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 sing...

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Autores principales:	Yun Feng, Yanru Wang, Hongliang Liu, Zhensheng Liu, Coleman Mills, Younghun Han, Rayjean J. Hung, Yonathan Brhane, John McLaughlin, Paul Brennan, Heike Bickeboeller, Albert Rosenberger, Richard S. Houlston, Neil E. Caporaso, Maria Teresa Landi, Irene Brueske, Angela Risch, Yuanqing Ye, Xifeng Wu, David C. Christiani, Christopher I. Amos, Qingyi Wei
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/88b185e7153d483f8d43da7299dbc53b
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spelling	oai:doaj.org-article:88b185e7153d483f8d43da7299dbc53b2021-12-02T16:06:14ZGenetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium10.1038/s41598-017-00850-02045-2322https://doaj.org/article/88b185e7153d483f8d43da7299dbc53b2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00850-0https://doaj.org/toc/2045-2322Abstract 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.Yun FengYanru WangHongliang LiuZhensheng LiuColeman MillsYounghun HanRayjean J. HungYonathan BrhaneJohn McLaughlinPaul BrennanHeike BickeboellerAlbert RosenbergerRichard S. HoulstonNeil E. CaporasoMaria Teresa LandiIrene BrueskeAngela RischYuanqing YeXifeng WuDavid C. ChristianiChristopher I. AmosQingyi WeiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yun Feng Yanru Wang Hongliang Liu Zhensheng Liu Coleman Mills Younghun Han Rayjean J. Hung Yonathan Brhane John McLaughlin Paul Brennan Heike Bickeboeller Albert Rosenberger Richard S. Houlston Neil E. Caporaso Maria Teresa Landi Irene Brueske Angela Risch Yuanqing Ye Xifeng Wu David C. Christiani Christopher I. Amos Qingyi Wei Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
description	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.
format	article
author	Yun Feng Yanru Wang Hongliang Liu Zhensheng Liu Coleman Mills Younghun Han Rayjean J. Hung Yonathan Brhane John McLaughlin Paul Brennan Heike Bickeboeller Albert Rosenberger Richard S. Houlston Neil E. Caporaso Maria Teresa Landi Irene Brueske Angela Risch Yuanqing Ye Xifeng Wu David C. Christiani Christopher I. Amos Qingyi Wei
author_facet	Yun Feng Yanru Wang Hongliang Liu Zhensheng Liu Coleman Mills Younghun Han Rayjean J. Hung Yonathan Brhane John McLaughlin Paul Brennan Heike Bickeboeller Albert Rosenberger Richard S. Houlston Neil E. Caporaso Maria Teresa Landi Irene Brueske Angela Risch Yuanqing Ye Xifeng Wu David C. Christiani Christopher I. Amos Qingyi Wei
author_sort	Yun Feng
title	Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
title_short	Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
title_full	Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
title_fullStr	Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
title_full_unstemmed	Genetic variants of PTPN2 are associated with lung cancer risk: a re-analysis of eight GWASs in the TRICL-ILCCO consortium
title_sort	genetic variants of ptpn2 are associated with lung cancer risk: a re-analysis of eight gwass in the tricl-ilcco consortium
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/88b185e7153d483f8d43da7299dbc53b
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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

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