Genome-wide association study identifies three new melanoma susceptibility loci
Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci. We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals...
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| Published in | Nature genetics Vol. 43; no. 11; pp. 1108 - 1113 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.11.2011
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci.
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. |
|---|---|
| AbstractList | 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 super(-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 super(-3): an SNP in ATM (rs1801516, overall P = 3.4 x 10 super(-9)), an SNP in MX2 (rs45430, P = 2.9 x 10 super(-9)) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 x 10 super(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 x 10 super(-7) under a fixed-effects model and P = 1.2 x 10 super(-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. 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. 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 x 10(-9)), an SNP in MX2 (rs45430, P = 2.9 x 10-9) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 x 10(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 x 10(-7) under a fixed-effects model and P = 1.2 x 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. Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci. 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^sup -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^sup -3^: an SNP in ATM (rs1801516, overall P = 3.4 × 10^sup -9^), an SNP in MX2 (rs45430, P = 2.9 × 10^sup -9^) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10^sup -10^). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10^sup -7^ under a fixed-effects model and P = 1.2 × 10^sup -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. [PUBLICATION 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. 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.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. Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci. 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. We report a genome-wide association study of melanoma, conducted by GenoMEL, of 2,981 cases, of European ancestry, and 1,982 study-specific controls, plus a further 6,426 French and UK population controls, all genotyped for 317,000 or 610,000 SNPs. The analysis confirmed previously known melanoma susceptibility loci. The 7 novel 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 Houston, Texas). Additional replication came from UK and Dutch case-control series. Three of the 7 regions replicated at p<10 −3 : an ATM missense polymorphism (rs1801516, overall p=3.4×10 −9 ); a polymorphism within MX2 (rs45430, p=2.9×10 −9 ) and a SNP adjacent to CASP8 (rs13016963, p=8.6×10 −10 ). A fourth region near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication. Unlike the previously known regions, the novel loci showed no association with nevus or pigmentation phenotypes in a large UK case-control series. |
| Audience | Academic |
| Author | Wei, Qingyi Bergman, Wilma Kefford, Richard F Höiom, Veronica Van Belle, Patricia van der Stoep, Nienke Lee, Jeffrey E Calista, Donato Novakovic, Srdjan Aitken, Joanne F Puig, Susana Amos, Christopher I Gillanders, Elizabeth M Fang, Shenying Avril, Marie-Francoise Barrett, Jennifer H Easton, Douglas F Montgomery, Grant W Hansson, Johan Han, Jiali Puig-Butille, Joan Anton Bianchi-Scarrà, Giovanna Demenais, Florence Dębniak, Tadeusz Corda, Eve Cannon-Albright, Lisa A Friedman, Eitan Hopper, John L Goldstein, Alisa M Gruis, Nelleke A Tuominen, Rainer van Nieuwpoort, Frans A Pastorino, Lorenza Iles, Mark M Mann, Graham J Mackie, Rona Duffy, David Hayward, Nicholas K Janssen, Bart Whiteman, David C Akslen, Lars A Zelenika, Diana Andresen, Per Arne Lang, Julie Malvehy, Josep Bishop, Julia A Newton Lubiński, Jan Bakker, Bert Harland, Mark Azizi, Esther Jönsson, Göran Brown, Kevin M Snowden, Helen Jenkins, Mark A Armstrong, Bruce K Molven, Anders Ingvar, Christian Landi, Giorgio Martin, Nicholas G Dunning, Alison M Randerson-Moor, Juliette Bressac-de Pa |
