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1. Genome-wide association study identifies novel loci predisposing to cutaneous melanoma†

Author

Amos, Ci, Wang, Le, Lee, Je, Gershenwald, Je, Chen, Wv, Fang, S, Kosoy, R, Zhang, M, Qureshi, Aa, Vattathil, S, Schacherer, Cw, Gardner, Jm, Wang, Y, Bishop, Dt, Barrett, Jh, Macgregor, S, Hayward, Nk, Martin, Ng, Duffy, Dl, Mann, Gj, Cust, A, Hopper, J, Brown, Km, Grimm, Ea, Xu, Y, Han, Y, Jing, K, Mchugh, C, Laurie, Cc, Doheny, Kf, Pugh, Ew, Seldin, Mf, Han, J, Wei, Q, Genomel, Investigators, Mega Investigators, Q., AMFS Investigators Mann GJ, Hopper, Jl, Aitken, Jf, Armstrong, Bk, Giles, Gg, Kefford, Rf, Cust, Ae, Jenkins, Ma, Schmid, H, Aguilera, P, Badenas, C, Carrera, C, Cuellar, F, Gabriel, D, Martinez, E, Gonzalez, M, Iglesias, P, Malvehy, J, Marti Laborda, R, Mila, M, Ogbah, Z, Butille, Ja, Puig, S, Alós, L, Arance, A, Arguís, P, Campo, A, Castel, T, Conill, C, Palou, J, Rull, R, Sánchez, M, Vidal Sicart, S, Vilalta, A, Vilella, R, Montgomery, Gw, Whiteman, Dc, Whiteman, D, Webb, P, Green, A, Parsons, P, Purdie, D, Hayward, N, Landi, Mt, Calista, D, Landi, G, Minghetti, P, Arcangeli, F, Bertazzi, Pa, Bianchi, Giovanna, Ghiorzo, Paola, Pastorino, Lorenza, Bruno, William, Battistuzzi, Linda, Gargiulo, Sara, Nasti, Sabina, Gliori, S, Origone, Paola, Andreotti, V, Queirolo, P, Mackie, R, Lang, J, Bishop, Ja, Affleck, P, Harrison, J, Iles, Mm, Randerson Moor, J, Harland, M, Taylor, Jc, Whittaker, L, Kukalizch, K, Leake, S, Karpavicius, B, Haynes, S, Mack, T, Chan, M, Taylor, Y, Davies, J, King, P, Gruis, Na, van Nieuwpoort FA, Out, C, van der Drift, C, Bergman, W, Kukutsch, N, Bavinck, Jn, Bakker, B, van der Stoep, N, ter Huurne, J, van der Rhee, H, Bekkenk, M, Snels, D, van Praag, M, Brochez, L, Gerritsen, R, Crijns, M, Vasen, H, Olsson, H, Ingvar, C, Jönsson, G, Borg, Å, Måsbäck, A, Lundgren, L, Baeckenhorn, K, Nielsen, K, Casslén, As, Helsing, P, Andresen, Pa, Rootwelt, H, Akslen, La, Molven, A, Avril, Mf, Bressac de Paillerets, B, Chaudru, V, Chateigner, N, Corda, E, Jeannin, P, Lesueur, F, de Lichy, M, Maubec, E, Mohamdi, H, Demenais, F, Andry Benzaquen, P, Bachollet, B, Bérard, F, Berthet, P, Boitier, F, Bonadona, V, Bonafé, Jl, Bonnetblanc, Jm, Cambazard, F, Caron, O, Caux, F, Chevrant Breton, J, Chompret, A, Dalle, S, Demange, L, Dereure, O, Doré, Mx, Doutre, Ms, Dugast, C, Faivre, L, Grange, F, Humbert, P, Joly, P, Kerob, D, Lasset, C, Leccia, Mt, Lenoir, G, Leroux, D, Levang, J, Lipsker, D, Mansard, S, Martin, L, Martin Denavit, T, Mateus, C, Michel, Jl, Morel, P, Olivier Faivre, L, Perrot, Jl, Robert, C, Ronger Savle, S, Sassolas, B, Souteyrand, P, Stoppa Lyonnet, D, Thomas, L, Vabres, P, Wierzbicka, E, Elder, D, Kanetsky, P, Knorr, J, Ming, M, Mitra, N, Ruffin, A, Van Belle, P, Debniak, T, Lubiński, J, Mirecka, A, Ertmański, S, Novakovic, S, Hocevar, M, Peric, B, Cerkovnik, P, Höiom, V, Hansson, J, Holland, Ea, Azizi, E, Galore Haskel, G, Friedman, E, Baron Epel, O, Scope, A, Pavlotsky, F, Yakobson, E, Cohen Manheim, I, Laitman, Y, Milgrom, R, Shimoni, I, and Kozlovaa, E.

