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Article: Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans

TitleGenome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans
Authors
KeywordsAngiogenic Proteins/genetics
Case-Control Studies
European Continental Ancestry Group/*genetics
Eye Color
Female
GTP-Binding Proteins/genetics
Genetic Predisposition to Disease
*Genome-Wide Association Study
Humans
Interferon Regulatory Factors/genetics
Male
Issue Date2013
PublisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/
Citation
Human Molecular Genetics, 2013, v. 22 n. 14, p. 2948-2959 How to Cite?
AbstractAiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 (P = 2.4 × 10-14; P = 5.4 × 10-9 in the discovery set and P = 1.2 × 10-6 in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye (P = 7.0 × 10-8; P = 5.3 × 10-5 in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color (P-value for interaction = 3.8 × 10-3). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 (P = 7.2 × 10-14; P = 1.8 × 10-8 in the discovery set and P = 6.7 × 10-7 in the replication set), rs12202284 between IRF4 and EXOC2 (P = 5.0 × 10-8; P = 6.6 × 10-7 in the discovery set and P = 3.0 × 10-3 in the replication set) and rs8015138 upstream of GNG2 (P = 6.6 × 10-8; P = 5.3 × 10-7 in the discovery set and P = 0.01 in the replication set).
Persistent Identifierhttp://hdl.handle.net/10722/219917
ISSN
2015 Impact Factor: 5.985
2015 SCImago Journal Rankings: 4.288
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorZhang, M-
dc.contributor.authorSong, F-
dc.contributor.authorLiang, L-
dc.contributor.authorNan, H-
dc.contributor.authorZhang, J-
dc.contributor.authorLiu, H-
dc.contributor.authorWang, LE-
dc.contributor.authorWei, Q-
dc.contributor.authorLee, JE-
dc.contributor.authorAmos, CI-
dc.contributor.authorKraft, P-
dc.contributor.authorQureshi, AA-
dc.contributor.authorHan, J-
dc.date.accessioned2015-10-02T08:21:20Z-
dc.date.available2015-10-02T08:21:20Z-
dc.date.issued2013-
dc.identifier.citationHuman Molecular Genetics, 2013, v. 22 n. 14, p. 2948-2959-
dc.identifier.issn0964-6906-
dc.identifier.urihttp://hdl.handle.net/10722/219917-
dc.description.abstractAiming to identify novel genetic loci for pigmentation and skin cancer, we conducted a series of genome-wide association studies on hair color, eye color, number of sunburns, tanning ability and number of non-melanoma skin cancers (NMSCs) among 10 183 European Americans in the discovery stage and 4504 European Americans in the replication stage (for eye color, 3871 males in the discovery stage and 2496 males in the replication stage). We targeted novel chromosome regions besides the known ones for replication. As a result, we identified a new region downstream of the EDNRB gene on 13q22 associated with hair color and the strongest association was the single-nucleotide polymorphism (SNP) rs975739 (P = 2.4 × 10-14; P = 5.4 × 10-9 in the discovery set and P = 1.2 × 10-6 in the replication set). Using blue, intermediate (including green) and brown eye colors as co-dominant outcomes, we identified the SNP rs3002288 in VASH2 on 1q32.3 associated with brown eye (P = 7.0 × 10-8; P = 5.3 × 10-5 in the discovery set and P = 0.02 in the replication set). Additionally, we identified a significant interaction between the SNPs rs7173419 and rs12913832 in the OCA2 gene region on brown eye color (P-value for interaction = 3.8 × 10-3). As for the number of NMSCs, we identified two independent SNPs on chr6 and one SNP on chromosome 14: rs12203592 in IRF4 (P = 7.2 × 10-14; P = 1.8 × 10-8 in the discovery set and P = 6.7 × 10-7 in the replication set), rs12202284 between IRF4 and EXOC2 (P = 5.0 × 10-8; P = 6.6 × 10-7 in the discovery set and P = 3.0 × 10-3 in the replication set) and rs8015138 upstream of GNG2 (P = 6.6 × 10-8; P = 5.3 × 10-7 in the discovery set and P = 0.01 in the replication set).-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://hmg.oxfordjournals.org/-
dc.relation.ispartofHuman Molecular Genetics-
dc.subjectAngiogenic Proteins/genetics-
dc.subjectCase-Control Studies-
dc.subjectEuropean Continental Ancestry Group/*genetics-
dc.subjectEye Color-
dc.subjectFemale-
dc.subjectGTP-Binding Proteins/genetics-
dc.subjectGenetic Predisposition to Disease-
dc.subject*Genome-Wide Association Study-
dc.subjectHumans-
dc.subjectInterferon Regulatory Factors/genetics-
dc.subjectMale-
dc.titleGenome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans-
dc.typeArticle-
dc.identifier.emailZhang, J: jzhang1@hku.hk-
dc.identifier.authorityZhang, J=rp01713-
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1093/hmg/ddt142-
dc.identifier.pmid23548203-
dc.identifier.pmcidPMC3690971-
dc.identifier.scopuseid_2-s2.0-84880271272-
dc.identifier.volume22-
dc.identifier.issue14-
dc.identifier.spage2948-
dc.identifier.epage2959-
dc.identifier.isiWOS:000321056500017-
dc.publisher.placeUnited Kingdom-

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