A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene

• Published in: PloS one 2011-04, Vol.6 (4), p.e19271-e19271
• Main Authors: Ibarrola-Villava, Maider, Fernandez, Lara P, Alonso, Santos, Boyano, M Dolores, Peña-Chilet, Maria, Pita, Guillermo, Aviles, Jose A, Mayor, Matias, Gomez-Fernandez, Cristina, Casado, Beatriz, Martin-Gonzalez, Manuel, Izagirre, Neskuts, De la Rua, Concepcion, Asumendi, Aintzane, Perez-Yarza, Gorka, Arroyo-Berdugo, Yoana, Boldo, Enrique, Lozoya, Rafael, Torrijos-Aguilar, Arantxa, Pitarch, Ana, Pitarch, Gerard, Sanchez-Motilla, Jose M, Valcuende-Cavero, Francisca, Tomas-Cabedo, Gloria, Perez-Pastor, Gemma, Diaz-Perez, Jose L, Gardeazabal, Jesus, Martinez de Lizarduy, Iñigo, Sanchez-Diez, Ana, Valdes, Carlos, Pizarro, Angel, Casado, Mariano, Carretero, Gregorio, Botella-Estrada, Rafael, Nagore, Eduardo, Lazaro, Pablo, Lluch, Ana, Benitez, Javier, Martinez-Cadenas, Conrado, Ribas, Gloria
• Format: Article
• Language: English
• Subjects: Adult; Aged; Aged, 80 and over; Albinism; Alleles; Analysis; Antigens, Neoplasm - genetics; Biology; Cyclin-dependent kinase 2; Deoxyribonucleic acid; DNA; Female; Gene Frequency; Genes; Genetic aspects; Genetic Predisposition to Disease; Genetic Variation; Genomes; Genotype; Haplotypes; Humans; Male; Medicine; Melanoma; Melanoma - epidemiology; Melanoma - genetics; Membrane Transport Proteins - genetics; Middle Aged; Mutation; Oligonucleotide Array Sequence Analysis; Ontology; Pathogenesis; Pigmentation; Polymorphism, Single Nucleotide; Risk; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Skin; Skin cancer; Spain; Statistical analysis; Tanning; Tanning (Leather finishing); Ultraviolet radiation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0019271

As the incidence of Malignant Melanoma (MM) reflects an interaction between skin colour and UV exposure, variations in genes implicated in pigmentation and tanning response to UV may be associated with susceptibility to MM. In this study, 363 SNPs in 65 gene regions belonging to the pigmentation pathway have been successfully genotyped using a SNP array. Five hundred and ninety MM cases and 507 controls were analyzed in a discovery phase I. Ten candidate SNPs based on a p-value threshold of 0.01 were identified. Two of them, rs35414 (SLC45A2) and rs2069398 (SILV/CKD2), were statistically significant after conservative Bonferroni correction. The best six SNPs were further tested in an independent Spanish series (624 MM cases and 789 controls). A novel SNP located on the SLC45A2 gene (rs35414) was found to be significantly associated with melanoma in both phase I and phase II (P