapira, Yilong Li, David Craft, Steven E. Schumacher, Marcin Imielinski, James E. Haber, Nicola Roberts, Xiaotong Yao, Chip Stewart, Cheng-Zhong Zhang, Jose Tubio, Young Seok Ju, Peter Campbell, Joachim Weischenfeldt, Rameen Beroukhim, PCAWG-Structural Variation Working Group, the PCAWG Network

bioRxiv posted September 14, 2017.

doi: https://doi.org/10.1101/187609


Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jonas Demeulemeester, Young Seok Ju, Jorge Zamora, Harald Detering, Yilong Li, Gianmarco Contino, Stefan C. Dentro, Alicia L. Bruzos, Ana Dueso-Barroso, Daniel Ardeljan, Marta Tojo, Nicola D. Roberts, Miguel G. Blanco, Paul A. W. Edwards, Joachim Weischenfeldt, Martin Santamarina, Montserrat Puiggros, Zechen Chong, Ken Chen, Eunjung Alice Lee, Jeremiah A. Wala, Keiran Raine, Adam Butler, Sebastian M. Waszak, Fabio C. P. Navarro, Steven E. Schumacher, Jean Monlong, Francesco Maura, Niccolo Bolli, Guillaume Bourque, Mark Gerstein, Peter J. Park, Rameen Berroukhim, David Torrents, Jan O. Korbel, Inigo Martincorena, Rebecca C. Fitzgerald, Peter Van Loo, Haig H. Kazazian, Kathleen H. Burns, Peter J. Campbell, Jose M. C. Tubio, PCAWG Structural Variation Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Net

bioRxiv posted August 24, 2017

doi: https://doi.org/10.1101/179705

Selection of past publications


2015


Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin.

Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ
Science (New York, N.Y.) 348 880-6 2015 May 22

PUBMED: 25999502; PMC: 4471149; DOI: 10.1126/science.aaa6806


The evolutionary history of lethal metastatic prostate cancer.

Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, ICGC Prostate Group., Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS
Nature 520 353-357 2015 Apr 16

PUBMED: 25830880; DOI: 10.1038/nature14347

2014


Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, Veer LV, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ, ICGC Breast Cancer Group., ICGC Bone Cancer Group., ICGC Prostate Cancer Group.
Science (New York, N.Y.) 345 1251343 2014 Aug 1

PUBMED: 25082706; PMC: 4380235; DOI: 10.1126/science.1251343


RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia.

Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O'Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ
Nature genetics 46 116-25 2014 Feb

PUBMED: 24413735; PMC: 3960636; DOI: 10.1038/ng.2874


Transmissible (corrected) dog cancer genome reveals the origin and history of an ancient cell lineage.

Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB, Donelan EM, Marino G, Fassati A, Campbell PJ, Yang F, Burt A, Weiss RA, Stratton MR
Science (New York, N.Y.) 343 437-440 2014 Jan 24

PUBMED: 24458646; PMC: 3918581; DOI: 10.1126/science.1247167

2013


Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma.

Tarpey PS, Behjati S, Cooke SL, Van Loo P, Wedge DC, Pillay N, Marshall J, O'Meara S, Davies H, Nik-Zainal S, Beare D, Butler A, Gamble J, Hardy C, Hinton J, Jia MM, Jayakumar A, Jones D, Latimer C, Maddison M, Martin S, McLaren S, Menzies A, Mudie L, Raine K, Teague JW, Tubio JM, Halai D, Tirabosco R, Amary F, Campbell PJ, Stratton MR, Flanagan AM, Futreal PA
Nature genetics 45 923-6 2013 Aug

PUBMED: 23770606; PMC: 3743157; DOI: 10.1038/ng.2668

2011


Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia.

Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, Ramsay AJ, Beà S, Pinyol M, Martínez-Trillos A, López-Guerra M, Colomer D, Navarro A, Baumann T, Aymerich M, Rozman M, Delgado J, Giné E, Hernández JM, González-Díaz M, Puente DA, Velasco G, Freije JM, Tubío JM, Royo R, Gelpí JL, Orozco M, Pisano DG, Zamora J, Vázquez M, Valencia A, Himmelbauer H, Bayés M, Heath S, Gut M, Gut I, Estivill X, López-Guillermo A, Puente XS, Campo E, López-Otín C
Nature genetics 44 47-52 2011 Dec 11

PUBMED: 22158541; DOI: 10.1038/ng.1032


Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.

Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, Tubío JM, López C, Navarro A, Tornador C, Aymerich M, Rozman M, Hernández JM, Puente DA, Freije JM, Velasco G, Gutiérrez-Fernández A, Costa D, Carrió A, Guijarro S, Enjuanes A, Hernández L, Yagüe J, Nicolás P, Romeo-Casabona CM, Himmelbauer H, Castillo E, Dohm JC, de Sanjosé S, Piris MA, de Alava E, San Miguel J, Royo R, Gelpí JL, Torrents D, Orozco M, Pisano DG, Valencia A, Guigó R, Bayés M, Heath S, Gut M, Klatt P, Marshall J, Raine K, Stebbings LA, Futreal PA, Stratton MR, Campbell PJ, Gut I, López-Guillermo A, Estivill X, Montserrat E, López-Otín C, Campo E
Nature 475 101-5 2011 Jun 5

PUBMED: 21642962; PMC: 3322590; DOI:10.1038/nature10113


Cancer: When catastrophe strikes a cell.
Tubio JM, Estivill X
Nature 470 476-7 2011 Feb 24

PUBMED: 21350479; DOI: doi:10.1038/470476a