| AuthorAffiliation | 39 Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA 29 Public Health and Health Policy, University of Glasgow, UK 33 Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA 13 Département de Biopathologie, Service de Génétique , Institut de Cancérologie Gustave Roussy, Villejuif, France 21 University of Cambridge, Cambridge, England, United Kingdom 16 Fondation Jean Dausset-CEPH, 75010, Paris, France 34 Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA 30 Melanoma Unit, Dermatology Department, Hospital Clinic, IDIBAPS, Barcelona, Spain and CIBER de Enfermedades Raras, Barcelona, Spain 32 Commissariat à l'énergie Atomique, Institut de Génomique, Centre National de Génotypage, Evry, France 3 Pathology Clinic, Oslo University Hospital, Rikshospitalet, N-0027 Oslo, Norway 15 Division of Genetic Epidemiology, Depa |
| AuthorAffiliation_xml | – name: 5 Dept. of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway – name: 43 Université Paris Diderot Paris 7, Institut Universitaire d'Hématologied'Hémtologie, Paris, France – name: 11 Department of Internal Medicine (DIMI), University of Genoa, V. le Benedetto XV 6, 16132 Genova, Italy – name: 28 Department of Medical Genetics, University of Glasgow, UK – name: 21 University of Cambridge, Cambridge, England, United Kingdom – name: 38 Department of Epidemiology Unit 1365, UT MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA – name: 18 Cancer Epidemiology and Services Research, Sydney School of Public Health, The University of Sydney, Sydney, Australia – name: 26 ServiceXS, Plesmanlaan 1d, 2333 BZ Leiden, The Netherlands – name: 1 Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital, Leeds, UK – name: 7 AP-HP, Hôpital Cochin, Service de Dermatologie, Faculté Paris 5, Paris, France – name: 40 Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Gaithersburg, MD 20892, USA – name: 17 Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology, School of Population Health, University of Melbourne, Melbourne, Australia – name: 16 Fondation Jean Dausset-CEPH, 75010, Paris, France – name: 31 Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA – name: 2 Viertel Centre for Research in Cancer Control, The Cancer Council, Queensland, Spring Hill, Brisbane, Australia – name: 42 Section of Computational and Genetic Epidemiology, Epidemiology, UT M.D. Anderson Cancer Center, 1155 Pressler St., Houston, TX 77030, USA – name: 27 Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute. NIH, Bethesda, MD 20892-7236, USA – name: 15 Division of Genetic Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA – name: 37 Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA – name: 22 UMR U557 Inserm; U1125 Inra; Cnam; Paris 13, CRNH Idf, 74 rue Marcel Cachin F-93017 Bobigny – name: 12 INSERM, U946, Fondation Jean-Dausset–CEPH, 75010 Paris, France – name: 4 The Gade Institute, University of Bergen, N-5020 Bergen, Norway – name: 19 International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland – name: 3 Pathology Clinic, Oslo University Hospital, Rikshospitalet, N-0027 Oslo, Norway – name: 24 Institute of Oncology Ljubljana, Zaloska 2, 1000 Ljubljana, Slovenia – name: 32 Commissariat à l'énergie Atomique, Institut de Génomique, Centre National de Génotypage, Evry, France – name: 35 Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA – name: 23 Department of Oncology-Pathology, Karolinska Institutet, SE-171 77 Stockholm, Sweden – name: 13 Département de Biopathologie, Service de Génétique , Institut de Cancérologie Gustave Roussy, Villejuif, France – name: 10 Department of Dermatology, Leiden University Medical Centre, Leiden, The Netherlands – name: 20 Queensland Institute of Medical Research, 300 Herston Rd, Brisbane, Queensland 4029, Australia – name: 36 Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, Texas – name: 14 Dermatology Unit, Maurizio Bufalini Hospital, 47023 Cesena, Italy – name: 8 Department of Dermatology, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel – name: 25 Department of Oncology, University