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Gowans LJJ, Comnick CL, Mossey PA, Eshete MA, Adeyemo WL, Naicker T, Awotoye WA, Petrin A, Adeleke C, Donkor P, Busch TD, James O, Ogunlewe MO, Li M, Olotu J, Hassan M, Adeniyan OA, Obiri-Yeboah S, Arthur FKN, Agbenorku P, Oti AA, Olatosi O, Adamson OO, Fashina AA, Zeng E, Marazita ML, Adeyemo AA, Murray JC, Butali A. Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P). Cleft Palate Craniofac J 2022; 59:841-851. [PMID: 34382870 PMCID: PMC9884465 DOI: 10.1177/10556656211036316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene-environment interactions, stochastic factors, gene-gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset. METHODS The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P. RESULTS We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16. CONCLUSION Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.
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Affiliation(s)
- LJJ Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - CL Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - PA Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - MA Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - WL Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, South Africa
| | - WA Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - A Petrin
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - P Donkor
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - TD Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - O James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - MO Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Nigeria
| | - M Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - OA Adeniyan
- NHS Foundation Trust (Queens Hospital, Belvedere Road, Burton-On-Trent), Staffordshire, UK
| | - S Obiri-Yeboah
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - FKN Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P Agbenorku
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - AA Oti
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - O Olatosi
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - OO Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - AA Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - ML Marazita
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AA Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - JC Murray
- Department of Pediatrics, University of Iowa, Iowa, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
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