Genome-wide linkage analysis of Swedish families to identify putative susceptibility loci for cutaneous malignant melanoma

Genes Chromosomes and Cancer

Volumn 50, Issue 12, 2011, Pages 1076-1084

  Höiom, Veronica ^a   Tuominen, Rainer ^a   Hansson, Johan ^a  

^a KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A;

ADULT; ARTICLE; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; LINKAGE ANALYSIS; MELANOMA; NONPARAMETRIC TEST; PARAMETRIC TEST; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SWEDEN;

ADULT; CHROMOSOMES, HUMAN, PAIR 17; FAMILY HEALTH; FEMALE; GENES, P16; GENETIC LINKAGE; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GERM-LINE MUTATION; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MELANOMA; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; SKIN NEOPLASMS; SWEDEN;

EID: 80053640638     PISSN: 10452257     EISSN: 10982264     Source Type: Journal    
DOI: 10.1002/gcc.20931     Document Type: Article

References (55)

1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30: 97-101.
2. Aitken JF, Duffy DL, Green A, Youl P, MacLennan R, Martin NG. 1994. Heterogeneity of melanoma risk in families of melanoma patients. Am J Epidemiol 140: 961-973.
3. Bale SJ, Dracopoli NC, Tucker MA, Clark WH, Jr., Fraser MC, Stanger BZ, Green P, Donis-Keller H, Housman DE, Greene MH. 1989. Mapping the gene for hereditary cutaneous malignant melanoma-dysplastic nevus to chromosome 1p. N Engl J Med 320: 1367-1372.
4. Bayle J, Letard S, Frank R, Dubreuil P, De Sepulveda P. 2004. Suppressor of cytokine signaling 6 associates with KIT and regulates KIT receptor signaling. J Biol Chem 279: 12249-12259.
5. Begg CB, Hummer A, Mujumdar U, Armstrong BK, Kricker A, Marrett LD, Millikan RC, Gruber SB, Anton-Culver H, Klotz JB, Zanetti R, Gallagher RP, Dwyer T, Rebbeck TR, Berwick M. 2004. Familial aggregation of melanoma risks in a large population-based sample of melanoma cases. Cancer Causes Control 15: 957-965.
6. Bishop DT, Demenais F, Goldstein AM, Bergman W, Bishop JN, Bressac-de Paillerets B, Chompret A, Ghiorzo P, Gruis N, Hansson J, et al. 2002. Geographical variation in the penetrance of CDKN2A mutations for melanoma. J Natl Cancer Inst 94: 894-903.
7. Bishop DT, Demenais F, Iles MM, Harland M, Taylor JC, Corda E, Randerson-Moor J, Aitken JF, Avril MF, Azizi E, et al. 2009. Genome-wide association study identifies three loci associated with melanoma risk. Nat Genet 41: 920-925.
8. Board of Health and Welfare. 2010. Cancer incidence in Sweden 2009 [Cancerförekomst i Sverige 2009]. Stockholm: Board of Health and Welfare.
9. Borg A, Johannsson U, Johannsson O, Hakansson S, Westerdahl J, Masback A, Olsson H, Ingvar C. 1996. Novel germline p16 mutation in familial malignant melanoma in southern Sweden. Cancer Res 56: 2497-2500.
10. Boyles AL, Scott WK, Martin ER, Schmidt S, Li YJ, Ashley-Koch A, Bass MP, Schmidt M, Pericak-Vance MA, Speer MC, Hauser ER. 2005. Linkage disequilibrium inflates type I error rates in multipoint linkage analysis when parental genotypes are missing. Hum Hered 59: 220-227.
11. Broberg K, Huynh E, Schlawicke Engstrom K, Bjork J, Albin M, Ingvar C, Olsson H, Hoglund M. 2009. Association between polymorphisms in RMI1, TOP3A, and BLM and risk of cancer, a case-control study. BMC Cancer 9: 140.
12. Brown KM, Macgregor S, Montgomery GW, Craig DW, Zhao ZZ, Iyadurai K, Henders AK, Homer N, Campbell MJ, Stark M, Thomas S, Schmid H, Holland EA, Gillanders EM, Duffy DL, Maskiell JA, Jetann J, Ferguson M, Stephan DA, Cust AE, Whiteman D, Green A, Olsson H, Puig S, Ghiorzo P, Hansson J, Demenais F, Goldstein AM, Gruis NA, Elder DE, Bishop JN, Kefford RF, Giles GG, Armstrong BK, Aitken JF, Hopper JL, Martin NG, Trent JM, Mann GJ, Hayward NK. 2008. Common sequence variants on 20q11.22 confer melanoma susceptibility. Nat Genet 40: 838-840.