Hospital Lund, Barngatan 2B, 221 85 Lund, Sweden – name: 34 Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA – name: 39 Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD 21224, USA – name: 33 Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA – name: 30 Melanoma Unit, Dermatology Department, Hospital Clinic, IDIBAPS, Barcelona, Spain and CIBER de Enfermedades Raras, Barcelona, Spain – name: 41 Centre for Clinical Epidemiology & Biostatistics and Department of Biostatistics & Epidemiology, 219 Blockley Hall, University of Pennsylvania, USA – name: 6 Westmead Millennium Institute, PO Box 412, Darcy Rd, Westmead, NSW, 2145, Australia – name: 29 Public Health and Health Policy, University of Glasgow, UK – name: 9 Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands |
| Author_xml | – sequence: 1 givenname: Jennifer H surname: Barrett fullname: Barrett, Jennifer H organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 2 givenname: Mark M surname: Iles fullname: Iles, Mark M organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 3 givenname: Mark surname: Harland fullname: Harland, Mark organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 4 givenname: John C surname: Taylor fullname: Taylor, John C organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 5 givenname: Joanne F surname: Aitken 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III (ISCIII) – sequence: 50 givenname: Joan Anton surname: Puig-Butille fullname: Puig-Butille, Joan Anton organization: Dermatology Department, Melanoma Unit, Hospital Clinic, Institut de Investigacó Biomèdica August Pi Suñe, Universitat de Barcelona, Centre of Biomedical Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII) – sequence: 51 givenname: Juliette surname: Randerson-Moor fullname: Randerson-Moor, Juliette organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 52 givenname: Helen surname: Snowden fullname: Snowden, Helen organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 53 givenname: Rainer surname: Tuominen fullname: Tuominen, Rainer organization: Department of Oncology-Pathology, Karolinska Institutet – sequence: 54 givenname: Patricia surname: Van Belle fullname: Van Belle, Patricia organization: Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine – sequence: 55 givenname: Nienke surname: van der Stoep fullname: van der Stoep, Nienke organization: Department of Clinical Genetics, Center of Human and Clinical Genetics, Leiden University Medical Center – sequence: 56 givenname: David C surname: Whiteman fullname: Whiteman, David C organization: Queensland Institute of Medical Research – sequence: 57 givenname: Diana surname: Zelenika fullname: Zelenika, Diana organization: Commissariat à l′Energie Atomique, Institut de Génomique, Centre National de Génotypage – sequence: 58 givenname: Jiali surname: Han fullname: Han, Jiali organization: Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Department of Medicine, Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, Department of Epidemiology, Harvard School 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University of Pennsylvania School of Medicine – sequence: 70 givenname: Christopher I surname: Amos fullname: Amos, Christopher I organization: Department of Genetics, University of Texas M.D. Anderson Cancer Center – sequence: 71 givenname: Nicholas K surname: Hayward fullname: Hayward, Nicholas K organization: Queensland Institute of Medical Research – sequence: 72 givenname: Nelleke A surname: Gruis fullname: Gruis, Nelleke A organization: Department of Dermatology, Leiden University Medical Centre – sequence: 73 givenname: Florence surname: Demenais fullname: Demenais, Florence organization: INSERM, U946, Fondation Jean-Dausset–CEPH, Fondation Jean Dausset–CEPH, Université Paris Diderot Paris 7, Institut Universitaire d'Hématologie – sequence: 74 givenname: Julia A Newton surname: Bishop fullname: Bishop, Julia A Newton organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital – sequence: 75 givenname: D Timothy surname: Bishop fullname: Bishop, D Timothy email: d.t.bishop@leeds.ac.uk organization: Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, Leeds Cancer Research UK Centre, St James's University Hospital |
