Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

Stuart MacGregor; Grant W. Montgomery; Jimmy Z. Liu; Zhen Zhen Zhao; Anjali K. Henders; Mitchell Stark; Helen Schmid; Elizabeth A. Holland; David L. Duffy; Mingfeng Zhang; Jodie N. Painter; Dale R. Nyholt; Judith A. Maskiell; Jodie Jetann; Megan Ferguson; Anne E. Cust; Mark A. Jenkins; David C. Whiteman; Håkan Olsson; Susana Puig; Giovanna Bianchi-Scarra; Johan Hansson; Florence Demenais; Maria Teresa Landi; Tadeusz Debniak; Rona Mackie; Esther Azizi; Brigitte Bressac-de Paillerets; Alisa M. Goldstein; Peter A. Kanetsky; Nelleke A. Gruis; David E. Elder; Julia A. Newton-Bishop; D. Timothy Bishop; Mark M. Iles; Per Helsing; Christopher I. Amos; Qingyi Wei; Li-E Wang; Jeffrey E. Lee; Abrar A. Qureshi; Richard F. Kefford; Graham G. Giles; Bruce K. Armstrong; Joanne F. Aitken; Jiali Han; John L. Hopper; Jeffrey M. Trent; Kevin M. Brown; Nicholas G. Martin; Graham J. Mann; Nicholas K. Hayward

doi:10.1038/ng.958

Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

Stuart MacGregor, Grant W. Montgomery, Jimmy Z. Liu, Zhen Zhen Zhao, Anjali K. Henders, Mitchell Stark, Helen Schmid, Elizabeth A. Holland, David L. Duffy, Mingfeng Zhang, Jodie N. Painter, Dale R. Nyholt, Judith A. Maskiell, Jodie Jetann, Megan Ferguson, Anne E. Cust, Mark A. Jenkins, David C. Whiteman, Håkan Olsson, Susana PuigGiovanna Bianchi-Scarra, Johan Hansson, Florence Demenais, Maria Teresa Landi, Tadeusz Debniak, Rona Mackie, Esther Azizi, Brigitte Bressac-de Paillerets, Alisa M. Goldstein, Peter A. Kanetsky, Nelleke A. Gruis, David E. Elder, Julia A. Newton-Bishop, D. Timothy Bishop, Mark M. Iles, Per Helsing, Christopher I. Amos, Qingyi Wei, Li-E Wang, Jeffrey E. Lee, Abrar A. Qureshi, Richard F. Kefford, Graham G. Giles, Bruce K. Armstrong, Joanne F. Aitken, Jiali Han, John L. Hopper, Jeffrey M. Trent, Kevin M. Brown, Nicholas G. Martin, Graham J. Mann, Nicholas K. Hayward

Research output: Contribution to journal › Article › peer-review

Abstract

We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 x 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 x 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.

Original language	English
Pages (from-to)	1114-1118
Journal	Nature Genetics
Volume	43
Issue number	11
DOIs	https://doi.org/10.1038/ng.958
Publication status	Published - 2011

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Cancer and Oncology

UN SDGs

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MacGregor, S., Montgomery, G. W., Liu, J. Z., Zhao, Z. Z., Henders, A. K., Stark, M., Schmid, H., Holland, E. A., Duffy, D. L., Zhang, M., Painter, J. N., Nyholt, D. R., Maskiell, J. A., Jetann, J., Ferguson, M., Cust, A. E., Jenkins, M. A., Whiteman, D. C., Olsson, H., ... Hayward, N. K. (2011). Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3. Nature Genetics, 43(11), 1114-1118. https://doi.org/10.1038/ng.958

@article{fe24832a21d84a129d3c24fb4f672090,

title = "Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3",

abstract = "We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 x 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 x 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.",

author = "Stuart MacGregor and Montgomery, {Grant W.} and Liu, {Jimmy Z.} and Zhao, {Zhen Zhen} and Henders, {Anjali K.} and Mitchell Stark and Helen Schmid and Holland, {Elizabeth A.} and Duffy, {David L.} and Mingfeng Zhang and Painter, {Jodie N.} and Nyholt, {Dale R.} and Maskiell, {Judith A.} and Jodie Jetann and Megan Ferguson and Cust, {Anne E.} and Jenkins, {Mark A.} and Whiteman, {David C.} and H{\aa}kan Olsson and Susana Puig and Giovanna Bianchi-Scarra and Johan Hansson and Florence Demenais and Landi, {Maria Teresa} and Tadeusz Debniak and Rona Mackie and Esther Azizi and {Bressac-de Paillerets}, Brigitte and Goldstein, {Alisa M.} and Kanetsky, {Peter A.} and Gruis, {Nelleke A.} and Elder, {David E.} and Newton-Bishop, {Julia A.} and Bishop, {D. Timothy} and Iles, {Mark M.} and Per Helsing and Amos, {Christopher I.} and Qingyi Wei and Li-E Wang and Lee, {Jeffrey E.} and Qureshi, {Abrar A.} and Kefford, {Richard F.} and Giles, {Graham G.} and Armstrong, {Bruce K.} and Aitken, {Joanne F.} and Jiali Han and Hopper, {John L.} and Trent, {Jeffrey M.} and Brown, {Kevin M.} and Martin, {Nicholas G.} and Mann, {Graham J.} and Hayward, {Nicholas K.}",

