Orofacial clefts (OFCs), which include non-syndromic cleft lip with or without cleft palate (CL/P), are among the most common birth defects in humans, affecting approximately 1 in 700 newborns. CL/P is phenotypically heterogeneous and has a complex etiology caused by genetic and environmental factors. Previous genome-wide association studies (GWASs) have identified at least 15 risk loci for CL/P. As these loci do not account for all of the genetic variance of CL/P, we hypothesized the existence of additional risk loci. We conducted a multiethnic GWAS in 6480 participants (823 unrelated cases, 1700 unrelated controls and 1319 case-parent trios) with European, Asian, African and Central and South American ancestry. Our GWAS revealed novel associations on 2p24 near FAM49A, a gene of unknown function (P = 4.22 × 10), and 19q13 near RHPN2, a gene involved in organizing the actin cytoskeleton (P = 4.17 × 10). Other regions reaching genome-wide significance were 1p36 (PAX7), 1p22 (ARHGAP29), 1q32 (IRF6), 8q24 and 17p13 (NTN1), all reported in previous GWASs. Stratification by ancestry group revealed a novel association with a region on 17q23 (P = 2.92 × 10) among individuals with European ancestry. This region included several promising candidates including TANC2, an oncogene required for development, and DCAF7, a scaffolding protein required for craniofacial development. In the Central and South American ancestry group, significant associations with loci previously identified in Asian or European ancestry groups reflected their admixed ancestry. In summary, we have identified novel CL/P risk loci and suggest new genes involved in craniofacial development, confirming the highly heterogeneous etiology of OFCs.

Nonsyndromic orofacial clefts (OFCs) are a heterogeneous group of common craniofacial birth defects with complex etiologies that include genetic and environmental risk factors. OFCs are commonly categorized as cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which have historically been analyzed as distinct entities. Genes for both CL/P and CP have been identified via multiple genome-wide linkage and association studies (GWAS), however, altogether, known variants account for a minority of the estimated heritability in risk to these craniofacial birth defects. We performed genome-wide meta-analyses of CL/P, CP, and all OFCs across two large, multiethnic studies. We then performed population specific meta-analyses in sub-samples of Asian and European ancestry. In addition to observing associations with known variants, we identified a novel genome-wide significant association between SNPs located in an intronic TP63 enhancer and CL/P (p = 1.16 × 10−8). Several novel loci with compelling candidate genes approached genome-wide significance on 4q21.1 (SHROOM3), 12q13.13 (KRT18), and 8p21 (NRG1). In the analysis of all OFCs combined, SNPs near FOXE1 reached genome-wide significance (p = 1.33 × 10−9). Our results support the highly heterogeneous nature of OFCs and illustrate the utility of meta-analysis for discovering new genetic risk factors.

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.

IntroductionPreterm birth is a dire complication of pregnancy that poses huge long-term medical and financial burdens for affected children, their families, and the health care system. The aim of the present study was to identify characteristics associated with preterm births at the Lagos University Teaching Hospital (LUTH), Lagos, Nigeria from 2011 to 2013.MethodsWe obtained Information from 5,561 maternal, fetal/neonatal and obstetric records from the labor ward. We excluded delivery at less than 22 weeks (0.25%), post-term birth at ≥42 weeks gestation (1.3%), and unknown gestation (1.4%). Additionally, we excluded records of multiple births (5.4%) and stillbirths (8.3%) leaving 4,691 records of singleton live-births for analysis. Logistic regression analysis was performed comparing preterm birth (22-36 weeks gestation) to term birth (37-41 weeks gestation). Multiple variable models adjusting for maternal age, parity, fetal position, delivery method and booking status were also evaluated. Multinomial regression was used to identify characteristics associated with preterm birth (PTB) defined as early PTB (22-31 weeks gestation), moderate PTB (32-34 weeks gestation), late PTB (35-36 weeks gestation), compared to term birth (37-41 completed weeks gestation).ResultsFrom our data, 16.8% of the singleton live-birth deliveries were preterm (<37 weeks gestation). Of these, 4.7% were early (22-31 weeks), 4.5% were moderate (32-34 weeks) and 7.7% were late (35-36) PTBs. Older maternal age (≥35 years) [odds ratio (OR) = 1.41], hypertension (OR = 3.44) and rupture of membranes (OR = 4.03) were significantly associated with increased odds of PTB. Women being treated for the prevention of mother-to-child transmission of HIV were at a significantly decreased risk for PTB (OR = 0.70). Sixteen percent of women in this cohort were not registered for antenatal care in LUTH. These non-registered subjects had significantly greater odds of all categories of PTB, including early (odds ratio (OR) = 20.8), moderate (OR = 8.68), and late (OR = 2.15).ConclusionPTB and risks for PTB remain high in Nigeria. We recommend that any high risk pregnancy should be referred to a tertiary center for prenatal care in order to significantly reduce adverse birth outcomes such as PTBs.

Orofacial clefts (OFC) are the most common malformations of the head and neck. In Africa, OFC is under-ascertained with little or no surveillance system in most parts for clefts and other birth defects. A Nigerian craniofacial anomalies study “NigeriaCRAN” was established in 2006 to support cleft research specifically for epidemiological studies, treatment outcomes and; studies into etiology and prevention. We pooled data from seven of the largest Smile Train treatment centers in the six geopolitical zones in Nigeria. Data from September 2006 to June 2011 were analyzed and clefts compared between sides and gender using the Fisher’s exact test. A total of 2197 cases were identified during the study period with an estimated prevalence rate of 0.5/1000. Of the total number of OFC, 53.3% are males and 47%.7 are females. There was a significant difference (p=0.0001) between unilateral left clefts and unilateral right clefts and; significant difference (p=0.0001) between bilateral clefts and either clefts on the left or right side. A significant gender difference (p=0.03) with more females than males was also observed for CP. A total of 103 (4.7 %) associated anomalies were identified, nine syndromic cleft cases and 10.4 % of the total number of clefts individuals have an affected relative. The significant difference between unilateral clefts and gender differences in the proportion of cleft palate only are consistent with the literature. The present study emphasizes the need for birth defects registries in developing countries in order to estimate the exact prevalence of birth defects including OFC.