Abstract
Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (~ 1/2,500), Asians have the highest prevalence (~1/500), Europeans and Latin Americans lie somewhere in the middle (~1/800 and 1/900, respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (~12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (<5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p = 6.27e-07), 10q22.2 (rs150952246, p = 3.14e-07), and 10q24.32 (rs118107597, p = 8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were (a) purely due to sample sizes, (b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.
Highlights
Orofacial clefts are among the most common birth defects in all populations worldwide and pose a significant health burden
More details on the Pittsburgh Orofacial Clefts (POFC) Multiethnic study can be found in the Database of Genotypes and Phenotypes and at the FaceBase resource for craniofacial research under dataset OFC4: Genetics of Orofacial Clefts and Related Phenotypes (URL https://www.facebase.org/id/1-50DT) (Marazita, 2019)
The current study extends previously published GWAS studies by using a substantially larger study sample than the previous GWAS study that included unrelated case trios, and singleton cases and controls
Summary
Orofacial clefts are among the most common birth defects in all populations worldwide and pose a significant health burden. Surgical treatment along with ongoing orthodontia, speech and other therapies, are very successful in ameliorating the physical health effects of OFC, but there is still a significant social, emotional, and financial burden for individuals with OFC, their families, and society (Wehby and Cassell, 2010; Nidey et al, 2016). There are disparities in access to such therapies for OFCs (Nidey and Wehby, 2019), similar to other malformations with complex medical and surgical needs. It is critical to identify etiologic factors leading to OFCs to improve diagnostics, treatments, and outcomes. The genetic causes of nonsyndromic OFCs are still largely undiscovered
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