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

dc.contributor.author

Feng, Yun

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Wang, Yanru

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Liu, Hongliang

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Liu, Zhensheng

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Mills, Coleman

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Han, Younghun

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Hung, Rayjean J

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Brhane, Yonathan

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McLaughlin, John

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Brennan, Paul

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Bickeboeller, Heike

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Rosenberger, Albert

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Houlston, Richard S

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Caporaso, Neil E

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Teresa Landi, Maria

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Brueske, Irene

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Risch, Angela

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Ye, Yuanqing

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Wu, Xifeng

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Christiani, David C

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Amos, Christopher I

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Wei, Qingyi

dc.date.accessioned

2019-02-01T15:01:05Z

dc.date.available

2019-02-01T15:01:05Z

dc.date.issued

2017-04-11

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2019-02-01T15:01:03Z

dc.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.

dc.identifier

10.1038/s41598-017-00850-0

dc.identifier.issn

2045-2322

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2045-2322

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https://hdl.handle.net/10161/17961

dc.language

eng

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Springer Science and Business Media LLC

dc.relation.ispartof

Scientific reports

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10.1038/s41598-017-00850-0

dc.subject

Humans

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Lung Neoplasms

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Polymorphism, Single Nucleotide

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Protein Tyrosine Phosphatase, Non-Receptor Type 2

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Genome-Wide Association Study

dc.title

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

dc.type

Journal article

duke.contributor.orcid

Wei, Qingyi|0000-0002-3845-9445|0000-0003-4115-4439

pubs.begin-page

825

pubs.issue

1

pubs.organisational-group

Staff

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Duke

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School of Medicine

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Duke Cancer Institute

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Institutes and Centers

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Population Health Sciences

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Basic Science Departments

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Medicine, Medical Oncology

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Medicine

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Clinical Science Departments

pubs.publication-status

Published

pubs.volume

7

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