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Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor

Abstract

Genome-wide association studies (GWAS) have transformed understanding of susceptibility to testicular germ cell tumors (TGCTs), but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totaling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, roughly doubling the number of known TGCT risk loci to 44. By performing in situ Hi-C in TGCT cells, we provide evidence for a network of physical interactions among all 44 TGCT risk SNPs and candidate causal genes. Our findings implicate widespread disruption of developmental transcriptional regulators as a basis of TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis1. Defective microtubule assembly and dysregulation of KIT–MAPK signaling also feature as recurrently disrupted pathways. Our findings support a polygenic model of risk and provide insight into the biological basis of TGCT.

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Figure 1
Figure 2: Circos plot of integrated functional analysis for all 44 TGCT risk loci.
Figure 3: Regional plots of three new TGCT loci.

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Acknowledgements

We thank the subjects with TGCT and the clinicians involved in their care for participation in this study. We thank the patients and all clinicians forming part of the UK Testicular Cancer Collaboration (UKTCC) for their participation in this study. This study would not have been possible without the contributions of M.K. Bolla (Breast Cancer Association Consortium (BCAC)), Q. Wang (BCAC), K. Michailido (BCAC), J. Dennis (BCAC), P. Hall (Collaborative Oncological Gene-environment Study (COGS)); D.F. Easton (BCAC), A. Berchuck (Ovarian Cancer Association Consortium), R. Eeles (PRACTICAL), G. Chenevix-Trench (The Consortium of Investigators of Modifiers of BRCA1/2), J. Dennis, P. Pharoah, A. Dunning, K. Muir, J. Peto, A. Lee and E. Dicks. We also thank the following for their contributions to this project: J. Simard, P. Kraft, C. Luccarini and the staff of the Centre for Genetic Epidemiology Laboratory; and K.F. Doheny and the staff of the Center for Inherited Disease Research (CIDR) genotyping facility. The results published here are based in part on data generated by the TCGA Research Network. This study makes use of data generated by the Wellcome Trust Case Control Consortium 2 (WTCCC2). We acknowledge the contribution of E. Rapley and M. Stratton to the generation of previously published UK GWAS case data. We thank all the individuals who took part in these studies and all the researchers, clinicians, technicians and administrative staff who have enabled this work to be carried out. We acknowledge National Health Service funding to the National Institute for Health Research Biomedical Research Centre. We thank the UK Genetics of Prostate Cancer Study (UKGPCS) study teams for the recruitment of the UKGPCS controls. Genotyping of the OncoArray was funded by the US National Institutes of Health (NIH) (U19 CA 148537 for Elucidating Loci Involved in Prostate cancer Susceptibility (ELLIPSE) project and X01HG007492 to the Center for Inherited Disease Research (CIDR) under contract number HHSN268201200008I). Additional analytical support was provided by NIH NCI U01 CA188392. The PRACTICAL consortium was supported by Cancer Research UK Grants C5047/A7357, C1287/A10118, C1287/A16563, C5047/A3354, C5047/A10692 and C16913/A6135; the European Commission's Seventh Framework Programme grant agreement 223175 (HEALTH-F2-2009-223175) (D.F.E., R.E. and Z.K.-J.); and the NIH Cancer Post-Cancer GWAS initiative grant 1 U19 CA 148537-01 (the GAME-ON initiative). We thank the following for funding support: the Institute of Cancer Research and the Everyman Campaign, the Prostate Cancer Research Foundation, Prostate Research Campaign UK (now Prostate Action), the Orchid Cancer Appeal, the National Cancer Research Network UK and the National Cancer Research Institute (NCRI) UK. We are grateful for NIHR funding to the Biomedical Research Centre at the Institute of Cancer Research and the Royal Marsden NHS Foundation Trust. We acknowledge funding from the Swedish Cancer Society (CAN2011/484 and CAN2012/823), the Norwegian Cancer Society (grants 418975-71081-PR-2006-0387 and PK01-2007-0375) and the Nordic Cancer Union (grant S-12/07). This study was supported by the Movember Foundation and the Institute of Cancer Research. K.L. is supported by a PhD fellowship from Cancer Research UK. R.S.H. and P.B. are supported by Cancer Research UK (C1298/A8362 Bobby Moore Fund for Cancer Research UK).

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C.T., K.L. and R.S.H. designed the study. Case samples were recruited by A.R., R.A.H. and through UKTCC. R.E., A.M.D., K.M., J.P., Z.K.-J., N.P. and D.F.E. supplied OncoArray control data. N.O. administrated genotyping of OncoArray case samples. D.D. coordinated all case sample administration and tracking. K.L., M.L., A.H. and P.B. prepared samples for genotyping experiments. K.L., M.L., G.O., C.L., K.F. and I.A. conducted all Promoter Hi-C and 3C laboratory experiments. C.T., R.S.H. and K.L. designed bioinformatics and statistical analyses. K.L., G.M., C.L. and M.L. conducted all Promoter Hi-C and 3C data analysis. K.L. and P.J.L. conducted transcription factor enrichment analysis. K.L., C.L. and M.L. performed all other bioinformatics and statistical analyses. R.K., T.B.H., W.K., T.G. and F.W. provided Scandinavian GWAS data. K.L. drafted the manuscript with assistance from C.T., R.S.H., M.L., J.S., J.N. and D.T.B. All authors reviewed and contributed to the manuscript.

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Correspondence to Clare Turnbull.

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A list of members appears in the Supplementary Note.

A list of members appears in the Supplementary Note.

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Litchfield, K., Levy, M., Orlando, G. et al. Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor. Nat Genet 49, 1133–1140 (2017). https://doi.org/10.1038/ng.3896

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