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GENOMES & DISEASE

'We investigate the patterns and mechanisms of genomic variation in disease'


2019


Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet

Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M and Paramio JM

Front. Genet. 10:1125.

doi: 10.3389/fgene.2019.01125


Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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

Nature Genetics (Expected publication: December 2019)


On the discovery of somatic driver events in >2,500 whole cancer genomes

Esther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A. Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M. Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, Radhakrishnan Sabarinathan, Tobias Madsen, Jaegil Kim, Loris Mularoni, Shimin Shuai, Andrés Lanzós, Carl Herrmann, Yosef E. Maruvka, Ciyue Shen, Samirkumar B. Amin, Pratiti Bandopadhayay, Johanna Bertl, Keith A. Boroevich, John Busanovich, Joana Carlevaro-Fita, Dimple Chakravarty, Calvin W.Y. Chan, David Craft, Priyanka Dhingra, Klev Diamanti, Nuno A. Fonseca, Abel Gonzalez-Perez, Qianyun Guo, Mark P. Hamilton, Nicholas J. Haradhvala, Chen Hong, Keren Isaev, Todd A. Johnson, Malene Juul, Andre Kahles, Abdullah Kahraman, Youngwook Kim, Jan Komorowski, Kiran Kumar, Sushant Kumar, Donghoon Lee, Kjong-Van Lehmann, Yilong Li, Eric Minwei Liu, Lucas Lochovsky, Keunchil Park, Oriol Pich, Nicola D. Roberts, Gordon Saksena, Steven E. Schumacher, Nikos Sidiropoulos, Lina Sieverling, Nicholas A. Sinnott-Armstrong, Chip Stewart, David Tamborero, Jose Tubio, Husen M. Umer, Liis Uusküla-Reimand, Claes Wadelius, Lina Wadi, Xiaotong Yao, ChengZhong Zhang, Jing Zhang, James E. Haber, Asger Hobolth, Marcin Imielinski, Manolis Kellis, Michael S. Lawrence, Christian von Mering, Hidewaki Nakagawa, Ben Raphael, Mark A. Rubin, Chris Sander, Lincoln Stein, Josh Stuart, Tatsuhiko Tsunoda, David A. Wheeler, Rory Johnson, Jüri Reimand, Mark B. Gerstein, Ekta Khurana, Peter J. Campbell, Núria López-Bigas, PCAWG Structural Variations Working Group, PCAWG Drivers and Functional Interpretation Working Group, Joachim Weischenfeldt, Rameen Beroukhim, Iñigo Martincorena, Jakob Skou Pedersen, Gad Getz

Nature (Expected publication: December 2019)


Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network

Nature (Expected publication: December 2019)


Genomic landscape and chronological reconstruction of driver events in multiple myeloma

Francesco Maura, Niccoló Bolli, Nicos Angelopoulos, Kevin Dawson, Daniel Leongamornlert, Inigo Martincorena, Thomas Mitchell, Anthony Fullam, Santiago Gonzalez, Raphael Szalat, Federico Abascal, Bernardo Rodriguez-Martin, Mehmet Samur, Dominik Glodzik, Marco Roncador, Mariateresa Fulciniti, Yu-Tzu Tai, Stephane Minvielle, Florence Magrangeas, Philippe Moreau, Paolo Corradini, Kenneth Anderson, Jose Tubio, David Wedge, Moritz Gerstung, Herve Avet-Loiseau, Nikhil Munshi, and Peter Campbell

Nature Communications, 10: 3835

doi: https://doi.org/10.1038/s41467-019-11680-1


Inhibition of a G9a/DNMT network triggers immune-mediated bladder cancer regression

Cristina Segovia *, Edurne San José-Enériz *, Ester Munera-Maravilla *, Mónica Martínez-Fernández, Leire Garate, Estíbaliz Miranda, Amaia Vilas-Zornoza, Iris Lodewijk, Carolina Rubio, Carmen Segrelles, Luis Vitores Valcárcel, Obdulia Rabal, Noelia Casares, Alejandra Bernardini, Cristian Suarez-Cabrera, Fernando F. López-Calderón, Puri Fortes, José A. Casado, Marta Dueñas, Felipe Villacampa, Juan José Lasarte, Félix Guerrero-Ramos, Guillermo de Velasco, Julen Oyarzabal, Daniel Castellano, Xabier Agirre, Felipe Prósper & Jesús M. Paramio. *Equal contributions

Nature Medicine volume 25, pages1073–1081 (2019)


Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status

Marta Dueñas, Andrés Pérez-Figueroa, Carla Oliveira, Cristian Suárez-Cabrera, Abel Sousa, Patricia Oliveira, Felipe Villacampa, Jesús M. Paramio & Mónica Martínez-Fernández

Scientific Reports volume 9, Article number: 10362 (2019)

DOI: 10.1038/s41598-019-46652-4


Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR

Cell, 176:1282-1294.

doi: 10.1016/j.cell.2019.02.012


2018


An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.

Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U.

Sci Rep. 2018 Sep 10;8(1):13537.

doi: 10.1038/s41598-018-31659-0.


The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.

Stammnitz MR, Coorens THH, Gori KC, Hayes D, Fu B, Wang J, Martin-Herranz DE, Alexandrov LB, Baez-Ortega A, Barthorpe S, Beck A, Giordano F, Knowles GW, Kwon YM, Hall G, Price S, Pye RJ, Tubio JMC, Siddle HVT, Sohal SS, Woods GM, McDermott U, Yang F, Garnett MJ, Ning Z, Murchison EP.

Cancer Cell. 2018 Apr 9;33(4):607-619.e15

doi: 10.1016/j.ccell.2018.03.013.


Genomic patterns of progression in smoldering multiple myeloma.

Bolli N, Maura F, Minvielle S, Gloznik D, Szalat R, Fullam A, Martincorena I, Dawson KJ, Samur MK, Zamora J, Tarpey P, Davies H, Fulciniti M, Shammas MA, Tai YT, Magrangeas F, Moreau P, Corradini P, Anderson K, Alexandrov L, Wedge DC, Avet-Loiseau H, Campbell P, Munshi N.

Nat Commun. 2018 Aug 22;9(1):3363.

doi: 10.1038/s41467-018-05058-y.


Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C; CAMCAP Study Group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C; TCGA Consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA,.

Nat Genet. 218 May;5(5):682-692.

doi: 1.138/s41588-18-86-z.

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