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This study was supported by the Ministerio de Economía y Competitividad, Grant n. SAF2015-67633-R ,and PI16/00420 which are part of Plan Nacional de I+D+I and are co-financed by the European Regional Development Fund (FEDER-"Una manera de hacer Europa") and the CERCA program from Generalitat Catalunya. European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement n. 306240; Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR1009, and Departament de Salut (SLT002-16-00350), Instituto de Salud Carlos III (ISCIII) International Cancer Genome Consortium for Chronic Lymphocytic Leukemia (ICGC-CLL Genome Project), and project PM15/00007, which is part of Plan Nacional de I+D+I and are co-financed by FEDER. NG is a recipient of a predoctoral fellowship from Agaur and EC is an Academia Researcher of the "Institució Catalana de Recerca i Estudis Avançats" (ICREA) of the Generalitat de Catalunya. ; Giménez, N., Martínez-Trillos, A., Montraveta, A., Lopez-Guerra, M., Rosich, L., Nadeu, F., Valero, J.G., Aymerich, M., Magnano, L., Rozman, M., Matutes, E., Delgado, J., Baumann, T., Gine, E., González, M., Alcoceba, M., Terol, M.J., Navarro, B., Colado, E., Payer, A.R., Puente, X.S., López-Otín, C., Lopez-Guillermo, A., Campo, E., Colomer, D., Villamor, N.

This work was supported by grants from Ministerio de Ciencia e Innovación-Spain, Fundación M. Botín, European Union (FP7 MicroEnviMet), Instituto de Salud Carlos III (ISCIII) and Red Temática de Investigación del Cáncer (RTICC) del ISCIII

This work was supported by the Spanish Ministry of Economy and Competitiveness, co-funded by FEDER funds - a way to build Europe - (grants SAF2016-80888-R to LValle, SAF2015-68016-R to GC and MP, and SAF2013-45836-R to XSP]; Carlos III National Health Institute [PI16/00563 to CL and CIBER-ONC]; the Government of Catalonia [Pla estrategic de recerca i innovacio en salut (PERIS) and 2014SGR338]; the Scientific Foundation Asociacion Espanola Contra el Cancer; and EU COST Action BM1206. PM holds a Juan de la Cierva postdoctoral fellowship from the Spanish Ministry of Economy and Competitiveness, and RMdV, a Dutch Cancer Society (KWF) Fellowship (KUN14-6666). ; Mur, P., De Voer, R.M., Olivera-Salguero, R., Rodríguez-Perales, S., Pons, T., Setién, F., Aiza, G., Valdés-Mas, R., Bertini, A., Pineda, M., Vreede, L., Navarro, M., Iglesias, S., González, S., Brunet, J., Valencia, A., Esteller, M., Lázaro, C., Kops, G.J.P.L., Urioste, M., Puente, X.S., Capellá, G., Valle, L.

Funding: European Union (CancerDegradome-FP6 and FP7); Ministerio de Ciencia e Innovación-Spain; Fundació M Botín; Fundación Lilly; Obra Social Cajastur (to the Instituto Universitario de Oncología). Funding for open access charge: Ministerio de Ciencia e Innovación-Spain.

This work was supported by grants from the Asociacion Espanola Contra el Cancer (AECC, Hereditary Cancer coordinated group, 2010; AECC Barcelona Ovarian Cancer 2015), the Generalitat de Catalunya (SGR 2014-364 and 2017-449), the Ministerio de Economia y Competitividad (SAF2013-45836-R and SAF2017-87811R), European Regional Development Fund (ERDF/FEDER "Una manera de hacer Europa"), the Instituto de Salud Carlos III (PIE13/00022-ONCOPROFILE, FIS PI13/01339, PI15/00854, PI16/01898 and RTICC RD12/0036/0008), and Fundacion Mutua Madrilena (AP150932014). A.D-N. is supported by the Department of Education of the Basque Government (PRE-2017-1-0100). ; Ruiz de Garibay, G., Mateo, F., Stradella, A., Valdés-Mas, R., Palomero, L., Serra-Musach, J., Puente, D.A., Dıáz-Navarro, A., Vargas-Parra, G., Tornero, E., Morilla, I., Farré, L., Martinez-Iniesta, M., Herranz, C., McCormack, E., Vidal, A., Petit, A., Soler, T., Lázaro, C., Puente, X.S., Villanueva, A., Pujana, M.A.

