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Gu F, Chen TH, Pfeiffer RM, Fargnoli MC, Calista D, Ghiorzo P, Peris K, Puig S, Menin C, De Nicolo A, Rodolfo M, Pellegrini C, Pastorino L, Evangelou E, Zhang T, Hua X, DellaValle CT, Timothy Bishop D, MacGregor S, Iles MI, Law MH, Cust A, Brown KM, Stratigos AJ, Nagore E, Chanock S, Shi J, Consortium MMA, Consortium M, Landi MT. Combining common genetic variants and non-genetic risk factors to predict risk of cutaneous melanoma. Hum Mol Genet 2018; 27:4145-4156. [PMID: 30060076 PMCID: PMC6240742 DOI: 10.1093/hmg/ddy282] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/14/2018] [Accepted: 07/24/2018] [Indexed: 02/04/2023] Open
Abstract
Melanoma heritability is among the highest for cancer and single nucleotide polymorphisms (SNPs) contribute to it. To date, only SNPs that reached statistical significance in genome-wide association studies or few candidate SNPs have been included in melanoma risk prediction models. We compared four approaches for building polygenic risk scores (PRS) using 12 874 melanoma cases and 23 203 controls from Melanoma Meta-Analysis Consortium as a training set, and newly genotyped 3102 cases and 2301 controls from the MelaNostrum consortium for validation. We estimated adjusted odds ratios (ORs) for melanoma risk using traditional melanoma risk factors and the PRS with the largest area under the receiver operator characteristics curve (AUC). We estimated absolute risks combining the PRS and other risk factors, with age- and sex-specific melanoma incidence and competing mortality rates from Italy as an example. The best PRS, including 204 SNPs (AUC = 64.4%; 95% confidence interval (CI) = 63-65.8%), developed using winner's curse estimate corrections, had a per-quintile OR = 1.35 (95% CI = 1.30-1.41), corresponding to a 3.33-fold increase comparing the 5th to the 1st PRS quintile. The AUC improvement by adding the PRS was up to 7%, depending on adjusted factors and country. The 20-year absolute risk estimates based on the PRS, nevus count and pigmentation characteristics for a 60-year-old Italian man ranged from 0.5 to 11.8% (relative risk = 26.34), indicating good separation.
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Affiliation(s)
- Fangyi Gu
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting-Huei Chen
- Department of Mathematics and Statistics, Laval University, Quebec, Canada
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
| | - Ketty Peris
- Institute of Dermatology, Catholic University, Rome, Italy
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Chiara Menin
- Department of Immunology and Molecular Oncology, Veneto Institute of Oncology IOV–IRCCS, Padua, Italy
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV–IRCCS, Padua, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Curt T DellaValle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark I Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anne Cust
- Sydney School of Public Health, and Melanoma Institute Australia, The University of Sydney, Sydney, Australia
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander J Stratigos
- 1 Department of Dermatology–Venereology, National and Kapodistrian University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Pellegrini C, Law M, Iles M, Machiela M, Stratigos A, Zhang T, Brown K, Newton-Bishop J, Hayward N, Martin N, Goldstein A, Yang R, Chanock S, Demenais F, Puig S, Nagore E, Shi J, Bishop T, McGregor S, Landi MT, Consortium G, Consortium M. Abstract 228: Association analysis across different populations identifies 26 new cutaneous melanoma risk loci. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Heritability of cutaneous melanoma is among the highest across cancer types and is mostly determined by common, noncoding genetic variants. Previous genome-wide association studies (GWAS), mostly including subjects from Australia and Northern European countries, had identified twenty genetic loci associated with melanoma risk. To characterize the genetic landscape of cutaneous melanoma across different populations, we conducted a new association study in Southern European countries including 6,043 melanoma cases and 10,383 controls from the MelaNostrum Consortium. Moreover, we largely expanded the analyses of melanoma cases and controls from other populations, for a total of 27,450 histologically confirmed melanoma cases and 49,888 controls from Northern Europe, Southern Europe, USA and Australia. Imputation was done using the Haplotype Reference Consortium as a reference panel. We assessed the association between cutaneous melanoma risk and single-nucleotide polymorphisms (SNPs) adjusting for country and ancestry-informative principal components. We identified 26 new genetic loci associated with melanoma risk achieving genome-wide significance. The pigmentation pathway, with TYRP1 and MITF, and the telomere-related pathway with RTEL1, TERC, and POT1 among the candidate genes, continued to show an important role for melanoma susceptibility. Additional candidate pathways emerged, including signaling (with GPRC5A and DOCK8), cell-cell junction (with CDH1), immune-related functions (with DCST2, involved in antigen processing), transcriptional regulation (with FOXD3, which represses MITF expression), or tumor-suppressor genes (TP53). Adding genotype data from 6,130 self-reported melanoma cases in a sensitivity analysis identified eight additional novel genetic loci involved in the HLA region, signaling transduction and transcription factor functions. A combined analysis of the melanoma GWAS with the GWAS of pigmentation characteristics from the UK Biobank including 500,000 UK persons, and with a GWAS of nevus density including over 52,000 persons, revealed substantial overlap across phenotypes. Although the effect size of the SNPs on melanoma risk was consistent across populations, substantial differences in minor allele frequency (MAF) were observed in pigmentation-related genes between Northern and Southern European populations; for example, MC1R, SLC45A2, and ASIP SNP MAF was 8.2, 3.1 and 14.2 in Northern and 2.6, 8.8, and 5.5 in Southern European subjects, respectively. Additional analyses based on melanoma histologic subtypes and body site distribution are ongoing. These results provide further insight into genetic susceptibility to cutaneous melanoma and provide the opportunity for genetic risk scores in risk-prediction models for early detection and targeted prevention of the disease.