Subjects
Genetic Markers, Candidate gene, Skin Neoplasms, Ubiquitin-Protein Ligases, Locus (genetics), Single-nucleotide polymorphism, Genome-wide association study, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, 0302 clinical medicine, Meta-Analysis as Topic, Genetics, Eye color, Guanine Nucleotide Exchange Factors, Humans, SNP, Genetic Predisposition to Disease, Melanoma, Molecular Biology, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Pigmentation, Association Studies Articles, General Medicine, 3. Good health, Chromosomes, Human, Pair 1, Genetic Loci, Genetic marker, Case-Control Studies, 030220 oncology & carcinogenesis, Cutaneous melanoma, Genome-Wide Association Study
Abstract

We performed a multistage genome-wide association study of melanoma. In a discovery cohort of 1804 melanoma cases and 1026 controls, we identified loci at chromosomes 15q13.1 (HERC2/OCA2 region) and 16q24.3 (MC1R) regions that reached genome-wide significance within this study and also found strong evidence for genetic effects on susceptibility to melanoma from markers on chromosome 9p21.3 in the p16/ARF region and on chromosome 1q21.3 (ARNT/LASS2/ANXA9 region). The most significant single-nucleotide polymorphisms (SNPs) in the 15q13.1 locus (rs1129038 and rs12913832) lie within a genomic region that has profound effects on eye and skin color; notably, 50% of variability in eye color is associated with variation in the SNP rs12913832. Because eye and skin colors vary across European populations, we further evaluated the associations of the significant SNPs after carefully adjusting for European substructure. We also evaluated the top 10 most significant SNPs by using data from three other genome-wide scans. Additional in silico data provided replication of the findings from the most significant region on chromosome 1q21.3 rs7412746 (P = 6 × 10(-10)). Together, these data identified several candidate genes for additional studies to identify causal variants predisposing to increased risk for developing melanoma.

Published
2011
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2. THE REFERENCE SITE COLLABORATIVE NETWORK OF THE EUROPEAN INNOVATION PARTNERSHIP ON ACTIVE AND HEALTHY AGEING