13. Carraway KL, Theodoropoulos G, Kozloski GA, Carothers Carraway CA. 2009. Muc4/MUC4 functions and regulation in cancer. Future Oncol 5: 1631-1640.
14. Cirulli ET, Goldstein DB. 2010. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11: 415-425.
15. Do KA, Aitken JF, Green AC, Martin NG. 2004. Analysis of melanoma onset: Assessing familial aggregation by using estimating equations and fitting variance components via Bayesian random effects models. Twin Res 7: 98-113.
16. Duffy DL, Iles MM, Glass D, Zhu G, Barrett JH, Hoiom V, Zhao ZZ, Sturm RA, Soranzo N, Hammond C, Kvaskoff M, Whiteman DC, Mangino M, Hansson J, Newton-Bishop JA, Bataille V, Hayward NK, Martin NG, Bishop DT, Spector TD, Montgomery GW. 2010. IRF4 variants have age-specific effects on nevus count and predispose to melanoma. Am J Hum Genet 87: 6-16.
17. Evans DM, Cardon LR. 2004. Guidelines for genotyping in genomewide linkage studies: Single-nucleotide-polymorphism maps versus microsatellite maps. Am J Hum Genet 75: 687-692.
18. Fletcher O, Houlston RS. 2010. Architecture of inherited susceptibility to common cancer. Nat Rev Cancer 10: 353-361.
19. Gillanders E, Juo SH, Holland EA, Jones M, Nancarrow D, Freas-Lutz D, Sood R, Park N, Faruque M, Markey C, Kefford RF, Palmer J, Bergman W, Bishop DT, Tucker MA, Bressac-de Paillerets B, Hansson J, Stark M, Gruis N, Bishop JN, Goldstein AM, Bailey-Wilson JE, Mann GJ, Hayward N, Trent J. 2003. Localization of a novel melanoma susceptibility locus to 1p22. Am J Hum Genet 73: 301-313.
20. Goldstein AM, Chan M, Harland M, Hayward NK, Demenais F, Bishop DT, Azizi E, Bergman W, Bianchi-Scarra G, Bruno W, Calista D, Albright LA, Chaudru V, Chompret A, Cuellar F, Elder DE, Ghiorzo P, Gillanders EM, Gruis NA, Hansson J, Hogg D, Holland EA, Kanetsky PA, Kefford RF, Landi MT, Lang J, Leachman SA, MacKie RM, Magnusson V, Mann GJ, Bishop JN, Palmer JM, Puig S, Puig-Butille JA, Stark M, Tsao H, Tucker MA, Whitaker L, Yakobson E. 2007a. Features associated with germline CDKN2A mutations: A GenoMEL study of melanoma-prone families from three continents. J Med Genet 44: 99-106.
21. Greene MH, Goldin LR, Clark WH, Jr., Lovrien E, Kraemer KH, Tucker MA, Elder DE, Fraser MC, Rowe S. 1983. Familial cutaneous malignant melanoma: Autosomal dominant trait possibly linked to the Rh locus. Proc Natl Acad Sci USA 80: 6071-6075.
22. Gudbjartsson DF, Sulem P, Stacey SN, Goldstein AM, Rafnar T, Sigurgeirsson B, Benediktsdottir KR, Thorisdottir K, Ragnarsson R, Sveinsdottir SG, Magnusson V, Lindblom A, Kostulas K, Botella-Estrada R, Soriano V, Juberias P, Grasa M, Saez B, Andres R, Scherer D, Rudnai P, Gurzau E, Koppova K, Kiemeney LA, Jakobsdottir M, Steinberg S, Helgason A, Gretarsdottir S, Tucker MA, Mayordomo JI, Nagore E, Kumar R, Hansson J, Olafsson JH, Gulcher J, Kong A, Thorsteinsdottir U, Stefansson K. 2008. ASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinoma. Nat Genet 40: 886-891.
23. Hansson J. 2008. Familial melanoma. Surg Clin North Am 88: 897-916, viii.
24. Hansson J, Bergenmar M, Hofer PA, Lundell G, Mansson-Brahme E, Ringborg U, Synnerstad I, Bratel AT, Wennberg AM, Rosdahl I. 2007. Monitoring of kindreds with hereditary predisposition for cutaneous melanoma and dysplastic nevus syndrome: Results of a Swedish preventive program. J Clin Oncol 25: 2819-2824.
25. Hashemi J, Bendahl PO, Sandberg T, Platz A, Linder S, Stierner U, Olsson H, Ingvar C, Hansson J, Borg A. 2001. Haplotype analysis and age estimation of the 113insR CDKN2A founder mutation in Swedish melanoma families. Genes Chromosomes Cancer 31: 107-116.