Citation Format: Cristina Pellegrini, Matthew Law, Mark Iles, Mitch Machiela, Alex Stratigos, Tongwu Zhang, Kevin Brown, Julia Newton-Bishop, Nick Hayward, Nick Martin, Alisa Goldstein, Rose Yang, Stephen Chanock, Florence Demenais, Susana Puig, Eduardo Nagore, Jianxin Shi, Tim Bishop, Stuart McGregor, Maria Teresa Landi, GenoMEL Consortium, MelaNostrum Consortium. Association analysis across different populations identifies 26 new cutaneous melanoma risk loci [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 228.
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Affiliation(s)
| | | | - Mark Iles
- 3University of Leeds, United Kingdom
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Rothuizen TC, Ocak G, Verschuren JJ, Dekker FW, Rabelink TJ, Jukema JW, Rotmans JI, Silva V, Raimann JG, Grassmann A, Marcelli D, Usvyat L, Canaud B, Kotanko P, Pecoits-Filho R, Consortium M, Strippoli GF, Sue YM, Tang CH, Chen TH, Hong CY, Ochi A, Ishimura E, Masuda M, Tsujimoto Y, Okuno S, Tabata T, Nishizawa Y, Inaba M, Moon Ki H, Do Hyoung K, Min Jee H, Hyun K, Wang Soo L, Su-Hyun K, Selim G, Stojceva-Taneva O, Tozija L, Dzekova-Vidimliski P, Trajceska L, Gelev S, Amitov V, Petronievic Z, Sikole A, Kee YK, Kim YL, Han JH, Oh HJ, Park JT, Han SH, Yoo TH, Kang SW, Okute Y, Shoji T, Sonoda M, Kuwamura Y, Tsujimoto Y, Tabata T, Shioi A, Tahara H, Emoto M, Inaba M, El Amrani M, Asserraji M, Benyahia M, Galloway PA, Yiu V, Hiemstra TF, Nilssen C, Zannad F, Jardine A, Schmieder R, Fellstrom B, Holdaas H, Mjoen G, Eftimovska - Otovic N, Babalj - Banskolieva E, Bogdanoska - Kostadinoska S, Grozdanovski R, Silva BC, Freitas GR, Silva VB, Abensur H, Luders C, Pereira BJ, Castro MC, Oliveira RB, Moyses RM, Elias RM, Perez De Jose A, Abad S, Vega A, Reque J, Quiroga B, Lopez-Gomez JM, Sasaki K, Yamguchi K, Hesaka A, Iwahashi E, Sakai S, Fujimoto T, Minami S, Fujita Y, Yokoyama K, Kidir V, Ersoy I, Altuntas A, Inal S, Do an A, Sezer MT, Azar H, Chacra D, Dabar G, Chelala D, Zhao L, Huang S, Liang T, Tang H, Turkmen K, Demirtas L, Akbas EM, Buyuklu M, Bakirci E, Kocyigit I, Ozcelik O, Guney I, Mumajesi S, Velaj A, Idrizi A, Pasko N, Cadri V, Barbullushi M, Bolleku E, Strakosh A, Cenaj A, Kacori V, Zekollari E, Rista E, Dusha D, Belba A, Thereska N, Gelev S, Toshev S, Trajceska L, Pavleska S, Selim G, Dzekova P, Shikole A, Naess H, Fellstrom B, Jardine AG, Schmieder RE, Zannad F, Holdaas H, Mjoen G, Sasaki K, Yamguchi S, Hesaka A, Iwahashi E, Sakai S, Fujimoto T, Minami S, Fujita Y, Yokoyama K, Bilevich O, Bunova S, Semchenko S, Schwermer K, Hoppe K, Klysz P, Baum E, Sikorska D, Radziszewska D, Sawatiuk P, Olejniczak P, Pawlaczyk K, Lindholm B, Oko A, El Amrani M, Asserraji M, Rbaibi A, El Kharass A, Benyahia M, Rroji ( Molla) M, Seferi S, Cafka M, Spahia N, Likaj E, Thereska N, Barbullushi M, Pelletier CC, Jolivot A, Kalbacher E, Panaye M, Bureau Du Colombier P, Juillard L, Burmeister JE, Mosmann CB, Bastos JP, Burmeister BO, Munaro G, Pereira JD, Youssef DW, Rosito GA. DIALYSIS CARDIOVASCULAR COMPLICATIONS 2. Nephrol Dial Transplant 2014. [DOI: 10.1093/ndt/gfu175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Bornstein J, McCullough K, Combe C, Bieber B, Jadoul M, Pisoni R, Mariani L, Robinson B, Saito A, Sen A, Tentori F, Guinsburg