Author

Bousquet, J., Illario, M., Farrell, J., Batey, N., Carriazo, A. M., Malva, J., Hajjam, J., Colgan, E., Guldemond, N., Perala-Heape, M., Onorato, G. L., Bedbrook, A., Leonardini, L., Stroetman, V., Birov, S., Abreu, C., Abrunhosa, A., Agrimi, A., Alalaakkola, T., Allegretti, N., Alonso-Trujillo, F., Alvarez-Benito, M., Angioli, S., Apostolo, J., Armitage, G., Arnavielhe, S., Baena-Parejo, M., Bamidis, P. D., Balenovic, A., Barbolini, M., Baroni, I., Blain, H., Bernard, P. L., Bersani, M., Berti, E., Bogatyrchuk, L., Bourret, R., Brehm, J., Brussino, L., Buhr, D., Bultje, D., Cabeza, E., Cano, A., Capitani, C., Carantona, E., Cardoso, A., Coll Clavero, J., Combe, B., Conforti, D., Coppola, L., Corti, F., Coscioni, E., Costa, E., Crooks, G., Cunha, A., Daien, C., Dantas, Darpon Sierra, J., Davoli, M., Dedeu Baraldes, A., Luca, V., Nardi, L., Di Ciano, M., Dozet, A., Ekinci, B., Erve, S., Espinoza Almendro, J. M., Fait, A., Fensli, R., Fernandez Nocelo, S., Galvez-Daza, P., Gamez-Paya, J., Garcia Saez, M., Garcia Sanchez, I., Gemicioglu, B., Goetzke, W., Goossens, E., Geurdens, M., Gutter, Z., Hansen, H., Hartman, S., Hegendorfer, G., Heikka, H., Henderson, D., Heran, D., Hirvonen, S., Iaccarino, G., Jansson, N., Kallasvaara, H., Kalyoncu, F., Kirchmayer, U., Kokko, J. A., Korpelainen, J., Kostka, T., Kuna, P., Lajarin Ortega, T., Lama, C. M., Laune, D., Lauri, D., Ledroit, V., Levato, G., Lewis, L., Liotta, G., Lundgren, L., Lupianez-Villanueva, F., Mc Garry, P., Maggio, M., Manuel Keenoy, E., Martinez, C., Martinez-Domene, M., Martinez-Lozano Aranaga, B., Massimilliano, M., Maurizio, A., Mayora, O., Melle, C., Mendez-Zorilla, A., Mengon, H., Mercier, G., Mercier, J., Meyer, I., Millet Pi-Figueras, A., Mitsias, P., Molloy, D. W., Monti, R., Moro, M. L., Muranko, H., Nalin, M., Nobili, A., Nogues, M., O Caoimh, R., Pais, S., Papini, D., Parkkila, P., Pattichis, C., Pavlickova, A., Peiponen, A., Pereira, S., Pepin, J. L., Piera Jimenez, J., Portheine, P., Potel, L., Pozzi, A. C., Quinonez, P., Lauritsen, Ramirez X., Ramos, M. J., Rannali-Kontturi, A., Risino, A., Robalo-Cordeiro, C., Rolla, G., Roller, R., Romano, M., Romano, V., Ruiz-Fernandez, J., Saccavini, C., Sachinopoulou, A., Sanchez Rubio, M. J., Santos, L., simonetta scalvini, Scopetani, E., Smedberg, D., Solana-Lara, R., Soltysik, B., Sorlini, M., Stericker, S., Badiale, Stramba M., Taillieu, I., Tervahauta, M., Teixeira, A., Tikanmaki, H., Todo-Bom, A., Tooley, A., Tuulonen, A., Tziraki, C., Ussai, S., Veen, S., Venchiarutti, A., Verdoy-Berastegi, D., Verissimo, M., Visconti, L., Vollenbroek-Hutten, M., Weinzerl, K., Wozniak, L., Yorgancioglu, A., Zavagli, V., Zurkuhlen, A. J., Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Contre les MAladies Chroniques pour un VIeillissement Actif en Languedoc-Roussillon (MACVIA-LR), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Nîmes (CHRU Nîmes)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-European Innovation Partnership on Active and Healthy Ageing Reference Site (EIP on AHA), Commission Européenne-Commission Européenne-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Hydraulic and Environmental Engineering, University of Pavia, Department of Geriatrics - Efficiency and Deficiency Laboratory, Università degli Studi di Firenze [Firenze], Groupe d'étude de l'atmosphère météorologique (CNRM-GAME), Institut national des sciences de l'Univers (INSU - CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), Mineralogisch-Petrographisches Institut (MPI), Mineralogisch-Petrographisches Institut, University of Coimbra [Portugal] (UC), Département de Rhumatologie[Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Hôpital Lapeyronie, Laboratoire d'océanographie de Villefranche (LOV), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Istituto di Astrofisica Spaziale, Hôpital Lapeyronie [Montpellier] (CHU), Centre d’Expertise National des Technologies de l’Information et de la Communication pour l’autonomie - CENTICH (FRANCE), Center for Turbulence Research (CTR), Stanford University [Stanford], Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Station de Palavas, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de magnétisme et d'optique de Versailles (LMOV), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire [Grenoble] (CHU), Epidemiology Unit, IRCCS Ospedale Pediatrico Bambino Gesù [Roma], Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo, Centre d'EPistémologie et d'ERgologie Comparatives - UMR 7304 (CEPERC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Ethics, Law & Medical humanities, APH - Aging & Later Life, Bousquet, J, Illario, M, Farrell, J, Batey, N, Carriazo, A M, Malva, J, Hajjam, J, Colgan, E, Guldemond, N, Perälä-Heape, M, Onorato, G L, Bedbrook, A, Leonardini, L, Stroetman, V, Birov, S, Abreu, C, Abrunhosa, A, Agrimi, A, Alalääkkölä, T, Allegretti, N, Alonso-Trujillo, F, Álvarez-Benito, M, Angioli, S, Apóstolo, J, Armitage, G, Arnavielhe, S, Baena-ParejoI, M, Bamidis, P D, Balenović, A, Barbolini, M, Baroni, I, Blain, H, Bernard, P L, Bersani, M, Berti, E, Bogatyrchuk, L, Bourret, R, Brehm, J, Brussino, L, Buhr, D, Bultje, D, Cabeza, E, Cano, A, De Capitani, C, Carantoña, E, Cardoso, A, Coll Clavero, J I, Combe, B, Conforti, D, Coppola, L, Corti, F, Coscioni, E, Costa, E, Crooks, G, Cunha, A, Daien, C, Dantas, Null, Darpón Sierra, J, Davoli, M, Dedeu Baraldes, A, De Luca, V, De Nardi, L, Di Ciano, M, Dozet, A, Ekinci, B, Erve, S, Espinoza Almendro, J M, Fait, A, Fensli, R, Fernandez Nocelo, S, Gálvez-Daza, P, Gámez-Payá, J, García Sáez, M, Garcia Sanchez, I, Gemicioğlu, B, Goetzke, W, Goossens, E, Geurdens, M, Gütter, Z, Hansen, H, Hartman, S, Hegendörfer, G, Heikka, H, Henderson, D, Héran, D, Hirvonen, S, Iaccarino, G, Jansson, N, Kallasvaara, H, Kalyoncu, F, Kirchmayer, U, Kokko, J A, Korpelainen, J, Kostka, T, Kuna, P, Lajarín Ortega, T, Lama, C M, Laune, D, Lauri, D, Ledroit, V, Levato, G, Lewis, L, Liotta, G, Lundgren, L, Lupiañez-Villanueva, F, Mc Garry, P, Maggio, M, Manuel de Keenoy, E, Martinez, C, Martínez-Domene, M, Martínez-Lozano Aranaga, B, Massimilliano, M, Maurizio, A, Mayora, O, Melle, C, Mendez-Zorilla, A, Mengon, H, Mercier, G, Mercier, J, Meyer, I, Millet Pi-Figueras, A, Mitsias, P, Molloy, D W, Monti, R, Moro, M L, Muranko, H, Nalin, M, Nobili, A, Noguès, M, O'Caoimh, R, Pais, S, Papini, D, Parkkila, P, Pattichis, C, Pavlickova, A, Peiponen, A, Pereira, S, Pépin, J L, Piera Jiménez, J, Portheine, P, Potel, L, Pozzi, A C, Quiñonez, P, Ramirez Lauritsen, X, Ramos, M J, Rännäli-Kontturi, A, Risino, A, Robalo-Cordeiro, C, Rolla, G, Roller, R, Romano, M, Romano, V, Ruiz-Fernández, J, Saccavini, C, Sachinopoulou, A, Sánchez Rubio, M J, Santos, L, Scalvini, S, Scopetani, E, Smedberg, D, Solana-Lara, R, Sołtysik, B, Sorlini, M, Stericker, S, Stramba Badiale, M, Taillieu, I, Tervahauta, M, Teixeira, A, Tikanmäki, H, Todo-Bom, A, Tooley, A, Tuulonen, A, Tziraki, C, Ussai, S, Van der Veen, S, Venchiarutti, A, Verdoy-Berastegi, D, Verissimo, M, Visconti, L, Vollenbroek-Hutten, M, Weinzerl, K, Wozniak, L, Yorgancıoğlu, A, Zavagli, V, Zurkuhlen, A J, Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Nîmes (CHU Nîmes)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-European Innovation Partnership on Active and Healthy Ageing Reference Site (EIP on AHA), Università degli Studi di Pavia = University of Pavia (UNIPV), Università degli Studi di Firenze = University of Florence (UniFI), Center for Turbulence Research [Stanford] (CTR), Stanford University, KYomed INNOV, Centre d'EPistémologie et d'ERgologie Comparatives (CEPERC), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Active and healthy ageing, DG CONNECT, DG Santé, EIP on AHA, European Innovation Partnership on Active and Healthy Ageing, Allergic Rhinitis, Operational Definition, Program, Turkey, DG Sante, [SDV]Life Sciences [q-bio], Eip, Diseases, Articles, 03 medical and health sciences, 0302 clinical medicine, Synergies, 030228 respiratory system, Aha, Settore MED/42, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; Seventy four Reference Sites of the European Innovation Partnership on Active and Healthy Ageing (EIP on AHA) have been recognised by the European Commission in 2016 for their commitment to excellence in investing and scaling up innovative solutions for active and healthy ageing. The Reference Site Collaborative Network (RSCN) brings together the EIP on AHA Reference Sites awarded by the European Commission, and Candidate Reference Sites into a single forum. The overarching goals are to promote cooperation, share and transfer good practice and solutions in the development and scaling up of health and care strategies, policies and service delivery models, while at the same time supporting the action groups in their work. The RSCN aspires to be recognized by the EU Commission as the principal forum and authority representing all EIP on AHA Reference Sites. The RSCN will contribute to achieve the goals of the EIP on AHA by improving health and care outcomes for citizens across Europe, and the development of sustainable economic growth and the creation of jobs.

