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Association between putative functional variants in the PSMB 9 gene and risk of melanoma – re‐analysis of published melanoma genome‐wide association studies
Author(s) -
Qian Ji,
Liu Hongliang,
Wei Sheng,
Liu Zhensheng,
Li Yangkai,
Wang LiE,
Chen Wei V.,
Amos Christopher I.,
Lee Jeffrey E.,
Iles Mark M.,
Law Matthew H.,
Cust Anne E.,
Barrett Jennifer H.,
Montgomery Grant W.,
Taylor John,
Bishop Julia A. Newton,
MacGregor Stuart,
Bishop D. Timothy,
Mann Graham J.,
Hayward Nicholas K.,
Wei Qingyi
Publication year - 2013
Publication title -
pigment cell and melanoma research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.618
H-Index - 105
eISSN - 1755-148X
pISSN - 1755-1471
DOI - 10.1111/pcmr.12069
Subject(s) - melanoma , genome wide association study , genetics , gene , biology , genetic association , association (psychology) , genome , computational biology , single nucleotide polymorphism , genotype , philosophy , epistemology
Summary To mine possibly hidden causal single‐nucleotide polymorphisms ( SNP s) of melanoma, we investigated the association of SNP s in 76 M/G1 transition genes with melanoma risk using our published genome‐wide association study ( GWAS ) data set with 1804 melanoma cases and 1026 cancer‐free controls. We found multiple SNP s with P < 0.01 and performed validation studies for 18 putative functional SNP s in PSMB9 in two other GWAS data sets. Two SNP s (rs1351383 and rs2127675) were associated with melanoma risk in the GenoMEL data set (P = 0.013 and 0.004, respectively), but failed in validation using the Australian data set. Genotype–phenotype analysis revealed these two SNP s were significantly correlated with mRNA expression level of PSMB9 . Further experiments revealed that SNP rs2071480, which is in high LD with rs1351383 and rs2127675, may have a weak effect on the promoter activity of PSMB9 . Taken together, our data suggested that functional variants in PSMB9 may contribute to melanoma susceptibility.