26. Hoiom V, Tuominen R, Kaller M, Linden D, Ahmadian A, Mansson-Brahme E, Egyhazi S, Sjoberg K, Lundeberg J, Hansson J. 2009. MC1R variation and melanoma risk in the Swedish population in relation to clinical and pathological parameters. Pigment Cell Melanoma Res 22: 196-204.
27. Holland EA, Beaton SC, Kefford RF, Mann GJ. 1997. Linkage analysis of familial melanoma and chromosome 6 in 14 Australian kindreds. Genes Chromosomes Cancer 19: 241-249.
28. John S, Shephard N, Liu G, Zeggini E, Cao M, Chen W, Vasavda N, Mills T, Barton A, Hinks A, Eyre S, Jones KW, Ollier W, Silman A, Gibson N, Worthington J, Kennedy GC. 2004. Whole-genome scan, in a complex disease, using 11, 245 single-nucleotide polymorphisms: Comparison with microsatellites. Am J Hum Genet 75: 54-64.
29. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA. 2001. Haplotype tagging for the identification of common disease genes. Nat Genet 29: 233-237.
30. Jonsson G, Bendahl PO, Sandberg T, Kurbasic A, Staaf J, Sunde L, Cruger DG, Ingvar C, Olsson H, Borg A. 2005. Mapping of a novel ocular and cutaneous malignant melanoma susceptibility locus to chromosome 9q21.32. J Natl Cancer Inst 97: 1377-1382.
31. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES. 1996. Parametric and nonparametric linkage analysis: A unified multipoint approach. Am J Hum Genet 58: 1347-1363.
32. Lai RH, Hsiao YW, Wang MJ, Lin HY, Wu CW, Chi CW, Li AF, Jou YS, Chen JY. 2010. SOCS6, down-regulated in gastric cancer, inhibits cell proliferation and colony formation. Cancer Lett 288: 75-85.
33. Lander E, Kruglyak L. 1995. Genetic dissection of complex traits: Guidelines for interpreting and reporting linkage results. Nat Genet 11: 241-247.
34. Lindor NM, Greene MH. 1998. The concise handbook of family cancer syndromes. Mayo Familial Cancer Program. J Natl Cancer Inst 90: 1039-1071.
35. Low SK, Kuchiba A, Zembutsu H, Saito A, Takahashi A, Kubo M, Daigo Y, Kamatani N, Chiku S, Totsuka H, Ohnami S, Hirose H, Shimada K, Okusaka T, Yoshida T, Nakamura Y, Sakamoto H. 2010. Genome-wide association study of pancreatic cancer in Japanese population. PLoS One 5: e11824.
36. Matichard E, Verpillat P, Meziani R, Gerard B, Descamps V, Legroux E, Burnouf M, Bertrand G, Bouscarat F, Archimbaud A, Picard C, Ollivaud L, Basset-Seguin N, Kerob D, Lanternier G, Lebbe C, Crickx B, Grandchamp B, Soufir N. 2004. Melanocortin 1 receptor (MC1R) gene variants may increase the risk of melanoma in France independently of clinical risk factors and UV exposure. J Med Genet 41: e13.
37. Molven A, Grimstvedt MB, Steine SJ, Harland M, Avril MF, Hayward NK, Akslen LA. 2005. A large Norwegian family with inherited malignant melanoma, multiple atypical nevi, and CDK4 mutation. Genes Chromosomes Cancer 44: 10-18.
38. Morris EJ, Michaud WA, Ji JY, Moon NS, Rocco JW, Dyson NJ. 2006. Functional identification of Api5 as a suppressor of E2F-dependent apoptosis in vivo. PLoS Genet 2: e196.
39. Ott J, Terwilliger J. 1994. Handbook of Human Genetic Linkage. Baltimore: Johns Hopkins University Press.
40. Palmer JS, Duffy DL, Box NF, Aitken JF, O'Gorman LE, Green AC, Hayward NK, Martin NG, Sturm RA. 2000. Melanocortin-1 receptor polymorphisms and risk of melanoma: Is the association explained solely by pigmentation phenotype? Am J Hum Genet 66: 176-186.
41. Platz A, Hansson J, Mansson-Brahme E, Lagerlof B, Linder S, Lundqvist E, Sevigny P, Inganas M, Ringborg U. 1997. Screening of germline mutations in the CDKN2A and CDKN2B genes in Swedish families with hereditary cutaneous melanoma. J Natl Cancer Inst 89: 697-702.