4. Pathway-Based Analysis of a Melanoma Genome-Wide Association Study: Analysis of Genes Related to Tumour-Immunosuppression

Author

Schoof, N, Iles, Mm, Bishop, Dt, Newton Bishop JA, Barrett, Jh, Mann, Gj, Hopper, Jl, Aitken, Jf, Armstrong, Bk, Giles, Gg, Kefford, Rf, Cust, A, Jenkins, M, Aguilera, P, Badenas, C, Carrera, C, Cuellar, F, Gabriel, D, Martinez, E, Gonzalez, M, Iglesias, P, Malvehy, J, Marti Laborda, R, Mila, M, Ogbah, Z, Butille, Ja, Puig, S, Alós, L, Arance, A, Arguís, P, Campo, A, Castel, T, Conill, C, Palou, J, Rull, R, Sánchez, M, Vidal Sicart, S, Vilalta, A, Vilella, R, Martin, Ng, Montgomery, Gw, Duffy, D, Whiteman, D, Macgregor, S, Hayward, Nk, Webb, P, Parsons, P, Purdie, D, Hayward, N, Landi, Mt, Calista, D, Landi, G, Minghetti, P, Arcangeli, F, Bertazzi, Pa, Bianchi, Giovanna, Ghiorzo, Paola, Pastorino, Lorenza, Bruno, William, Battistuzzi, Linda, Gargiulo, Sara, Nasti, Sabina, Gliori, S, Origone, Paola, Queirolo, P, Mackie, R, Lang, J, Bishop, Ja, Affleck, P, Harrison, J, Randerson Moor, J, Harland, M, Taylor, Jc, Whittaker, L, Kukalizch, K, Leake, S, Karpavicius, B, Haynes, S, Mack, T, Chan, M, Taylor, Y, Davies, J, King, P, Gruis, Na, van Nieuwpoort FA, Out, C, van der Drift, C, Bergman, W, Kukutsch, N, Bavinck, Jn, Bakker, B, van der Stoep, N, ter Huurne, J, van der Rhee, H, Bekkenk, M, Snels, D, van Praag, M, Brochez, L, Gerritsen, R, Crijns, M, Vasen, H, Olsson, H, Ingvar, C, Jönsson, G, Borg, Å, Måsbäck, A, Lundgren, L, Baeckenhorn, K, Nielsen, K, Casslén, As, Helsing, P, Andresen, Pa, Rootwelt, H, Akslen, La, Molven, A, Avril, Mf, Bressac de Paillerets, B, Chaudru, V, Chateigner, N, Corda, E, Jeannin, P, Lesueur, F, de Lichy, M, Maubec, E, Mohamdi, H, Demenais, F, Andry Benzaquen, P, Bachollet, B, Bérard, F, Berthet, P, Boitier, F, Bonadona, V, Bonafé, Jl, Bonnetblanc, Jm, Cambazard, F, Caron, O, Caux, F, Chevrant Breton, J, Chompret, A, Dalle, S, Demange, L, Dereure, O, Doré, Mx, Doutre, Ms, Dugast, C, Faivre, L, Grange, F, Humbert, P, Joly, P, Kerob, D, Lasset, C, Leccia, Mt, Lenoir, G, Leroux, D, Levang, J, Lipsker, D, Mansard, S, Martin, L, Martin Denavit, T, Mateus, C, Michel, Jl, Morel, P, Olivier Faivre, L, Perrot, Jl, Robert, C, Ronger Savle, S, Sassolas, B, Souteyrand, P, Stoppa Lyonnet, D, Thomas, L, Vabres, P, Wierzbicka, E, Elder, D, Kanetsky, P, Knorr, J, Ming, M, Mitra, N, Ruffin, A, Van Belle, P, Dębniak, T, Lubiński, J, Mirecka, A, Ertmański, S, Novakovic, S, Hocevar, M, Peric, B, Cerkovnik, P, Höiom, V, Hansson, J, Schmid, H, Holland, Ea, Azizi, E, Galore Haskel, G, Friedman, E, Baron Epel, O, Scope, A, Pavlotsky, F, Yakobson, E, Cohen Manheim, I, Laitman, Y, Milgrom, R, Shimoni, I, Kozlovaa, E., Biostatistiques santé, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Martí Laborda, Rosa Ma., and Universitat de Barcelona

