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

Qian, J., Liu, H., Wei, S., Liu, Z., Li,Y., Wang, L..-E., Chen, W.V., Amos, C.I., Lee, J.E., Iles, M.M., Law, M.H., Cust, A.E., Barrett, J.H., Montgomery, G.W., Taylor, J., Bishop, J.A.N., Macgregor, S., Bishop, D.T., Mann, G.J., Hayward, N.K. and Wei, Q. (2013) Association between putative functional variants in the PSMB9 gene and risk of melanoma - re-analysis of published melanoma genome-wide association studies. Pigment Cell and Melanoma Research, 26 3: 392-401. doi:10.1111/pcmr.12069

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Author Qian, J.
Liu, H.
Wei, S.
Liu, Z.
Li,Y.
Wang, L..-E.
Chen, W.V.
Amos, C.I.
Lee, J.E.
Iles, M.M.
Law, M.H.
Cust, A.E.
Barrett, J.H.
Montgomery, G.W.
Taylor, J.
Bishop, J.A.N.
Macgregor, S.
Bishop, D.T.
Mann, G.J.
Hayward, N.K.
Wei, Q.
Title Association between putative functional variants in the PSMB9 gene and risk of melanoma - re-analysis of published melanoma genome-wide association studies
Journal name Pigment Cell and Melanoma Research   Check publisher's open access policy
ISSN 1755-1471
1755-148X
Publication date 2013-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1111/pcmr.12069
Open Access Status Not Open Access
Volume 26
Issue 3
Start page 392
End page 401
Total pages 10
Place of publication Malden, MA, U.S.A.
Publisher Wiley-Blackwell Publishing, Inc.
Language eng
Subject 2708 Dermatology
2730 Oncology
1300 Biochemistry, Genetics and Molecular Biology
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.
Keyword Cell cycle
Genome-wide association study
Melanoma
Polymorphism
PSMB9
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID R01 CA100264
P50 CA093459
LSHC-CT-2006-018702
CA83115
C588/A4994
CA83115
107359
WT084766/Z/08/Z
496674
1011143
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Medicine Publications
 
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Created: Sat, 22 Feb 2014, 23:35:32 EST by Matthew Lamb on behalf of School of Medicine