Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium.
Abstract
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.
Type
Journal articleSubject
HumansLung Neoplasms
Polymorphism, Single Nucleotide
Protein Tyrosine Phosphatase, Non-Receptor Type 2
Genome-Wide Association Study
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https://hdl.handle.net/10161/17961Published Version (Please cite this version)
10.1038/s41598-017-00850-0Publication Info
Feng, Yun; Wang, Yanru; Liu, Hongliang; Liu, Zhensheng; Mills, Coleman; Han, Younghun;
... Wei, Qingyi (2017). Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight
GWASs in the TRICL-ILCCO consortium. Scientific reports, 7(1). pp. 825. 10.1038/s41598-017-00850-0. Retrieved from https://hdl.handle.net/10161/17961.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Zhensheng Liu
Assistant Professor of Medicine
Qingyi Wei
Professor in Population Health Sciences
Qingyi Wei, MD, PhD, Professor in the Department of Medicine, is Associate Director
for Cancer Control and Population Sciences, Co-leader of CCPS and Co-leader of Epidemiology
and Population Genomics (Focus Area 1). He is a professor of Medicine and an internationally
recognized epidemiologist focused on the molecular and genetic epidemiology of head
and neck cancers, lung cancer, and melanoma. His research focuses on biomarkers and
genetic determinants for the DNA repair deficient phenotype and
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