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 Orofacial clefts (interaction). The EFO term Orofacial clefting syndrome, cleft lip 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: Orofacial clefting syndrome, cleft lip

SCORE TYPE:

P-Value

DATE ADDED:

2017-05-02

DATE UPDATED:

2024-04-25

SPECIES:

AUTHORS:

TH Beaty, I Ruczinski, JC Murray, ML Marazita, RG Munger, JB Hetmanski, T Murray, RJ Redett, MD Fallin, KY Liang, T Wu, PJ Patel, SC Jin, TX Zhang, H Schwender, YH Wu-Chou, PK Chen, SS Chong, F Cheah, V Yeow, X Ye, H Wang, S Huang, EW Jabs, B Shi, AJ Wilcox, RT Lie, SH Jee, K Christensen, KF Doheny, EW Pugh, H Ling, AF Scott

TITLE:

Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate.

JOURNAL:

Genetic epidemiology Sep 2011, Vol 35, pp. 469-78

ABSTRACT:

Nonsyndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome-wide association study (GWAS) using 550 case-parent trios, ascertained through a CP case collected in an international consortium. Family-based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene-environment (G × E) interaction simultaneously, plus a separate 1 df test for G × E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome-wide significance when considered alone, markers in several genes attained or approached genome-wide significance when G × E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in an increased risk if the mother consumed alcohol during the peri-conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G × E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP. PUBMED: 21618603
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