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An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs.

Publication ,  Journal Article
Yu, H; Zhao, H; Wang, L-E; Han, Y; Chen, WV; Amos, CI; Rafnar, T; Sulem, P; Stefansson, K; Landi, MT; Caporaso, N; Albanes, D; Thun, M ...
Published in: DNA Repair (Amst)
April 3, 2011

DNA repair genes are important for maintaining genomic stability and limiting carcinogenesis. We analyzed all single nucleotide polymorphisms (SNPs) of 125 DNA repair genes covered by the Illumina HumanHap300 (v1.1) BeadChips in a previously conducted genome-wide association study (GWAS) of 1154 lung cancer cases and 1137 controls and replicated the top-hits of XRCC4 SNPs in an independent set of 597 cases and 611 controls in Texas populations. We found that six of 20 XRCC4 SNPs were associated with a decreased risk of lung cancer with a P-value of 0.01 or lower in the discovery dataset, of which the most significant SNP was rs10040363 (P for allelic test=4.89 x 10⁻⁴). Moreover, the data in this region allowed us to impute a potentially functional SNP rs2075685 (imputed P for allelic test=1.3 x 10⁻³). A luciferase reporter assay demonstrated that the rs2075685G>T change in the XRCC4 promoter increased expression of the gene. In the replication study of rs10040363, rs1478486, rs9293329, and rs2075685, however, only rs10040363 achieved a borderline association with a decreased risk of lung cancer in a dominant model (adjusted OR=0.80, 95% CI=0.62-1.03 and P=0.079). In the final combined analysis of both the Texas GWAS discovery and replication datasets, the strength of the association was increased for rs10040363 (adjusted OR=0.77, 95% CI=0.66-0.89, P(dominant)=5 x 10⁻⁴ and P for trend=5 x 10⁻⁴) and rs1478486 (adjusted OR=0.82, 95% CI=0.71-0.94, P(dominant)=6 x 10⁻³ and P for trend=3.5 x 10⁻³). Finally, we conducted a meta-analysis of these XRCC4 SNPs with available data from published GWA studies of lung cancer with a total of 12,312 cases and 47,921 controls, in which none of these XRCC4 SNPs was associated with lung cancer risk. It appeared that rs2075685, although associated with increased expression of a reporter gene and lung cancer risk in the Texas populations, did not have an effect on lung cancer risk in other populations. This study underscores the importance of replication using published data in larger populations.

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Published In

DNA Repair (Amst)

DOI

EISSN

1568-7856

Publication Date

April 3, 2011

Volume

10

Issue

4

Start / End Page

398 / 407

Location

Netherlands

Related Subject Headings

  • Texas
  • Polymorphism, Single Nucleotide
  • Middle Aged
  • Male
  • Lung Neoplasms
  • Humans
  • Hela Cells
  • HeLa Cells
  • Genotype
  • Genome-Wide Association Study
 

Citation

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Yu, H., Zhao, H., Wang, L.-E., Han, Y., Chen, W. V., Amos, C. I., … Wei, Q. (2011). An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs. DNA Repair (Amst), 10(4), 398–407. https://doi.org/10.1016/j.dnarep.2011.01.005
Yu, Hongping, Hui Zhao, Li-E Wang, Younghun Han, Wei V. Chen, Christopher I. Amos, Thorunn Rafnar, et al. “An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs.DNA Repair (Amst) 10, no. 4 (April 3, 2011): 398–407. https://doi.org/10.1016/j.dnarep.2011.01.005.
Yu, Hongping, et al. “An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs.DNA Repair (Amst), vol. 10, no. 4, Apr. 2011, pp. 398–407. Pubmed, doi:10.1016/j.dnarep.2011.01.005.
Yu H, Zhao H, Wang L-E, Han Y, Chen WV, Amos CI, Rafnar T, Sulem P, Stefansson K, Landi MT, Caporaso N, Albanes D, Thun M, McKay JD, Brennan P, Wang Y, Houlston RS, Spitz MR, Wei Q. An analysis of single nucleotide polymorphisms of 125 DNA repair genes in the Texas genome-wide association study of lung cancer with a replication for the XRCC4 SNPs. DNA Repair (Amst). 2011 Apr 3;10(4):398–407.
Journal cover image

Published In

DNA Repair (Amst)

DOI

EISSN

1568-7856

Publication Date

April 3, 2011

Volume

10

Issue

4

Start / End Page

398 / 407

Location

Netherlands

Related Subject Headings

  • Texas
  • Polymorphism, Single Nucleotide
  • Middle Aged
  • Male
  • Lung Neoplasms
  • Humans
  • Hela Cells
  • HeLa Cells
  • Genotype
  • Genome-Wide Association Study