A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption

F1000Research
Øystein A HaalandAstanand Jugessur

Abstract

Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. Our new methodology detects if PoO effects are different across environmental strata and is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with tw...Continue Reading

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Citations

Oct 31, 2020·Birth Defects Research·Michael A GarlandChengji J Zhou
Jun 5, 2021·Mutation Research. Reviews in Mutation Research·Ghenwa NasreddineMichella Ghassibe-Sabbagh
Aug 13, 2021·The Cleft Palate-craniofacial Journal : Official Publication of the American Cleft Palate-Craniofacial Association·Lord J J GowansAzeez Butali
Aug 27, 2021·Frontiers in Genetics·Dongjing LiuJohn R Shaffer

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Software Mentioned

BGee
Haplin
GeneCards
PoOxSmoke
PoOxVitamin
PoOxE
Commons
Hetionet
1000 Genomes browser
R package BgeeDB _

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