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| ContentType | Journal Article |
| Contributor | Castel, Teresa Bergman, Wilma Harrison, Jane Kefford, Richard F van der Stoep, Nienke Aitken, Joanne F Puig, Susana Marti-Laborda, Rosa Bertazzi, Pier Alberto Taylor, C Barrett, Jennifer H Brochez, Lieve Montgomery, Grant W Purdie, David Schmid, Helen Vilalta, Antonio Gabriel, Daniel Bruno, William Hopper, John L van Praag, Marinus Pastorino, Lorenza Arcangeli, Fabio Crijns, Marianne Mann, Graham J Bouwes Bavinck, Jan Nico Mackie, Rona Duffy, David Hayward, Nicholas K Iles, M Snels, Dyon Arguís, Pedro Affleck, Paul Gliori, Sara Bakker, Bert Out, Coby Karpavicius, Birute Bekkenk, Marcel Armstrong, Bruce K Queirolo, Paola Haynes, Sue Jenkins, Mark Kukalizch, Kairen Parsons, Peter Gonzalez, Melinda Nasti, Sabina Battistuzzi, Linda Puig Butille, Joan-Anton Rull, Ramon Landi, Maria Teresa Giles, Graham G van der Drift, Clasine Gargiulo, Sara Sánchez, Marcelo Taylor, Yvonne Mack, Tricia Vilella, Ramon Green, Adele Cuellar, Francisco Minghetti, Paola Newton Bishop, Julia A Calista, Donato Campo, Antonio Randerson, Juliette Bianchi, Giovanna Gerritsen, Ria Universitat de Barcelona |
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| Copyright | Springer Nature America, Inc. 2011 2015 INIST-CNRS COPYRIGHT 2011 Nature Publishing Group Copyright Nature Publishing Group Nov 2011 (c) Barrett, Jennifer H. et al., 2011 info:eu-repo/semantics/openAccess Distributed under a Creative Commons Attribution 4.0 International License |
| Copyright_xml | – notice: Springer Nature America, Inc. 2011 – notice: 2015 INIST-CNRS – notice: COPYRIGHT 2011 Nature Publishing Group – notice: Copyright Nature Publishing Group Nov 2011 – notice: (c) Barrett, Jennifer H. et al., 2011 info:eu-repo/semantics/openAccess – notice: Distributed under a Creative Commons Attribution 4.0 International License |
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| Keywords | Identification Malignant tumor Locus Malignant melanoma Cancer WOMEN CUTANEOUS MALIGNANT-MELANOMA POPULATION METAANALYSIS GENE PHENOTYPIC CHARACTERISTICS RISK SEQUENCE VARIANTS CANCER NEVI |
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Cancer20091259099171:CAS:528:DC%2BD1MXnsFeltb8%3D10.1002/ijc.24327 Newton-BishopJASerum 25-hydroxyvitamin D3 levels are associated with breslow thickness at presentation and survival from melanomaJ. Clin. Oncol.200927543954441:CAS:528:DC%2BD1MXhsFKkt7vK10.1200/JCO.2009.22.1135 GarnerCUpward bias in odds ratio estimates from genome-wide association studiesGenet. Epidemiol.20073128829510.1002/gepi.20209 FernandezLPSLC45A2: a novel malignant melanoma-associated geneHum. Mutat.200829116111671:CAS:528:DC%2BD1cXht1ShtrjM10.1002/humu.20804 RaimondiSMC1R variants, melanoma and red hair color phenotype: a meta-analysisInt. J. Cancer2008122275327601:CAS:528:DC%2BD1cXht1eku7rJ10.1002/ijc.23396 DerSimonianRLairdNMeta-analysis in clinical trialsControl. Clin. Trials198671771881:STN:280:DyaL2s7gsVamtA%3D%3D10.1016/0197-2456(86)90046-2 GudbjartssonDFASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinomaNat. Genet.2008408868911:CAS:528:DC%2BD1cXnslKktbg%3D10.1038/ng.161 BrownKMCommon sequence variants on 20q11.22 confer melanoma susceptibilityNat. Genet.2008408388401:CAS:528:DC%2BD1cXnslKkurw%3D10.1038/ng.163 HollyEAAstonDACressRDAhnDKKristiansenJJCutaneous melanoma in women. I. Exposure to sunlight, ability to tan, and other risk factors related to ultraviolet lightAm. J. Epidemiol.19951419239331:STN:280:DyaK2M3lvFKrtA%3D%3D10.1093/oxfordjournals.aje.a117359 CurtinJADistinct sets of genetic alterations in melanomaN. Engl. J. Med.2005353213521471:CAS:528:DC%2BD2MXht1ajtLjP10.1056/NEJMoa050092 HigginsJPThompsonSGQuantifying heterogeneity in a meta-analysisStat. Med.2002211539155810.1002/sim.1186 HollyEAAstonDACressRDAhnDKKristiansenJJCutaneous melanoma in women. II. Phenotypic characteristics and other host-related factorsAm. J. 