Subjects
Melanomas, Skin Neoplasms, Epidemiology, medicine.medical_treatment, [SDV]Life Sciences [q-bio], lcsh:Medicine, Genome-wide association study, 0302 clinical medicine, Polymorphism (computer science), Genetics of the Immune System, lcsh:Science, Melanoma, Genetics, 0303 health sciences, Multidisciplinary, Cancer Risk Factors, Statistics, Immunosuppression, Genomics, Oncology, Genetic Epidemiology, 030220 oncology & carcinogenesis, Medicine, Research Article, medicine.medical_specialty, Immunology, Genetic Causes of Cancer, Malignant Skin Neoplasms, Single-nucleotide polymorphism, Dermatology, Biostatistics, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genome Analysis Tools, Molecular genetics, Genome-Wide Association Studies, medicine, Humans, SNP, Genetic Predisposition to Disease, Statistical Methods, Gene, 030304 developmental biology, Immunosuppression Therapy, Evolutionary Biology, Population Biology, Immunosupressió, lcsh:R, Computational Biology, Human Genetics, medicine.disease, Genetic Polymorphism, Clinical Immunology, lcsh:Q, Population Genetics, Mathematics, Genome-Wide Association Study
Abstract

Systemic immunosuppression is a risk factor for melanoma, and sunburn-induced immunosuppression is thought to be causal. Genes in immunosuppression pathways are therefore candidate melanoma-susceptibility genes. If variants within these genes individually have a small effect on disease risk, the association may be undetected in genome-wide association (GWA) studies due to low power to reach a high significance level. Pathway-based approaches have been suggested as a method of incorporating a priori knowledge into the analysis of GWA studies. In this study, the association of 1113 single nucleotide polymorphisms (SNPs) in 43 genes (39 genomic regions) related to immunosuppression have been analysed using a gene-set approach in 1539 melanoma cases and 3917 controls from the GenoMEL consortium GWA study. The association between melanoma susceptibility and the whole set of tumour-immunosuppression genes, and also predefined functional subgroups of genes, was considered. The analysis was based on a measure formed by summing the evidence from the most significant SNP in each gene, and significance was evaluated empirically by case-control label permutation. An association was found between melanoma and the complete set of genes (pemp = 0.002), as well as the subgroups related to the generation of tolerogenic dendritic cells (pemp = 0.006) and secretion of suppressive factors (pemp = 0.0004), thus providing preliminary evidence of involvement of tumour-immunosuppression gene polymorphisms in melanoma susceptibility. The analysis was repeated on a second phase of the GenoMEL study, which showed no evidence of an association. As one of the first attempts to replicate a pathway-level association, our results suggest that low power and heterogeneity may present challenges.

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