This work was funded by the Spanish Ministry of Economy and Competitiveness (SAF2012-38885 [LV], SAF2012-31881 [JS], SAF2013-45836R [XSP] and SAF2012-33636 [GC] and Ramón y Cajal Contract to LV);the Carlos III Health Institute (PI11-01439 [VM], PI13/00285 [CL] and fellowship to NS); CIBERESP (CB07/02/2005 [VM]); RTICC (RD12/0036/0031,RD12/0036/0006, RD12/0036/0008 and RD12/0036/0067); the EU FP7 project ASSET (grant agreement 259348 to AV); L'Oréal-UNESCO "For Women in Science"; the Scientific Foundation Asociación Española Contra el Cáncer; and the Government of Catalonia (2014SGR338 [GC] and 2009SGR0489 [JS]). JS is also funded by ICREA Academia and the European Regional Development FEDER Funds. CIBERER is an initiative of the Carlos III Health Institute ; Seguí, N., Mina, L.B., Lázaro, C., Sanz-Pamplona, R., Pons, T., Navarro, M., Bellido, F., López-Doriga, A., Valdés-Mas, R., Pineda, M., Guinó, E., Vidal, A., Soto, J.L., Caldés, T., Durán, M., Urioste, M., Rueda, D., Brunet, J., Balbín, M., Blay, P., Iglesias, S., Garré, P., Lastra, E., Sánchez-Heras, A.B., Valencia, A., Moreno, V., Pujana, M.Á., Villanueva, A., Blanco, I., Capellá, G., Surrallés, J., Puente, X.S., Valle, L.

This work has been supported by grants from Ministerio de Ciencia e Innovación-Spain, Fundación M. Botín, and European Union (FP7 MicroEnviMet). The Instituto Universitario de Oncología is supported by Obra Social Cajastur and Acción Transversal del Cáncer-RTICC.

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research. ; We thank all the members of the Boutros lab for insightful discussions. This study was conducted with the support of the Ontario Institute for Cancer Research to P.C.B. through funding provided by the Government of Ontario. This work was supported by the Discovery Frontiers: Advancing Big Data Science in Genomics Research program, which is jointly funded by the Natural Sciences and Engineering Research Council (NSERC) of Canada, the Canadian Institutes of Health Research (CIHR), Genome Canada and the Canada Foundation for Innovation (CFI). P.C.B. was supported by a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award. This work was supported by an NSERC Discovery grant and by Canadian Institutes of Health Research, grant #SVB-145586, to P.C.B. This work was supported by the NIH/NCI under award number P30CA016042 and an operating grant from the National Cancer Institute Early Detection Research Network (1U01CA214194-01). We acknowledge the contributions of the many clinical networks across ICGC and TCGA who provided samples and data to the PCAWG Consortium, and the contributions of ...

Fundación Asociación Española contra el Cáncer (AECC), FERO (EDM), Ramón Areces Foundation, Cellex Foundation, BBVA (CAIMI), the ISCIII, FIS (PI16/01278) and the Juan de la Cierva fellowship (L.E). X.S.P. is supported by Ministerio de Economía y Competitividad (MINECO) SAF2013-45836-R and CIBERONC; A.D.N. is supported by the Department of Education of the Basque Government (grant number PRE_2017_1_0100). ; Escudero, L., Llort, A., Arias, A., Diaz-Navarro, A., Martínez-Ricarte, F., Rubio-Perez, C., Mayor, R., Caratù, G., Martínez-Sáez, E., Vázquez-Méndez, É., Lesende-Rodríguez, I., Hladun, R., Gros, L., Ramón y Cajal, S., Poca, M.A., Puente, X.S., Sahuquillo, J., Gallego, S., Seoane, J.

This work has been supported by grants from Ministerio de Ciencia e Innovación-Spain, PCTI-FICYT Asturias, Fundación Centro Médico de Asturias, Fundación María Cristina Masaveu Peterson, and the European Union (FP7 Micro- EnviMet). C.L-O. is an investigator in the Botin Foundation. The Instituto Universitario de Oncología is supported by Obra Social Cajastur and Acción Transversal del Cáncer-RTICC

This work was funded by the European Union's Seventh Framework Programme through the Blueprint Consortium (grant agreement 282510), the International Cancer Genome Consortium (Chronic Lymphocytic Leukemia Genome consortium to E.C. and C.L.-O.), La Caixa Foundation (CLLEvolution-HE17–00221, to E.C. and C.L.-O.), the World Wide Cancer Research Foundation Grant No. 16–1285 (to J.I.M.-S.), the Spanish Ministerio de Economía y Competitividad (MINECO), Grant No. SAF2015-64885-R (to E.C.) and Grant No. PMP15/00007