Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi

Nature Genetics

Volumn 41, Issue 8, 2009, Pages 915-919

  Falchi, Mario ^a,b   Bataille, Veronique ^a,c   Hayward, Nicholas K ^d   Duffy, David L ^d   Bishop, Julia A Newton ^e   Pastinen, Tomi ^f   Cervino, Alessandra ^a   Zhao, Zhen Z ^d   Deloukas, Panos ^g   Soranzo, Nicole ^a,g   Elder, David E ^h   Barrett, Jennifer H ^e   Martin, Nicholas G ^d   Bishop, D Timothy ^e   Montgomery, Grant W ^d   Spector, Timothy D ^a  

^a ST THOMAS HOSPITAL   (United Kingdom)

^b HAMMERSMITH HOSPITAL   (United Kingdom)

^c Hemel Hempstead General Hospital   (United Kingdom)

^d QIMR BERGHOFER MEDICAL RESEARCH INSTITUTE   (Australia)

^e UNIVERSITY OF LEEDS   (United Kingdom)

^f MCGILL UNIVERSITY   (Canada)

^g WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^h UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; UNTRANSLATED RNA;

ALLELE; ARTICLE; ATTRIBUTABLE RISK; AUSTRALIA; CANCER RISK; CANCER SUSCEPTIBILITY; CHROMOSOME 22Q; CHROMOSOME 9P; COHORT ANALYSIS; FAMILIAL CANCER; GENE FREQUENCY; GENE LOCUS; GENE MAPPING; GENETIC ASSOCIATION; GENOME; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MELANOCYTIC NEVUS; MELANOMA; NEVUS; POPULATION RISK; PRIORITY JOURNAL; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM; TWINS; UNITED KINGDOM;

ALLELES; CHROMOSOMES, HUMAN, PAIR 22; CHROMOSOMES, HUMAN, PAIR 9; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GREAT BRITAIN; HOMOZYGOTE; HUMANS; MELANOMA; NEVUS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRECANCEROUS CONDITIONS; SKIN NEOPLASMS;

EID: 68149100807     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.410     Document Type: Article

References (31)

