Genome-wide association study identifies three new melanoma susceptibility loci

Jennifer H. Barrett; Mark M. Iles; Mark Harland; John C. Taylor; Joanne F. Aitken; Per Arne Andresen; Lars A. Akslen; Bruce K. Armstrong; Marie Francoise Avril; Esther Azizi; Bert Bakker; Wilma Bergman; Giovanna Bianchi-Scarrà; Brigitte Bressac-De Paillerets; Donato Calista; Lisa A. Cannon-Albright; Eve Corda; Anne E. Cust; Tadeusz Dȩbniak; David Duffy; Alison M. Dunning; Douglas F. Easton; Eitan Friedman; Pilar Galan; Paola Ghiorzo; Graham G. Giles; Johan Hansson; Marko Hocevar; Veronica Höiom; John L. Hopper; Christian Ingvar; Bart Janssen; Mark A. Jenkins; Göran Jönsson; Richard F. Kefford; Giorgio Landi; Maria Teresa Landi; Julie Lang; Jan Lubiński; Rona MacKie; Josep Malvehy; Nicholas G. Martin; Anders Molven; Grant W. Montgomery; Frans A. Van Nieuwpoort; Srdjan Novakovic; Håkan Olsson; Lorenza Pastorino; Susana Puig; Joan Anton Puig-Butille; Juliette Randerson-Moor; Helen Snowden; Rainer Tuominen; Patricia Van Belle; Nienke Van Der Stoep; David C. Whiteman; Diana Zelenika; Jiali Han; Shenying Fang; Jeffrey E. Lee; Qingyi Wei; G. Mark Lathrop; Elizabeth M. Gillanders; Kevin M. Brown; Alisa M. Goldstein; Peter A. Kanetsky; Graham J. Mann; Stuart MacGregor; David E. Elder; Christopher I. Amos; Nicholas K. Hayward; Nelleke A. Gruis; Florence Demenais; Julia A.Newton Bishop; D. Timothy Bishop

doi:10.1038/ng.959

Genome-wide association study identifies three new melanoma susceptibility loci

Jennifer H. Barrett, Mark M. Iles, Mark Harland, John C. Taylor, Joanne F. Aitken, Per Arne Andresen, Lars A. Akslen, Bruce K. Armstrong, Marie Francoise Avril, Esther Azizi, Bert Bakker, Wilma Bergman, Giovanna Bianchi-Scarrà, Brigitte Bressac-De Paillerets, Donato Calista, Lisa A. Cannon-Albright, Eve Corda, Anne E. Cust, Tadeusz Dȩbniak, David DuffyAlison M. Dunning, Douglas F. Easton, Eitan Friedman, Pilar Galan, Paola Ghiorzo, Graham G. Giles, Johan Hansson, Marko Hocevar, Veronica Höiom, John L. Hopper, Christian Ingvar, Bart Janssen, Mark A. Jenkins, Göran Jönsson, Richard F. Kefford, Giorgio Landi, Maria Teresa Landi, Julie Lang, Jan Lubiński, Rona MacKie, Josep Malvehy, Nicholas G. Martin, Anders Molven, Grant W. Montgomery, Frans A. Van Nieuwpoort, Srdjan Novakovic, Håkan Olsson, Lorenza Pastorino, Susana Puig, Joan Anton Puig-Butille, Juliette Randerson-Moor, Helen Snowden, Rainer Tuominen, Patricia Van Belle, Nienke Van Der Stoep, David C. Whiteman, Diana Zelenika, Jiali Han, Shenying Fang, Jeffrey E. Lee, Qingyi Wei, G. Mark Lathrop, Elizabeth M. Gillanders, Kevin M. Brown, Alisa M. Goldstein, Peter A. Kanetsky, Graham J. Mann, Stuart MacGregor, David E. Elder, Christopher I. Amos, Nicholas K. Hayward, Nelleke A. Gruis, Florence Demenais, Julia A.Newton Bishop, D. Timothy Bishop

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Abstract

We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10 ^-5 and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10 ^-3: an SNP in ATM (rs1801516, overall P = 3.4 × 10 ^-9), an SNP in MX2 (rs45430, P = 2.9 × 10 ^-9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10 ^-10). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10 ^-7 under a fixed-effects model and P = 1.2 × 10 ^-3 under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.

