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Study Description

The focus of this project is to identify genetic variants that are associated with orofacial clefts in African populations in sub-Saharan Africa. Most genetic studies of CLP (including the vast majority of GWAS) have been conducted in populations of European origin with only a few focused on Asian or African populations. We choose to study the genetics of these complex traits in African populations because, African populations have the greatest genetic variation amongst the various populations in the world by virtue of being the primary ancestral population to modern humans (Cavalli-Sforza and Feldman, 2003; Ramsay et al., 2011). Therefore, the potential for finding novel loci for CLP is quite high. To date 6 genome wide association studies (GWAS) for cleft lip with or without cleft palate (CL/P) have been conducted and 18 risk loci identified (Birnbaum et al., 2009; Grant et al., 2009 ; Beaty et al., 2010; Mangold et al., 2010; Ludwig et al., 2012; Sun et al., 2015). All these studies have either been conducted in European populations, Asian populations or both. There is currently no published GWAS for clefts in African populations. African populations represent a novel and richly productive populations for genetic and environmental exposure studies for CL/P. Investigating the presence of genetic variants in diverse population groups can identify novel variants and candidate genes that are population specific. Environmental factors may also increase the risks in certain population groups due to genetic susceptibility and/or specific exposures. Understanding the role these susceptibility genes play in the effects of environmental risk factors can inform strategies designed towards reducing the outcome of these complex traits, e.g. through the modification of the environmental influences.

The study population comprises a large number of individuals (3205 individuals) from Africa (Ghana, Ethiopia and Nigeria). There are cases, case triads (nuclear families), as well as controls with no history of OFC nor other developmental defects.

  • Study Types: Case-Control, Parent-Offspring, Parent-Offspring Trios, Nuclear Families
  • Number of study subjects that have individual level data available through Authorized Access: 3179

Authorized Access
Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Eligible subjects are individuals with non-syndromic clefts and their families born to Ghanaian, Ethiopian and Nigerian parents. Births from Caucasians and Asians were excluded. Controls were recruited in Ethiopia, Ghana and Lagos, Nigeria to match cases at these sites. The recruitment exercise in Ile-Ife, Nigeria was for case families only. Controls were Africans, born alive without any congenital birth defects, in Ethiopia, Ghana and Nigeria (Lagos) and their parents.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
Targeted Genomic Sequencing Illumina MEGA Consortium.v2 15070954_A2 N/A N/A Custom array, developed by CIDR
Study History

This study started in Nigeria through the Nigerian Craniofacial Anomalies project (NigeriaCRAN); a multi-center collaboration between the University of Dundee, Scotland and 11 hospitals in Nigeria that started in September 2006. All participating hospitals obtained ethical permission. In 2012, the project evolved into the African Craniofacial Anomalies Network (AfriCRAN) and the included sample collection started in Ethiopia and then Ghana.

Selected publications
Diseases/Traits Related to Study (MESH terms)
Links to Related Resources
Authorized Data Access Requests
Study Attribution