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Cancer20091244204281:CAS:528:DC%2BD1MXhvFejug%3D%3D10.1002/ijc.23869 PattersonNPriceALReichDPopulation structure and eigenanalysisPLoS Genet.20062e19010.1371/journal.pgen.0020190 NaldiLCutaneous malignant melanoma in women. Phenotypic characteristics, sun exposure, and hormonal factors: a case-control study from ItalyAnn. Epidemiol.20051554555010.1016/j.annepidem.2004.10.005 Gauderman, W.J. & Morrison, J.M. QUANTO 1.1: A Computer Program for Power and Sample Size Calculations for Genetic-Epidemiology Studies. (2006). Available from http://hydra.usc.edu/gxe. Titus-ErnstoffLPigmentary characteristics and moles in relation to melanoma riskInt. J. Cancer20051161441491:CAS:528:DC%2BD2MXls1KjtL4%3D10.1002/ijc.21001 BishopDTGenome-wide association study identifies three loci associated with melanoma riskNat. Genet.2009419209251:CAS:528:DC%2BD1MXotVClsb8%3D10.1038/ng.411 ClaytonDTesting for association on the X chromosomeBiostatistics2008959360010.1093/biostatistics/kxn007 KanetskyPAPopulation-based study of natural variation in the melanocortin-1 receptor gene and melanomaCancer Res.200666933093371:CAS:528:DC%2BD28Xps1ahs78%3D10.1158/0008-5472.CAN-06-1634 DuffyDLIRF4 variants have age-specific effects on nevus count and predispose to melanomaAm. J. Hum. Genet.2010876161:CAS:528:DC%2BC3cXpsFegs7s%3D10.1016/j.ajhg.2010.05.017 S Raimondi (BFng959_CR9) 2008; 122 L Titus-Ernstoff (BFng959_CR3) 2005; 116 EA Holly (BFng959_CR5) 1995; 141 J Han (BFng959_CR19) 2008; 4 N Patterson (BFng959_CR28) 2006; 2 AL Price (BFng959_CR29) 2006; 38 R DerSimonian (BFng959_CR32) 1986; 7 M Yin (BFng959_CR22) 2010; 31 L Naldi (BFng959_CR2) 2005; 15 DF Gudbjartsson (BFng959_CR11) 2008; 40 H Nan (BFng959_CR17) 2009; 125 M Guedj (BFng959_CR16) 2008; 29 JP Higgins (BFng959_CR31) 2002; 21 DL Duffy (BFng959_CR15) 2010; 130 EA Holly (BFng959_CR4) 1995; 141 DT Bishop (BFng959_CR8) 2009; 41 RJ Pruim (BFng959_CR27) 2010; 26 MF Lavin (BFng959_CR23) 2008; 9 LP Fernandez (BFng959_CR20) 2008; 29 JA Curtin (BFng959_CR25) 2005; 353 JA Newton-Bishop (BFng959_CR26) 2010; 19 DM Baird (BFng959_CR21) 2010; 12 PA Kanetsky (BFng959_CR10) 2006; 66 D Clayton (BFng959_CR30) 2008; 9 YM Chang (BFng959_CR7) 2009; 124 BFng959_CR35 DL Duffy (BFng959_CR14) 2010; 87 C Garner (BFng959_CR24) 2007; 31 BFng959_CR1 JA Newton-Bishop (BFng959_CR34) 2009; 27 KM Brown (BFng959_CR13) 2008; 40 V Bataille (BFng959_CR6) 1996; 73 M Falchi (BFng959_CR12) 2009; 41 T Rafnar (BFng959_CR18) 2009; 41 JA Newton-Bishop (BFng959_CR33) 2011; 47 |
| References_xml | – reference: ChangYMA pooled analysis of melanocytic nevus phenotype and the risk of cutaneous melanoma at different latitudesInt. J. Cancer20091244204281:CAS:528:DC%2BD1MXhvFejug%3D%3D10.1002/ijc.23869 – reference: RaimondiSMC1R variants, melanoma and red hair color phenotype: a meta-analysisInt. J. Cancer2008122275327601:CAS:528:DC%2BD1cXht1eku7rJ10.1002/ijc.23396 – reference: PattersonNPriceALReichDPopulation structure and eigenanalysisPLoS Genet.20062e19010.1371/journal.pgen.0020190 – reference: Newton-BishopJASerum 25-hydroxyvitamin D3 levels are associated with breslow thickness at presentation and survival from melanomaJ. Clin. Oncol.200927543954441:CAS:528:DC%2BD1MXhsFKkt7vK10.1200/JCO.2009.22.1135 – reference: GudbjartssonDFASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinomaNat. Genet.2008408868911:CAS:528:DC%2BD1cXnslKktbg%3D10.1038/ng.161 – reference: PruimRJLocusZoom: regional visualization of genome-wide association scan resultsBioinformatics201026233623371:CAS:528:DC%2BC3cXhtFGhu73E10.1093/bioinformatics/btq419 – reference: HollyEAAstonDACressRDAhnDKKristiansenJJCutaneous melanoma in women. I. Exposure to sunlight, ability to tan, and other risk factors related to ultraviolet lightAm. J. Epidemiol.19951419239331:STN:280:DyaK2M3lvFKrtA%3D%3D10.1093/oxfordjournals.aje.a117359 – reference: NaldiLCutaneous malignant melanoma in women. Phenotypic characteristics, sun exposure, and hormonal factors: a case-control study from ItalyAnn. Epidemiol.20051554555010.1016/j.annepidem.2004.10.005 – reference: YinMYanJWeiSWeiQCASP8 polymorphisms contribute to cancer