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

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 pat...

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Autores principales:	Maider Ibarrola-Villava, Lara P Fernandez, Santos Alonso, M Dolores Boyano, Maria Peña-Chilet, Guillermo Pita, Jose A Aviles, Matias Mayor, Cristina Gomez-Fernandez, Beatriz Casado, Manuel Martin-Gonzalez, Neskuts Izagirre, Concepcion De la Rua, Aintzane Asumendi, Gorka Perez-Yarza, Yoana Arroyo-Berdugo, Enrique Boldo, Rafael Lozoya, Arantxa Torrijos-Aguilar, Ana Pitarch, Gerard Pitarch, Jose M Sanchez-Motilla, Francisca Valcuende-Cavero, Gloria Tomas-Cabedo, Gemma Perez-Pastor, Jose L Diaz-Perez, Jesus Gardeazabal, Iñigo Martinez de Lizarduy, Ana Sanchez-Diez, Carlos Valdes, Angel Pizarro, Mariano Casado, Gregorio Carretero, Rafael Botella-Estrada, Eduardo Nagore, Pablo Lazaro, Ana Lluch, Javier Benitez, Conrado Martinez-Cadenas, Gloria Ribas
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/54eddd4350a44dff8928703af2a4810d
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spelling	oai:doaj.org-article:54eddd4350a44dff8928703af2a4810d2021-11-18T06:54:51ZA customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.1932-620310.1371/journal.pone.0019271https://doaj.org/article/54eddd4350a44dff8928703af2a4810d2011-04-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21559390/?tool=EBIhttps://doaj.org/toc/1932-6203As 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<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.Maider Ibarrola-VillavaLara P FernandezSantos AlonsoM Dolores BoyanoMaria Peña-ChiletGuillermo PitaJose A AvilesMatias MayorCristina Gomez-FernandezBeatriz CasadoManuel Martin-GonzalezNeskuts IzagirreConcepcion De la RuaAintzane AsumendiGorka Perez-YarzaYoana Arroyo-BerdugoEnrique BoldoRafael LozoyaArantxa Torrijos-AguilarAna PitarchGerard PitarchJose M Sanchez-MotillaFrancisca Valcuende-CaveroGloria Tomas-CabedoGemma Perez-PastorJose L Diaz-PerezJesus GardeazabalIñigo Martinez de LizarduyAna Sanchez-DiezCarlos ValdesAngel PizarroMariano CasadoGregorio CarreteroRafael Botella-EstradaEduardo NagorePablo LazaroAna LluchJavier BenitezConrado Martinez-CadenasGloria RibasPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 4, p e19271 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Maider Ibarrola-Villava Lara P Fernandez Santos Alonso M Dolores Boyano Maria Peña-Chilet Guillermo Pita Jose A Aviles Matias Mayor Cristina Gomez-Fernandez Beatriz Casado Manuel Martin-Gonzalez Neskuts Izagirre Concepcion De la Rua Aintzane Asumendi Gorka Perez-Yarza Yoana Arroyo-Berdugo Enrique Boldo Rafael Lozoya Arantxa Torrijos-Aguilar Ana Pitarch Gerard Pitarch Jose M Sanchez-Motilla Francisca Valcuende-Cavero Gloria Tomas-Cabedo Gemma Perez-Pastor Jose L Diaz-Perez Jesus Gardeazabal Iñigo Martinez de Lizarduy Ana Sanchez-Diez Carlos Valdes Angel Pizarro Mariano Casado Gregorio Carretero Rafael Botella-Estrada Eduardo Nagore Pablo Lazaro Ana Lluch Javier Benitez Conrado Martinez-Cadenas Gloria Ribas A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
description	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<0.0001). None of the other five SNPs were replicated in this second phase of the study. However, three SNPs in TYR, SILV/CDK2 and ADAMTS20 genes (rs17793678, rs2069398 and rs1510521 respectively) had an overall p-value<0.05 when considering the whole DNA collection (1214 MM cases and 1296 controls). Both the SLC45A2 and the SILV/CDK2 variants behave as protective alleles, while the TYR and ADAMTS20 variants seem to function as risk alleles. Cumulative effects were detected when these four variants were considered together. Furthermore, individuals carrying two or more mutations in MC1R, a well-known low penetrance melanoma-predisposing gene, had a decreased MM risk if concurrently bearing the SLC45A2 protective variant. To our knowledge, this is the largest study on Spanish sporadic MM cases to date.
format	article
author	Maider Ibarrola-Villava Lara P Fernandez Santos Alonso M Dolores Boyano Maria Peña-Chilet Guillermo Pita Jose A Aviles Matias Mayor Cristina Gomez-Fernandez Beatriz Casado Manuel Martin-Gonzalez Neskuts Izagirre Concepcion De la Rua Aintzane Asumendi Gorka Perez-Yarza Yoana Arroyo-Berdugo Enrique Boldo Rafael Lozoya Arantxa Torrijos-Aguilar Ana Pitarch Gerard Pitarch Jose M Sanchez-Motilla Francisca Valcuende-Cavero Gloria Tomas-Cabedo Gemma Perez-Pastor Jose L Diaz-Perez Jesus Gardeazabal Iñigo Martinez de Lizarduy Ana Sanchez-Diez Carlos Valdes Angel Pizarro Mariano Casado Gregorio Carretero Rafael Botella-Estrada Eduardo Nagore Pablo Lazaro Ana Lluch Javier Benitez Conrado Martinez-Cadenas Gloria Ribas
author_facet	Maider Ibarrola-Villava Lara P Fernandez Santos Alonso M Dolores Boyano Maria Peña-Chilet Guillermo Pita Jose A Aviles Matias Mayor Cristina Gomez-Fernandez Beatriz Casado Manuel Martin-Gonzalez Neskuts Izagirre Concepcion De la Rua Aintzane Asumendi Gorka Perez-Yarza Yoana Arroyo-Berdugo Enrique Boldo Rafael Lozoya Arantxa Torrijos-Aguilar Ana Pitarch Gerard Pitarch Jose M Sanchez-Motilla Francisca Valcuende-Cavero Gloria Tomas-Cabedo Gemma Perez-Pastor Jose L Diaz-Perez Jesus Gardeazabal Iñigo Martinez de Lizarduy Ana Sanchez-Diez Carlos Valdes Angel Pizarro Mariano Casado Gregorio Carretero Rafael Botella-Estrada Eduardo Nagore Pablo Lazaro Ana Lluch Javier Benitez Conrado Martinez-Cadenas Gloria Ribas
author_sort	Maider Ibarrola-Villava
title	A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
title_short	A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
title_full	A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
title_fullStr	A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
title_full_unstemmed	A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.
title_sort	customized pigmentation snp array identifies a novel snp associated with melanoma predisposition in the slc45a2 gene.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/54eddd4350a44dff8928703af2a4810d
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A customized pigmentation SNP array identifies a novel SNP associated with melanoma predisposition in the SLC45A2 gene.

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