Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)

Lord J. J Gowans; Carissa L Comnick; Peter A Mossey; Mekonen A Eshete; Wasiu L Adeyemo; Thirona Naicker; Waheed A Awotoye; Aline Petrin; Chinyere Adeleke; Peter Donkor; Tamara D Busch; Olutayo James; Mobolanle O Ogunlewe; Mary Li; Joy Olotu; Mohaned Hassan; Oluwole A Adeniyan; Solomon Obiri-Yeboah; Fareed K. N Arthur; Pius Agbenorku; Alexander A Oti; Olubukola Olatosi; Olawale O Adamson; Azeez A Fashina; Erliang Zeng; Mary L Marazita; Adebowale A Adeyemo; Jeffrey C Murray; Azeez Butali

doi:10.1177/10556656211036316

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Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)

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Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)

Lord J. J Gowans, Carissa L Comnick, Peter A Mossey, Mekonen A Eshete, Wasiu L Adeyemo, Thirona Naicker, Waheed A Awotoye, Aline Petrin, Chinyere Adeleke, Peter Donkor, …

The Cleft palate-craniofacial journal, Vol.59(7), pp.841-851

07/2022

DOI: 10.1177/10556656211036316

PMCID: PMC9884465

PMID: 34382870

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https://discovery.dundee.ac.uk/ws/files/65917229/POO_PAPER_v3.pdfView

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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.

Dentistry

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Title: Subtitle: Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P)
Creators: Lord J. J Gowans - Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Carissa L Comnick - Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa
Peter A Mossey - Department of Orthodontics, University of Dundee
Mekonen A Eshete - Department of Surgery, School of Medicine, Addis Ababa University
Wasiu L Adeyemo - Department of Oral and Maxillofacial Surgery, University of Lagos
Thirona Naicker - Department of Pediatrics, Universityof KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital
Waheed A Awotoye - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Aline Petrin - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Chinyere Adeleke - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Peter Donkor - School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology
Tamara D Busch - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Olutayo James - Department of Oral and Maxillofacial Surgery, University of Lagos
Mobolanle O Ogunlewe - Department of Oral and Maxillofacial Surgery, University of Lagos
Mary Li - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Joy Olotu - Department of Anatomy, University of Port Harcourt
Mohaned Hassan - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Oluwole A Adeniyan - NHS Foundation Trust (Queens Hospital
Solomon Obiri-Yeboah - School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology
Fareed K. N Arthur - Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology
Pius Agbenorku - School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology
Alexander A Oti - School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology
Olubukola Olatosi - Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh
Olawale O Adamson - Department of Oral and Maxillofacial Surgery, University of Lagos
Azeez A Fashina - Department of Oral and Maxillofacial Surgery, University of Lagos
Erliang Zeng - Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa
Mary L Marazita - Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Graduate School of Public Health, University of Pittsburgh, Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh
Adebowale A Adeyemo - Center for Research on Genomics and Global Health, National Human Genome Research Institute
Jeffrey C Murray - Department of Pediatrics, University of Iowa
Azeez Butali - Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa
Resource Type: Journal article
Publication Details: The Cleft palate-craniofacial journal, Vol.59(7), pp.841-851
DOI: 10.1177/10556656211036316
PMID: 34382870
PMCID: PMC9884465
NLM abbreviation: Cleft Palate Craniofac J
ISSN: 1055-6656
eISSN: 1545-1569
Grant note: DOI: 10.13039/100000002, name: National Institutes of Health, award: R37 DE-08559; DOI: 10.13039/100000867, name: Robert Wood Johnson Foundation, award: 72429; DOI: 10.13039/100000072, name: National Institute of Dental and Craniofacial Research, award: K43DE029427, R00 DE022378, R01DE028300
Language: English
Electronic publication date: 08/12/2021
Date published: 07/2022
Academic Unit: Preventive and Community Dentistry; Roy J. Carver Department of Biomedical Engineering; Orthodontics; Oral Pathology, Radiology and Medicine; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Epidemiology; Iowa Neuroscience Institute; Biostatistics; Pediatric Dentistry; Craniofacial Anomalies Research Center; Dental Research
Record Identifier: 9984120579902771

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