Original language	English
Pages (from-to)	1108-1113
Number of pages	6
Journal	Nature Genetics
Volume	43
Issue number	11
DOIs	https://doi.org/10.1038/ng.959
Publication status	Published - Nov 2011
Externally published	Yes

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Barrett, J. H., Iles, M. M., Harland, M., Taylor, J. C., Aitken, J. F., Andresen, P. A., Akslen, L. A., Armstrong, B. K., Avril, M. F., Azizi, E., Bakker, B., Bergman, W., Bianchi-Scarrà, G., Bressac-De Paillerets, B., Calista, D., Cannon-Albright, L. A., Corda, E., Cust, A. E., Dȩbniak, T., ... Bishop, D. T. (2011). Genome-wide association study identifies three new melanoma susceptibility loci. Nature Genetics, 43(11), 1108-1113. https://doi.org/10.1038/ng.959

@article{d2faad287e4440f69e9824b7738bd43a,

title = "Genome-wide association study identifies three new melanoma susceptibility loci",

abstract = "We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10 -5 and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10 -3: an SNP in ATM (rs1801516, overall P = 3.4 × 10 -9), an SNP in MX2 (rs45430, P = 2.9 × 10 -9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10 -10). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10 -7 under a fixed-effects model and P = 1.2 × 10 -3 under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.",

author = "Barrett, {Jennifer H.} and Iles, {Mark M.} and Mark Harland and Taylor, {John C.} and Aitken, {Joanne F.} and Andresen, {Per Arne} and Akslen, {Lars A.} and Armstrong, {Bruce K.} and Avril, {Marie Francoise} and Esther Azizi and Bert Bakker and Wilma Bergman and Giovanna Bianchi-Scarr{\`a} and {Bressac-De Paillerets}, Brigitte and Donato Calista and Cannon-Albright, {Lisa A.} and Eve Corda and Cust, {Anne E.} and Tadeusz Dȩbniak and David Duffy and Dunning, {Alison M.} and Easton, {Douglas F.} and Eitan Friedman and Pilar Galan and Paola Ghiorzo and Giles, {Graham G.} and Johan Hansson and Marko Hocevar and Veronica H{\"o}iom and Hopper, {John L.} and Christian Ingvar and Bart Janssen and Jenkins, {Mark A.} and G{\"o}ran J{\"o}nsson and Kefford, {Richard F.} and Giorgio Landi and Landi, {Maria Teresa} and Julie Lang and Jan Lubi{\'n}ski and Rona MacKie and Josep Malvehy and Martin, {Nicholas G.} and Anders Molven and Montgomery, {Grant W.} and {Van Nieuwpoort}, {Frans A.} and Srdjan Novakovic and H{\aa}kan Olsson and Lorenza Pastorino and Susana Puig and Puig-Butille, {Joan Anton} and Juliette Randerson-Moor and Helen Snowden and Rainer Tuominen and {Van Belle}, Patricia and {Van Der Stoep}, Nienke and Whiteman, {David C.} and Diana Zelenika and Jiali Han and Shenying Fang and Lee, {Jeffrey E.} and Qingyi Wei and Lathrop, {G. Mark} and Gillanders, {Elizabeth M.} and Brown, {Kevin M.} and Goldstein, {Alisa M.} and Kanetsky, {Peter A.} and Mann, {Graham J.} and Stuart MacGregor and Elder, {David E.} and Amos, {Christopher I.} and Hayward, {Nicholas K.} and Gruis, {Nelleke A.} and Florence Demenais and Bishop, {Julia A.Newton} and Bishop, {D. Timothy}",

year = "2011",

month = nov,

doi = "10.1038/ng.959",

language = "English",

volume = "43",

pages = "1108--1113",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group - Macmillan Publishers",

number = "11",

}

Barrett, JH, Iles, MM, Harland, M, Taylor, JC, Aitken, JF, Andresen, PA, Akslen, LA, Armstrong, BK, Avril, MF, Azizi, E, Bakker, B, Bergman, W, Bianchi-Scarrà, G, Bressac-De Paillerets, B, Calista, D, Cannon-Albright, LA, Corda, E, Cust, AE, Dȩbniak, T, Duffy, D, Dunning, AM, Easton, DF, Friedman, E, Galan, P, Ghiorzo, P, Giles, GG, Hansson, J, Hocevar, M, Höiom, V, Hopper, JL, Ingvar, C, Janssen, B, Jenkins, MA, Jönsson, G, Kefford, RF, Landi, G, Landi, MT, Lang, J, Lubiński, J, MacKie, R, Malvehy, J, Martin, NG, Molven, A, Montgomery, GW, Van Nieuwpoort, FA, Novakovic, S, Olsson, H, Pastorino, L, Puig, S, Puig-Butille, JA, Randerson-Moor, J, Snowden, H, Tuominen, R, Van Belle, P, Van Der Stoep, N, Whiteman, DC, Zelenika, D, Han, J, Fang, S, Lee, JE, Wei, Q, Lathrop, GM, Gillanders, EM, Brown, KM, Goldstein, AM, Kanetsky, PA, Mann, GJ, MacGregor, S, Elder, DE, Amos, CI, Hayward, NK, Gruis, NA, Demenais, F, Bishop, JAN & Bishop, DT 2011, 'Genome-wide association study identifies three new melanoma susceptibility loci', Nature Genetics, vol. 43, no. 11, pp. 1108-1113. https://doi.org/10.1038/ng.959

