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 Oral cavity cancer. The EFO term oral cavity cancer 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: oral cavity cancer

SCORE TYPE:

P-Value

DATE ADDED:

2017-05-02

DATE UPDATED:

2024-04-25

SPECIES:

AUTHORS:

C Lesseur, B Diergaarde, AF Olshan, V Wünsch-Filho, AR Ness, G Liu, M Lacko, J Eluf-Neto, S Franceschi, P Lagiou, GJ Macfarlane, L Richiardi, S Boccia, J Polesel, K Kjaerheim, D Zaridze, M Johansson, AM Menezes, MP Curado, M Robinson, W Ahrens, C Canova, A Znaor, X Castellsagué, DI Conway, I Holcátová, D Mates, M Vilensky, CM Healy, N Szeszenia-Dąbrowska, E Fabiánová, J Lissowska, JR Grandis, MC Weissler, EH Tajara, FD Nunes, MB de Carvalho, S Thomas, RJ Hung, WH Peters, R Herrero, G Cadoni, HB Bueno-de-Mesquita, A Steffen, A Agudo, O Shangina, X Xiao, V Gaborieau, A Chabrier, D Anantharaman, P Boffetta, CI Amos, JD McKay, P Brennan

TITLE:

Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.

JOURNAL:

Nature genetics Dec 2016, Vol 48, pp. 1544-1550

ABSTRACT:

We conducted a genome-wide association study of oral cavity and pharyngeal cancer in 6,034 cases and 6,585 controls from Europe, North America and South America. We detected eight significantly associated loci (P < 5 × 10(-8)), seven of which are new for these cancer sites. Oral and pharyngeal cancers combined were associated with loci at 6p21.32 (rs3828805, HLA-DQB1), 10q26.13 (rs201982221, LHPP) and 11p15.4 (rs1453414, OR52N2-TRIM5). Oral cancer was associated with two new regions, 2p23.3 (rs6547741, GPN1) and 9q34.12 (rs928674, LAMC3), and with known cancer-related loci-9p21.3 (rs8181047, CDKN2B-AS1) and 5p15.33 (rs10462706, CLPTM1L). Oropharyngeal cancer associations were limited to the human leukocyte antigen (HLA) region, and classical HLA allele imputation showed a protective association with the class II haplotype HLA-DRB1*1301-HLA-DQA1*0103-HLA-DQB1*0603 (odds ratio (OR) = 0.59, P = 2.7 × 10(-9)). Stratified analyses on a subgroup of oropharyngeal cases with information available on human papillomavirus (HPV) status indicated that this association was considerably stronger in HPV-positive (OR = 0.23, P = 1.6 × 10(-6)) than in HPV-negative (OR = 0.75, P = 0.16) cancers. PUBMED: 27749845
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