42. Ryschich E, Huszty G, Knaebel HP, Hartel M, Buchler MW, Schmidt J. 2004. Transferrin receptor is a marker of malignant phenotype in human pancreatic cancer and in neuroendocrine carcinoma of the pancreas. Eur J Cancer 40: 1418-1422.
43. Schaid DJ, Guenther JC, Christensen GB, Hebbring S, Rosenow C, Hilker CA, McDonnell SK, Cunningham JM, Slager SL, Blute ML, Thibodeau SN. 2004. Comparison of microsatellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci. Am J Hum Genet 75: 948-965.
44. Smith R, Healy E, Siddiqui S, Flanagan N, Steijlen PM, Rosdahl I, Jacques JP, Rogers S, Turner R, Jackson IJ, Birch-Machin MA, Rees JL. 1998. Melanocortin 1 receptor variants in an Irish population [see comment]. J Invest Dermatol 111: 119-122.
45. Soufir N, Avril MF, Chompret A, Demenais F, Bombled J, Spatz A, Stoppa-Lyonnet D, Benard J, Bressac-de Paillerets B. 1998. Prevalence of p16 and CDK4 germline mutations in 48 melanoma-prone families in France. The French Familial Melanoma Study Group [erratum appears in Hum Mol Genet 1998 May;7(5):941]. Hum Mol Genet 7: 209-216.
46. Stanford JL, FitzGerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K, Hood L, Ostrander EA, Schaid DJ. 2009. Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet 18: 1839-1848.
47. Stratigos AJ, Dimisianos G, Nikolaou V, Poulou M, Sypsa V, Stefanaki I, Papadopoulos O, Polydorou D, Plaka M, Christofidou E, Gogas H, Tsoutsos D, Kastana O, Antoniou C, Hatzakis A, Kanavakis E, Katsambas AD. 2006. Melanocortin receptor-1 gene polymorphisms and the risk of cutaneous melanoma in a low-risk southern European population. J Invest Dermatol 126: 1842-1849.
48. Tavtigian SV, Simard J, Teng DH, Abtin V, Baumgard M, Beck A, Camp NJ, Carillo AR, Chen Y, Dayananth P, Desrochers M, Dumont M, Farnham JM, Frank D, Frye C, Ghaffari S, Gupte JS, Hu R, Iliev D, Janecki T, Kort EN, Laity KE, Leavitt A, Leblanc G, McArthur-Morrison J, Pederson A, Penn B, Peterson KT, Reid JE, Richards S, Schroeder M, Smith R, Snyder SC, Swedlund B, Swensen J, Thomas A, Tranchant M, Woodland AM, Labrie F, Skolnick MH, Neuhausen S, Rommens J, Cannon-Albright LA. 2001. A candidate prostate cancer susceptibility gene at chromosome 17p. Nat Genet 27: 172-180.
49. Tsao H, Benoit E, Sober AJ, Thiele C, Haluska FG. 1998. Novel mutations in the p16/CDKN2A binding region of the cyclin-dependent kinase-4 gene. Cancer Res 58: 109-113.
50. Valverde P, Healy E, Jackson I, Rees JL, Thody AJ. 1995. Variants of the melanocyte-stimulating hormone receptor gene are associated with red hair and fair skin in humans [see comment]. Nat Genet 11: 328-330.
51. Valverde P, Healy E, Sikkink S, Haldane F, Thody AJ, Carothers A, Jackson IJ, Rees JL. 1996. The Asp84Glu variant of the melanocortin 1 receptor (MC1R) is associated with melanoma. Hum Mol Genet 5: 1663-1666.
52. Wada S, Noguchi T, Takeno S, Kawahara K. 2006. PIK3CA and TFRC located in 3q are new prognostic factors in esophageal squamous cell carcinoma. Ann Surg Oncol 13: 961-966.
53. Walsh MC, Kim GK, Maurizio PL, Molnar EE, Choi Y. 2008. TRAF6 autoubiquitination-independent activation of the NFkappaB and MAPK pathways in response to IL-1 and RANKL. PLoS One 3: e4064.
54. Wang Z, Liu H, Liu B, Ma W, Xue X, Chen J, Zhou Q. 2010. Gene expression levels of CSNK1A1 and AAC-11, but not NME1, in tumor tissues as prognostic factors in NSCLC patients. Med Sci Monit 16: CR357-CR364.
55. Zuo L, Weger J, Yang Q, Goldstein AM, Tucker MA, Walker GJ, Hayward N, Dracopoli NC. 1996. Germline mutations in the p16INK4a binding domain of CDK4 in familial melanoma. Nat Genet 12: 97-99.