susceptibility: evidence from a meta-analysis of 23 publications with 55 individual studiesCarcinogenesis2010318508571:CAS:528:DC%2BC3cXlvVWjsLo%3D10.1093/carcin/bgq047 – reference: GarnerCUpward bias in odds ratio estimates from genome-wide association studiesGenet. Epidemiol.20073128829510.1002/gepi.20209 – reference: BrownKMCommon sequence variants on 20q11.22 confer melanoma susceptibilityNat. Genet.2008408388401:CAS:528:DC%2BD1cXnslKkurw%3D10.1038/ng.163 – reference: NanHKraftPHunterDJHanJGenetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in CaucasiansInt. J. Cancer20091259099171:CAS:528:DC%2BD1MXnsFeltb8%3D10.1002/ijc.24327 – reference: BatailleVRisk of cutaneous melanoma in relation to the numbers, types and sites of naevi: a case-control studyBr. J. Cancer199673160516111:STN:280:DyaK283mt1Wnuw%3D%3D10.1038/bjc.1996.302 – reference: BairdDMVariation at the TERT locus and predisposition for cancerExpert Rev. Mol. Med.201012e1610.1017/S146239941000147X – reference: KanetskyPAPopulation-based study of natural variation in the melanocortin-1 receptor gene and melanomaCancer Res.200666933093371:CAS:528:DC%2BD28Xps1ahs78%3D10.1158/0008-5472.CAN-06-1634 – reference: FalchiMGenome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous neviNat. Genet.2009419159191:CAS:528:DC%2BD1MXotVCltro%3D10.1038/ng.410 – reference: Newton-BishopJARelationship between sun exposure and melanoma risk for tumours in different body sites in a large case-control study in a temperate climateEur. J. Cancer20114773274110.1016/j.ejca.2010.10.008 – reference: ClaytonDTesting for association on the X chromosomeBiostatistics2008959360010.1093/biostatistics/kxn007 – reference: CurtinJADistinct sets of genetic alterations in melanomaN. Engl. J. Med.2005353213521471:CAS:528:DC%2BD2MXht1ajtLjP10.1056/NEJMoa050092 – reference: PriceALPrincipal components analysis corrects for stratification in genome-wide association studiesNat. Genet.2006389049091:CAS:528:DC%2BD28XnsVCgsrg%3D10.1038/ng1847 – reference: Gauderman, W.J. & Morrison, J.M. QUANTO 1.1: A Computer Program for Power and Sample Size Calculations for Genetic-Epidemiology Studies. (2006). Available from http://hydra.usc.edu/gxe. – reference: DuffyDLMultiple pigmentation gene polymorphisms account for a substantial proportion of risk of cutaneous malignant melanomaJ. Invest. 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| Snippet | Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci.
We... We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with... Timothy Bishop and colleagues of the GenoMEL Consortium report a genome-wide association study for melanoma, identifying three new susceptibility loci. We report a genome-wide association study of melanoma, conducted by GenoMEL, of 2,981 cases, of European ancestry, and 1,982 study-specific controls, plus a... |
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| SubjectTerms | 631/208/205/2138 631/208/727/2000 692/699/67/1813/1634 Agriculture Analysis Animal Genetics and Genomics Awards & honors Biological and medical sciences Biomedical and Life Sciences Biomedicine Cancer Cancer and Oncology Cancer och onkologi Cancer Research Case-Control Studies Chromosomes Clinical Medicine Càncer de pell Dermatology Disease susceptibility Family medical history Fundamental and applied biological sciences. Psychology Gene Function Genealogy Genes Genetic aspects Genetic Predisposition to Disease Genetic research Genetics of eukaryotes. Biological and molecular evolution Genome-Wide Association Study Genomes Genomics Genètica mèdica Human Genetics Humans Kirurgi Klinisk medicin letter Life Sciences Medical and Health Sciences Medical genetics Medical research Medical sciences Medicin och hälsovetenskap Melanoma Melanoma - genetics Pigmentation Polymorphism, Single Nucleotide Single nucleotide polymorphisms Skin cancer Skin Neoplasms - genetics Statistical analysis Studies Surgery Tumors of the skin and soft tissue. Premalignant lesions |
| Title | Genome-wide association study identifies three new melanoma susceptibility loci |
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