year = "2011",

doi = "10.1038/ng.958",

language = "English",

volume = "43",

pages = "1114--1118",

journal = "Nature Genetics",

issn = "1546-1718",

publisher = "Nature Publishing Group",

number = "11",

}

MacGregor, S, Montgomery, GW, Liu, JZ, Zhao, ZZ, Henders, AK, Stark, M, Schmid, H, Holland, EA, Duffy, DL, Zhang, M, Painter, JN, Nyholt, DR, Maskiell, JA, Jetann, J, Ferguson, M, Cust, AE, Jenkins, MA, Whiteman, DC, Olsson, H, Puig, S, Bianchi-Scarra, G, Hansson, J, Demenais, F, Landi, MT, Debniak, T, Mackie, R, Azizi, E, Bressac-de Paillerets, B, Goldstein, AM, Kanetsky, PA, Gruis, NA, Elder, DE, Newton-Bishop, JA, Bishop, DT, Iles, MM, Helsing, P, Amos, CI, Wei, Q, Wang, L-E, Lee, JE, Qureshi, AA, Kefford, RF, Giles, GG, Armstrong, BK, Aitken, JF, Han, J, Hopper, JL, Trent, JM, Brown, KM, Martin, NG, Mann, GJ & Hayward, NK 2011, 'Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3', Nature Genetics, vol. 43, no. 11, pp. 1114-1118. https://doi.org/10.1038/ng.958

TY - JOUR

T1 - Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

AU - MacGregor, Stuart

AU - Montgomery, Grant W.

AU - Liu, Jimmy Z.

AU - Zhao, Zhen Zhen

AU - Henders, Anjali K.

AU - Stark, Mitchell

AU - Schmid, Helen

AU - Holland, Elizabeth A.

AU - Duffy, David L.

AU - Zhang, Mingfeng

AU - Painter, Jodie N.

AU - Nyholt, Dale R.

AU - Maskiell, Judith A.

AU - Jetann, Jodie

AU - Ferguson, Megan

AU - Cust, Anne E.

AU - Jenkins, Mark A.

AU - Whiteman, David C.

AU - Olsson, Håkan

AU - Puig, Susana

AU - Bianchi-Scarra, Giovanna

AU - Hansson, Johan

AU - Demenais, Florence

AU - Landi, Maria Teresa

AU - Debniak, Tadeusz

AU - Mackie, Rona

AU - Azizi, Esther

AU - Bressac-de Paillerets, Brigitte

AU - Goldstein, Alisa M.

AU - Kanetsky, Peter A.

AU - Gruis, Nelleke A.

AU - Elder, David E.

AU - Newton-Bishop, Julia A.

AU - Bishop, D. Timothy

AU - Iles, Mark M.

AU - Helsing, Per

AU - Amos, Christopher I.

AU - Wei, Qingyi

AU - Wang, Li-E

AU - Lee, Jeffrey E.

AU - Qureshi, Abrar A.

AU - Kefford, Richard F.

AU - Giles, Graham G.

AU - Armstrong, Bruce K.

AU - Aitken, Joanne F.

AU - Han, Jiali

AU - Hopper, John L.

AU - Trent, Jeffrey M.

AU - Brown, Kevin M.

AU - Martin, Nicholas G.

AU - Mann, Graham J.

AU - Hayward, Nicholas K.

PY - 2011

Y1 - 2011

N2 - We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 x 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 x 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.

AB - We performed a genome-wide association study of melanoma in a discovery cohort of 2,168 Australian individuals with melanoma and 4,387 control individuals. In this discovery phase, we confirm several previously characterized melanoma-associated loci at MC1R, ASIP and MTAP-CDKN2A. We selected variants at nine loci for replication in three independent case-control studies (Europe: 2,804 subjects with melanoma, 7,618 control subjects; United States 1: 1,804 subjects with melanoma, 1,026 control subjects; United States 2: 585 subjects with melanoma, 6,500 control subjects). The combined meta-analysis of all case-control studies identified a new susceptibility locus at 1q21.3 (rs7412746, P = 9.0 x 10(-11), OR in combined replication cohorts of 0.89 (95% CI 0.85-0.95)). We also show evidence suggesting that melanoma associates with 1q42.12 (rs3219090, P = 9.3 x 10(-8)). The associated variants at the 1q21.3 locus span a region with ten genes, and plausible candidate genes for melanoma susceptibility include ARNT and SETDB1. Variants at the 1q21.3 locus do not seem to be associated with human pigmentation or measures of nevus density.

U2 - 10.1038/ng.958

DO - 10.1038/ng.958

M3 - Article

C2 - 21983785

SN - 1546-1718

VL - 43

SP - 1114

EP - 1118

JO - Nature Genetics

JF - Nature Genetics

IS - 11

ER -

Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3

Abstract

Subject classification (UKÄ)

UN SDGs

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