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Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium.

Publication ,  Journal Article
Feng, Y; Wang, Y; Liu, H; Liu, Z; Mills, C; Han, Y; Hung, RJ; Brhane, Y; McLaughlin, J; Brennan, P; Bickeboeller, H; Rosenberger, A; Risch, A ...
Published in: Sci Rep
April 11, 2017

The T-cell protein tyrosine phosphatase (TCPTP) pathway consists of signaling events mediated by TCPTP. Mutations and genetic variants of some genes in the TCPTP pathway are associated with lung cancer risk and survival. In the present study, we first investigated associations of 5,162 single nucleotide polymorphisms (SNPs) in 43 genes of this TCPTP pathway with lung cancer risk by using summary data of six published genome-wide association studies (GWAS) of 12,160 cases and 16,838 controls. We identified 11 independent SNPs in eight genes after correction for multiple comparisons by a false discovery rate <0.20. Then, we performed in silico functional analyses for these 11 SNPs by eQTL analysis, two of which, PTPN2 SNPs rs2847297 and rs2847282, were chosen as tagSNPs. We further included two additional GWAS datasets of Harvard University (984 cases and 970 controls) and deCODE (1,319 cases and 26,380 controls), and the overall effects of these two SNPs among all eight GWAS studies remained significant (OR = 0.95, 95% CI = 0.92-0.98, and P = 0.004 for rs2847297; OR = 0.95, 95% CI = 0.92-0.99, and P = 0.009 for rs2847282). In conclusion, the PTPN2 rs2847297 and rs2847282 may be potential susceptible loci for lung cancer risk.

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Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

April 11, 2017

Volume

7

Issue

1

Start / End Page

825

Location

England

Related Subject Headings

  • Protein Tyrosine Phosphatase, Non-Receptor Type 2
  • Polymorphism, Single Nucleotide
  • Lung Neoplasms
  • Humans
  • Genome-Wide Association Study
 

Citation

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Feng, Y., Wang, Y., Liu, H., Liu, Z., Mills, C., Han, Y., … Wei, Q. (2017). Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium. Sci Rep, 7(1), 825. https://doi.org/10.1038/s41598-017-00850-0
Feng, Yun, Yanru Wang, Hongliang Liu, Zhensheng Liu, Coleman Mills, Younghun Han, Rayjean J. Hung, et al. “Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium.Sci Rep 7, no. 1 (April 11, 2017): 825. https://doi.org/10.1038/s41598-017-00850-0.
Feng Y, Wang Y, Liu H, Liu Z, Mills C, Han Y, et al. Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium. Sci Rep. 2017 Apr 11;7(1):825.
Feng, Yun, et al. “Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium.Sci Rep, vol. 7, no. 1, Apr. 2017, p. 825. Pubmed, doi:10.1038/s41598-017-00850-0.
Feng Y, Wang Y, Liu H, Liu Z, Mills C, Han Y, Hung RJ, Brhane Y, McLaughlin J, Brennan P, Bickeboeller H, Rosenberger A, Houlston RS, Caporaso NE, Teresa Landi M, Brueske I, Risch A, Ye Y, Wu X, Christiani DC, Amos CI, Wei Q. Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium. Sci Rep. 2017 Apr 11;7(1):825.

Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

April 11, 2017

Volume

7

Issue

1

Start / End Page

825

Location

England

Related Subject Headings

  • Protein Tyrosine Phosphatase, Non-Receptor Type 2
  • Polymorphism, Single Nucleotide
  • Lung Neoplasms
  • Humans
  • Genome-Wide Association Study