1. Karim-Kos, H.E. et al. Recent trends of cancer in Europe: a combined approach of incidence, survival and mortality for 17 cancer sites since the 1990s. Eur. J. Cancer 44, 1345-1389 (2008).
2. Goldstein, A.M. et al. Features associated with germline CDKN2A mutations: a GenoMEL study of melanoma-prone families from three continents. J. Med. Genet. 44, 99-106 (2007).
3. Palmieri, G. et al. Definition of the role of chromosome 9p21 in sporadic melanoma through genetic analysis of primary tumours and their metastases. The Melanoma Cooperative Group. Br. J. Cancer 83, 1707-1714 (2000).
4. Fountain, J.W., Bale, S.J., Housman, D.E. & Dracopoli, N.C. Genetics of melanoma. Cancer Surv. 9, 645-671 (1990).
5. Gandini, S. et al. Meta-analysis of risk factors for cutaneous melanoma: I. Common and atypical naevi. Eur. J. Cancer 41, 28-44 (2005).
6. Falchi, M., Spector, T.D., Perks, U., Kato, B.S. & Bataille, V. Genome-wide search for nevus density shows linkage to two melanoma loci on chromosome 9 and identifies a new QTL on 5q31 in an adult twin cohort. Hum. Mol. Genet. 15, 2975-2979 (2006).
7. Zhu, G. et al. A genome-wide scan for naevus count: linkage to CDKN2A and to other chromosome regions. Eur. J. Hum. Genet. 15, 94-102 (2007).
8. Ma, Z., Wang, X., Nowatzke, W., Ramanadham, S. & Turk, J. Human pancreatic islets express mRNA species encoding two distinct catalytically active isoforms of group VI phospholipase A2 (iPLA2) that arise from an exon-skipping mechanism of alternative splicing of the transcript from the iPLA2 gene on chromosome 22q13.1. J. Biol. Chem. 274, 9607-9616 (1999).
9. Garcia-Castellano, J.M. et al. Methylthioadenosine phosphorylase gene deletions are common in osteosarcoma. Clin. Cancer Res. 8, 782-787 (2002).
10. Hori, Y. et al. The methylthioadenosine phosphorylase gene is frequently co-deleted with the p16INK4a gene in acute type adult T-cell leukemia. Int. J. Cancer 75, 51-56 (1998).
11. Christopher, S.A., Diegelman, P., Porter, C.W. & Kruger, W.D. Methylthioadenosine phosphorylase, a gene frequently codeleted with p16(cdkN2a/ARF), acts as a tumor suppressor in a breast cancer cell line. Cancer Res. 62, 6639-6644 (2002).
12. Behrmann, I. et al. Characterization of methylthioadenosin phosphorylase (MTAP) expression in malignant melanoma. Am. J. Pathol. 163, 683-690 (2003).
13. Pasmant, E. et al. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 67, 3963-3969 (2007).
14. Easton, D.F. & Eeles, R.A. Genome-wide association studies in cancer. Hum. Mol. Genet. 17, R109-R115 (2008).
15. Hosgood, H.D. III et al. Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. Carcinogenesis 29, 1938-1943 (2008).
16. 2+-independent phospholipase A2 in cell growth and signaling. Biochem. Pharmacol. 76, 1059-1067 (2008).
17. 2+-independent phospholipase A2 but not cytosolic phospholipase A2, which undergoes proteolytic inactivation. J. Biol. Chem. 273, 13870-13877 (1998).
18. Bao, S. et al. Effects of stable suppression of Group VIA phospholipase A2 expression on phospholipid content and composition, insulin secretion, and proliferation of INS-1 insulinoma cells. J. Biol. Chem. 281, 187-198 (2006).
19. Song, Y. et al. Inhibition of calcium-independent phospholipase A2 suppresses proliferation and tumorigenicity of ovarian carcinoma cells. Biochem. J. 406, 427-436 (2007).
20. 2+-independent phospholipase A2 decreases prostate cancer cell growth by p53-dependent and independent mechanisms. J. Pharmacol. Exp. Ther. 326, 59-68 (2008).
21. Bishop, D.T. et al. Genome-wide association study identifies three loci associated with melanoma risk. Nat. Genet advance online publication, doi:10.1038/ng.411 (5 July 2009).
22. Bataille, V., Snieder, H., MacGregor, A.J., Sasieni, P. & Spector, D.T. Genetics of risk factors for melanoma: an adult twin study of nevi and freckles. J. Natl. Cancer Inst. 92, 457-463 (2000).
23. Sturm, R.A. et al. A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am. J. Hum. Genet. 82, 424-431 (2008).
24. Baxter, A.J. et al. The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA); study design, baseline characteristics, and repeatability of phenotype and sun exposure measures. Twin Res. Hum. Genet. 11, 183-196 (2008).
25. Richards, J.B. et al. Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study. Lancet 371, 1505-1512 (2008).
26. Zhao, Z.Z. et al. Genetic variation in tumour necrosis factor and lymphotoxin is not associated with endometriosis in an Australian sample. Hum. Reprod. 22, 2389-2397 (2007).
27. Chen, W.M. & Abecasis, G.R. Family-based association tests for genomewide association scans. Am. J. Hum. Genet. 81, 913-926 (2007).
28. Devlin, B., Roeder, K. & Wasserman, L. Genomic control, a new approach to genetic-based association studies. Theor. Popul. Biol. 60, 155-166 (2001).
29. Lange, K., Weeks, D. & Boehnke, M. Programs for Pedigree Analysis: MENDEL, FISHER, and dGENE. Genet. Epidemiol. 5, 471-472 (1988).
30. Saxena, R. et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316, 1331-1336 (2007).
31. Prokopenko, I. et al. Variants in MTNR1B influence fasting glucose levels. Nat. Genet. 41, 77-81 (2009).