A germline variant in the TP53 polyadenylation signal confers cancer susceptibility

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Abstract

To identify new risk variants for cutaneous basal cell carcinoma, we performed a genome-wide association study of 16 million SNPs identified through whole-genome sequencing of 457 Icelanders. We imputed genotypes for 41,675 Illumina SNP chip-typed Icelanders and their relatives. In the discovery phase, the strongest signal came from rs78378222[C] (odds ratio (OR) = 2.36, P = 5.2 × 10−17), which has a frequency of 0.0192 in the Icelandic population. We then confirmed this association in non-Icelandic samples (OR = 1.75, P = 0.0060; overall OR = 2.16, P = 2.2 × 10−20). rs78378222 is in the 3′ untranslated region of TP53 and changes the AATAAA polyadenylation signal to AATACA, resulting in impaired 3′-end processing of TP53 mRNA. Investigation of other tumor types identified associations of this SNP with prostate cancer (OR = 1.44, P = 2.4 × 10−6), glioma (OR = 2.35, P = 1.0 × 10−5) and colorectal adenoma (OR = 1.39, P = 1.6 × 10−4). However, we observed no effect for breast cancer, a common Li-Fraumeni syndrome tumor (OR = 1.06, P = 0.57, 95% confidence interval 0.88–1.27).

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Figure 1: Overview of single-point SNP association data obtained from genomic sequencing in the 17p13 region covered by haplotypes A6 and A8.

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Acknowledgements

The work at deCODE genetics was funded in part by contract number 202059 (PROMARK) from the 7th Framework Program of the European Union. The Danish study 'Diet, Cancer and Health' was supported by grants from the Danish Cancer Society and 'Europe against cancer': European Prospective Investigation into Cancer and Nutrition (EPIC). The Inter99 study 'A population-based primary prevention study on cardiovascular disease and type 2 diabetes' was initiated by T. Jørgensen (principal investigator), K. Borch-Johnsen (co-principal investigator), H. Ibsen and T.F. Thomsen. The steering committee comprises the former two individuals and C. Pisinger. The establishment of the cohort was financially supported by research grants from the Danish Research Council, The Danish Centre for Health Technology Assessment, Novo Nordisk Inc., Research Foundation of Copenhagen County, the Ministry of Internal Affairs and Health, The Danish Heart Foundation, The Danish Pharmaceutical Association, The Augustinus Foundation, The Ib Henriksen Foundation and the Becket Foundation. The University of California, San Francisco (UCSF) Adult Glioma Study also acknowledges the people who have made substantial contributions to subject recruitment, specimen processing, pathology review and data analysis, including L.S. McCoy, I. Smirnov, J.S. Patoka, M.D. Prados, S.M. Chang and M.S. Berger (Department of Neurological Surgery, UCSF), J.L. Wiemels (Department of Epidemiology and Biostatistics, UCSF) and T. Tihan (Department of Pathology, UCSF). Work at the University of California, San Francisco has been supported by US National Institutes of Health (NIH) grants R01CA52689 and UCSF Brain Tumor SPORE, P50CA097257, as well as by grants from the National Brain Tumor Foundation, the UCSF Lewis Chair in Brain Tumor Research and by donations from families and friends of J. Berardi, H. Glaser, E. Olsen, R.E. Cooper and W. Martinusen. Work at the Mayo Clinic has been supported by the Mayo Clinic Brain Tumor SPORE (NIH P50 CA108961), the Mayo Clinic Comprehensive Cancer Center (NIH P30 CA15083) and an American Recovery and Reinvestment Act (ARRA) Recovery grant (NIH NS068222). Members of the Swedish Low-risk Colorectal Cancer Study Group are: D. Edler, Karolinska Universitetssjukhuset, Solna, Stockholm, Sweden; C. Lenander, Mag-tarm-centrum, Ersta sjukhus, Stockholm, Sweden; J. Dalén, St Görans sjukhus, Stockholm, Sweden; F. Hjern, Danderyds sjukhus, Danderyd, Sweden; N. Lundqvist, Norrtälje sjukhus, Norrtälje, Sweden; U. Lindforss, Södertälje sjukhus, Södertälje, Sweden; L. Påhlman, Akademiska sjukhuset, Uppsala, Sweden; K. Smedh, Centrallasarettet, Västerås, Sweden; A. Törnqvist, Centralsjukhuset, Karlstad, Sweden; J. Holm, Länssjukhuset Gävle-Sandviken, Gävle. Sweden; M. Janson, Karolinska Universitetssjukhuset, Huddinge, Huddinge, Sweden; M. Andersson, Universitetssjukhuset, Örebro, Sweden; S. Ekelund, Södersjukhuset, Stockholm, Sweden; and E. Olsson, Mälarsjukhuset, Eskilstuna, Sweden. Work on the US Prostate Cancer sample set was supported in part by the Urological Research Foundation, Prostate SPORE grant (P50 CA90386-05S2) and the Robert H. Lurie Comprehensive Cancer Center grant (P30 CA60553). For the UK Prostate Cancer sample set, the UK Department of Health funded the ProtecT study through the National Institute for Health Research (NIHR) Health Technology Assessment programme (projects 96/20/06, 96/20/99). We acknowledge the contribution of all members of the ProtecT study research group. We acknowledge the support of the NIHR Cambridge Biomedical Research Centre and the National Cancer Research Institute (ProMPT) Prostate Cancer Collaborative. The views and opinions expressed herein are those of the authors and do not necessarily reflect those of the UK Department of Health. Sample collection in Romania was supported in part by the Romanian National Council For Scientific Research (CNCSIS-UEFISCSU), grant PNII-IDEI 1184/2008. In Spain, J.I.M. is funded by Red Tematica de Investigacion Cooperative en Cancer RD06/0020/1054.

