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. Hayward; Qingyi Wei

doi:10.1111/pcmr.12069

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

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

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 language	English (US)
Pages (from-to)	392-401
Number of pages	10
Journal	Pigment Cell and Melanoma Research
Volume	26
Issue number	3
DOIs	https://doi.org/10.1111/pcmr.12069
State	Published - May 2013

Keywords

Cell cycle
Genome-wide association study
Melanoma
PSMB9
Polymorphism

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology
Oncology
Dermatology

MD Anderson CCSG core facilities

Clinical Trials Office

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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., ... 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. https://doi.org/10.1111/pcmr.12069

Qian, J, Liu, H, Wei, S, Liu, Z, Li, Y, Wang, LE, Chen, WV, Amos, CI, Lee, JE, Iles, MM, Law, MH, Cust, AE, Barrett, JH, Montgomery, GW, Taylor, J, Bishop, JAN, Macgregor, S, Bishop, DT, Mann, GJ, Hayward, NK & 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, vol. 26, no. 3, pp. 392-401. https://doi.org/10.1111/pcmr.12069

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

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.",

keywords = "Cell cycle, Genome-wide association study, Melanoma, PSMB9, Polymorphism",

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

year = "2013",

month = may,

doi = "10.1111/pcmr.12069",

language = "English (US)",

volume = "26",

pages = "392--401",

journal = "Pigment Cell and Melanoma Research",

issn = "1755-1471",

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T1 - Association between putative functional variants in the PSMB9 gene and risk of melanoma - re-analysis of published melanoma genome-wide association studies

AU - Qian, Ji

AU - Liu, Hongliang

AU - Wei, Sheng

AU - Liu, Zhensheng

AU - Li, Yangkai

AU - Wang, Li E.

AU - Chen, Wei V.

AU - Amos, Christopher I.

AU - Lee, Jeffrey E.

AU - Iles, Mark M.

AU - Law, Matthew H.

AU - Cust, Anne E.

AU - Barrett, Jennifer H.

AU - Montgomery, Grant W.

AU - Taylor, John

AU - Bishop, Julia A.Newton

AU - Macgregor, Stuart

AU - Bishop, D. Timothy

AU - Mann, Graham J.

AU - Hayward, Nicholas K.

AU - Wei, Qingyi

PY - 2013/5

Y1 - 2013/5

N2 - 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.

AB - 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.

KW - Cell cycle

KW - Genome-wide association study

KW - Melanoma

KW - PSMB9

KW - Polymorphism

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

Abstract

Keywords

ASJC Scopus subject areas

MD Anderson CCSG core facilities

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