TY - JOUR

T1 - Genome-wide association study identifies three new melanoma susceptibility loci

AU - Barrett, Jennifer H.

AU - Iles, Mark M.

AU - Harland, Mark

AU - Taylor, John C.

AU - Aitken, Joanne F.

AU - Andresen, Per Arne

AU - Akslen, Lars A.

AU - Armstrong, Bruce K.

AU - Avril, Marie Francoise

AU - Azizi, Esther

AU - Bakker, Bert

AU - Bergman, Wilma

AU - Bianchi-Scarrà, Giovanna

AU - Bressac-De Paillerets, Brigitte

AU - Calista, Donato

AU - Cannon-Albright, Lisa A.

AU - Corda, Eve

AU - Cust, Anne E.

AU - Dȩbniak, Tadeusz

AU - Duffy, David

AU - Dunning, Alison M.

AU - Easton, Douglas F.

AU - Friedman, Eitan

AU - Galan, Pilar

AU - Ghiorzo, Paola

AU - Giles, Graham G.

AU - Hansson, Johan

AU - Hocevar, Marko

AU - Höiom, Veronica

AU - Hopper, John L.

AU - Ingvar, Christian

AU - Janssen, Bart

AU - Jenkins, Mark A.

AU - Jönsson, Göran

AU - Kefford, Richard F.

AU - Landi, Giorgio

AU - Landi, Maria Teresa

AU - Lang, Julie

AU - Lubiński, Jan

AU - MacKie, Rona

AU - Malvehy, Josep

AU - Martin, Nicholas G.

AU - Molven, Anders

AU - Montgomery, Grant W.

AU - Van Nieuwpoort, Frans A.

AU - Novakovic, Srdjan

AU - Olsson, Håkan

AU - Pastorino, Lorenza

AU - Puig, Susana

AU - Puig-Butille, Joan Anton

AU - Randerson-Moor, Juliette

AU - Snowden, Helen

AU - Tuominen, Rainer

AU - Van Belle, Patricia

AU - Van Der Stoep, Nienke

AU - Whiteman, David C.

AU - Zelenika, Diana

AU - Han, Jiali

AU - Fang, Shenying

AU - Lee, Jeffrey E.

AU - Wei, Qingyi

AU - Lathrop, G. Mark

AU - Gillanders, Elizabeth M.

AU - Brown, Kevin M.

AU - Goldstein, Alisa M.

AU - Kanetsky, Peter A.

AU - Mann, Graham J.

AU - MacGregor, Stuart

AU - Elder, David E.

AU - Amos, Christopher I.

AU - Hayward, Nicholas K.

AU - Gruis, Nelleke A.

AU - Demenais, Florence

AU - Bishop, Julia A.Newton

AU - Bishop, D. Timothy

PY - 2011/11

Y1 - 2011/11

N2 - We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10 -5 and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10 -3: an SNP in ATM (rs1801516, overall P = 3.4 × 10 -9), an SNP in MX2 (rs45430, P = 2.9 × 10 -9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10 -10). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10 -7 under a fixed-effects model and P = 1.2 × 10 -3 under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.

AB - We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10 -5 and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10 -3: an SNP in ATM (rs1801516, overall P = 3.4 × 10 -9), an SNP in MX2 (rs45430, P = 2.9 × 10 -9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10 -10). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10 -7 under a fixed-effects model and P = 1.2 × 10 -3 under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.

UR - http://www.scopus.com/inward/record.url?scp=80054996042&partnerID=8YFLogxK

U2 - 10.1038/ng.959

DO - 10.1038/ng.959

M3 - Article

C2 - 21983787

AN - SCOPUS:80054996042

SN - 1061-4036

VL - 43

SP - 1108

EP - 1113

JO - Nature Genetics

JF - Nature Genetics

IS - 11

ER -

Genome-wide association study identifies three new melanoma susceptibility loci

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