A, Marelli C, Marcelli D, Usvyat L, Maddux D, Canaud B, Kotanko P, Hwang SJ, Hsieh HM, Chen HF, Mau LW, Lin MY, Hsu CC, Yang WC, Pitcher D, Rao A, Phelps R, Canaud B, Barbieri C, Marcelli D, Bellocchio F, Bowry S, Mari F, Amato C, Gatti E, Zitt E, Hafner-Giessauf H, Wimmer B, Herr A, Horn S, Friedl C, Sprenger-Maehr H, Kramar R, Rosenkranz AR, Lhotta K, Ferris M, Marcelli D, Marelli C, Etter M, Xu X, Grassmann A, Von Gersdorff GD, Pecoits-Filho R, Sylvestre L, Kotanko P, Usvyat L, Consortium M, Dzekova-Vidimliski P, Nikolov I, Trajceska L, Selim G, Gelev S, Matevska Geshkovska N, Dimovski A, Sikole A, Suleymanlar G, Utas C, Ecder T, Ates K, Bieber B, Robinson BM, Pisoni RL, Laplante S, Liu FX, Culleton B, Tomilina N, Bikbov B, Andrusev A, Zemchenkov A, Bieber B, Robinson BM, Pisoni RL, Bikbov B, Tomilina N, Kotenko O, Andrusev A, Panaye M, Jolivot A, Lemoine S, Guebre-Egziabher F, Doret M, Juillard L, Filiopoulos V, Hadjiyannakos D, Papakostoula A, Takouli L, Biblaki D, Dounavis A, Vlassopoulos D, Bikbov B, Tomilina N, Al Wakeel J, Bieber B, Al Obaidli AA, Ahmed Almaimani Y, Al-Arrayed S, Alhelal B, Fawzy A, Robinson BM, Pisoni RL, Aucella F, Girotti G, Gesuete A, Cicchella A, Seresin C, Vinci C, Scaparrotta G, Naso A, Pilotto A, Hoffmann TR, Flusser V, Santoro LF, Almeida FA, Aucella F, Girotti G, Gesuete A, Cicchella A, Seresin C, Vinci C, Scaparrotta G, Ganugi S, Gnerre T, Russo GE, Amato M, Naso A, Pilotto A, Trigka K, Douzdampanis P, Chouchoulis K, Mpimpi A, Kaza M, Pipili C, Kyritsis I, Fourtunas C, Ortalda V, Tomei P, Ybarek T, Lupo A, Torreggiani M, Esposito V, Catucci D, Arazzi M, Colucci M, Montagna G, Semeraro L, Efficace E, Piazza V, Picardi L, Esposito C, Hekmat R, Mohebi M, Ahmadzadehhashemi S, Park J, Hwang E, Jang M, Park S, Resende LL, Dantas MA, Martins MTS, Lopes GB, Lopes AA, Engelen W, Elseviers M, Gheuens E, Colson C, Muyshondt I, Daelemans R, He Y, Chen J, Luan S, Wan Q, Cuoghi A, Bellei E, Monari E, Bergamini S, Tomasi A, Atti M, Caiazzo M, Palladino G, Bruni F, Tekce H, Ozturk S, Aktas G, Kin Tekce B, Erdem A, Uyeturk U, Ozyasar M, Taslamacioglu Duman T, Yazici M, Schaubel DE, McCullough KP, Morgenstern H, Gallagher MP, Hasegawa T, Pisoni RL, Robinson BM, Nacak H, Van Diepen M, Suttorp MM, Hoorn EJ, Rotmans JI, Dekker FW, Speyer E, Beauger D, Gentile S, Isnard Bagnis C, Caille Y, Baudelot C, Mercier S, Jacquelinet C, Briancon S, Sosorburam T, Baterdene B, Delger A, Daelemans R, Gheuens E, Engelen W, De Boeck K, Marynissen J, Bouman K, Mann M, Exner DV, Hemmelgarn BR, Hanley D, Ahmed SB. DIALYSIS. EPIDEMIOLOGY, OUTCOME RESEARCH, HEALTH SERVICES 2. Nephrol Dial Transplant 2014. [DOI: 10.1093/ndt/gfu178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Komaba H, Taniguchi M, Yamamoto S, Nomura T, Fukagawa M, Pasch A, De Francisco AL, Covic A, Marzell B, Arens HJ, Passlick-Deetjen J, Jahnen-Dechent W, Castellano A, Ruggiero P, Pedrini LA, Barreto F, Grassmann A, Marcelli D, Canaud B, Kotanko P, Silva VC, Usvyat L, Pecoits-Filho R, Consortium M, Drueke TB, Moe SM, Abdalla S, Parfrey PS, Chertow GM. DIALYSIS MINERAL BONE DISEASE. Nephrol Dial Transplant 2014. [DOI: 10.1093/ndt/gfu127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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