Author information

The study was designed and the results were interpreted by S.N.S., P.S., G.M., D.F.G., O.T.M., J.H.O., A.K., U.T., T. Rafnar and K.S. Subject ascertainment and recruitment was carried out by S.N.S., J.G., B.S., K.T., R.R., K.R.B., B.A.N., A.T., K.O., P.R., E.G., K.K., K.H., C.C., V.F., P.G., S.N., F.F., M.D.G.-P., E.S., A.P., A.D.J., A.G., F.R., D.P., V. Soriano, C.R., K.K.A., M.M.v.R., R.G.H.M.C., I.M.v.O., D.-J.v.S., J.A.S., W.H.M.P., B.T.H., J.L.D., F.C.H., D.B., O.C., M.J., I.E.C., V.C., P.B., I.N.M., D.E.D., A.C., D.M., S.K., B.A.A., E.J., R.B.B., G.V.E., F.S., P.H.M., T.S., T.V., O.T.J., H.S., T. Jonsson, J.G.J., L.T., T. Rice, H.M.H., Y.X., D.H.L., B.P.O., M.L.K., P.A.D., V. Steinthorsdottir, A.L., R.S.S., T.O.K., K.B., T. Jørgensen, D.R.W., T.H., O.P., V.J., D.E.N., W.J.C., M.W., J.W., R.B.J., E.N., U.V., L.A.K., R.K., J.I.M., J.H.O., U.T. and T. Rafnar. The sequencing, genotyping and expression analysis was carried out by S.N.S., A.J., J.G., O.T.M., H.J., H.T.H., A.S. and U.T. The statistical and bioinformatics analysis was carried out by S.N.S., P.S., G.M., D.F.G., S.A.G., G.T. and A.K. S.N.S., P.S., D.F.G., T. Rafnar and K.S. drafted the manuscript. All authors contributed to the final version of the paper. Principal collaborators for the case-control population samples were: S.K. (Colorectal Adenoma), G.V.E. (Iceland Prostate), V.J. (Romania Prostate), D.E.N. (UK Prostate), W.J.C. (US Prostate), M.W. (US UCSF Glioma), R.B.J. (US Mayo Clinic Glioma), E.J. and J.I.M. (Spain BCC and Prostate), U.V. and O.P. (Denmark BCC), L.A.K. (Netherlands Prostate), R.K. (Eastern Europe BCC) and J.H.O. (Iceland BCC).

Correspondence to Simon N Stacey or Kari Stefansson.

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deCODE Genetics is a private biotechnology company that markets genetic tests.

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A full list of members is provided in the Acknowledgements Section.

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Supplementary Figures 1–3, Supplementary Tables 1–6 and Supplementary Note. (PDF 2304 kb)

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