DESCRIPTION:

List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Lung cancer. The EFO term squamous cell carcinoma was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.

LABEL:

GWAS: squamous cell carcinoma

SCORE TYPE:

P-Value

DATE ADDED:

2017-05-02

DATE UPDATED:

2024-04-25

SPECIES:

AUTHORS:

Y Wang, JD McKay, T Rafnar, Z Wang, MN Timofeeva, P Broderick, X Zong, M Laplana, Y Wei, Y Han, A Lloyd, M Delahaye-Sourdeix, D Chubb, V Gaborieau, W Wheeler, N Chatterjee, G Thorleifsson, P Sulem, G Liu, R Kaaks, M Henrion, B Kinnersley, M Vallée, F LeCalvez-Kelm, VL Stevens, SM Gapstur, WV Chen, D Zaridze, N Szeszenia-Dabrowska, J Lissowska, P Rudnai, E Fabianova, D Mates, V Bencko, L Foretova, V Janout, HE Krokan, ME Gabrielsen, F Skorpen, L Vatten, I Njølstad, C Chen, G Goodman, S Benhamou, T Vooder, K Välk, M Nelis, A Metspalu, M Lener, J Lubiński, M Johansson, P Vineis, A Agudo, F Clavel-Chapelon, HB Bueno-de-Mesquita, D Trichopoulos, KT Khaw, M Johansson, E Weiderpass, A Tjønneland, E Riboli, M Lathrop, G Scelo, D Albanes, NE Caporaso, Y Ye, J Gu, X Wu, MR Spitz, H Dienemann, A Rosenberger, L Su, A Matakidou, T Eisen, K Stefansson, A Risch, SJ Chanock, DC Christiani, RJ Hung, P Brennan, MT Landi, RS Houlston, CI Amos

TITLE:

Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer.

JOURNAL:

Nature genetics Jul 2014, Vol 46, pp. 736-41

ABSTRACT:

We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data. PUBMED: 24880342
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