Association between putative functional variants in the PSMB9 gene and risk of melanoma - re-analysis of published melanoma genome-wide association studies

Ji Qian, Hongliang Liu, Sheng Wei, Zhensheng Liu, Yangkai Li, Li E. Wang, Wei V. Chen, Christopher I. Amos, Jeffrey E. Lee, Mark M. Iles, Matthew H. Law, Anne E. Cust, Jennifer H. Barrett, Grant W. Montgomery, John Taylor, Julia A.Newton Bishop, Stuart Macgregor, D. Timothy Bishop, Graham J. Mann, Nicholas K. HaywardQingyi Wei*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

8 Citations (Scopus)

Abstract

To mine possibly hidden causal single-nucleotide polymorphisms (SNPs) of melanoma, we investigated the association of SNPs 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 SNPs with P < 0.01 and performed validation studies for 18 putative functional SNPs in PSMB9 in two other GWAS data sets. Two SNPs (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 SNPs 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.

Original languageEnglish
Pages (from-to)392-401
Number of pages10
JournalPigment Cell and Melanoma Research
Volume26
Issue number3
DOIs
Publication statusPublished - May 2013
Externally publishedYes

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