A Genome-wide Association Study of Nonsyndromic Cleft Palate Identifies an Etiologic Missense Variant in GRHL3

Abstract

Cleft palate (CP) is a common birth defect occurring in 1 in 2,500 live births. Approximately half of infants with CP have a syndromic form, exhibiting other physical and cognitive disabilities. The other half have nonsyndromic CP, and to date, few genes associated with risk for nonsyndromic CP have been characterized. To identify such risk factors, we performed a genome-wide association study of this disorder. We discovered a genome-wide significant association with a missense variant in GRHL3 (p.Thr454Met [c.1361C>T]; rs41268753; p = 4.08 × 10(-9)) and replicated the result in an independent sample of case and control subjects. In both the discovery and replication samples, rs41268753 conferred increased risk for CP (OR = 8.3, 95% CI 4.1-16.8; OR = 2.16, 95% CI 1.43-3.27, respectively). In luciferase transactivation assays, p.Thr454Met had about one-third of the activity of wild-type GRHL3, and in zebrafish embryos, perturbed periderm development. We conclude that this mutation is an etiologic variant for nonsyndromic CP and is one of few functional variants identified to date for nonsyndromic orofacial clefting. This finding advances our understanding of the genetic basis of craniofacial development and might ultimately lead to improvements in recurrence risk prediction, treatment, and prognosis.

Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate

“…Participants were recruited from 13 countries in North America (United States), Central or South America (Guatemala, Argentina, Colombia, Puerto Rico), Asia (China, Philippines), Europe (Denmark, Turkey, Spain), and Africa (Ethiopia, Nigeria). Additional details on recruitment, genotyping, and quality controls are described in Leslie et al (2016b) and Leslie et al (2016a). Briefly, samples were genotyped for 539,473 SNPs on the Illumina HumanCore+Exome array.…”

“…Quality control procedures were completed in each contributing study and have been described extensively in the original publications (Leslie et al (2016b), Leslie et al (2016a), Beaty et al (2010) and Beaty et al (2011)). In the POFC study, SNPs with minor allele frequencies (MAF) less than 1% or those deviating from Hardy-Weinberg Equilibrium (HWE p < 0.0001) in genetically-defined, unrelated European controls were excluded.…”

“…Multiple successful genome-wide linkage and association studies have contributed to the substantial progress in identifying potentially causal genes for OFCs over the last ten years. To date, there have been eight CL/P GWASs (Beaty et al 2010; Birnbaum et al 2009; Camargo et al 2012; Grant et al 2009; Leslie et al 2016a; Mangold et al 2010; Sun et al 2015; Wolf et al 2015), a genome-wide meta-analysis of two CL/P GWASs (Ludwig et al 2012), and two GWASs of CP (Beaty et al 2011; Leslie et al 2016b). …”

“…The first study, despite interrogating 400 CP case-parent trios, did not identify any statistically significant SNP main effects (Beaty et al 2011). The second study identified a single locus associated with CP, but this association signal was limited to European populations because of very low frequencies of the risk allele in other populations (Leslie et al 2016b; Mangold et al 2016). For both CL/P and CP, the identified risk loci only account for a modest portion of the genetic variance of OFCs, suggesting that additional genetic risk factors may be involved.…”

Mutations in HYAL2, Encoding Hyaluronidase 2, Cause a Syndrome of Orofacial Clefting and Cor Triatriatum Sinister in Humans and Mice

“…They are clinically categorized dependent upon the absence (non-syndromic CL/P; 70% of cases) or presence (syndromic CL/P; 30% of cases) of additional congenital anomalies [5, 6]. For non-syndromic CL/P, 17 genetic risk loci have been defined and replicated with genome wide association studies worldwide [7–11]. As well as environmental influences, more recent evidence implicates non-coding or regulatory genomic regions in non-syndromic CL/P [12–14], perhaps explaining why re-sequencing of candidate genes or exome sequencing strategies rarely identify mutations in these cases [15].…”