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Butali A, Mossey PA, Adeyemo WL, Eshete MA, Gowans LJJ, Busch TD, Jain D, Yu W, Huan L, Laurie CA, Laurie CC, Nelson S, Li M, Sanchez-Lara PA, Magee WP, Magee KS, Auslander A, Brindopke F, Kay DM, Caggana M, Romitti PA, Mills JL, Audu R, Onwuamah C, Oseni GO, Owais A, James O, Olaitan PB, Aregbesola BS, Braimah RO, Oginni FO, Oladele AO, Bello SA, Rhodes J, Shiang R, Donkor P, Obiri-Yeboah S, Arthur FKN, Twumasi P, Agbenorku P, Plange-Rhule G, Oti AA, Ogunlewe OM, Oladega AA, Adekunle AA, Erinoso AO, Adamson OO, Elufowoju AA, Ayelomi OI, Hailu T, Hailu A, Demissie Y, Derebew M, Eliason S, Romero-Bustillous M, Lo C, Park J, Desai S, Mohammed M, Abate F, Abdur-Rahman LO, Anand D, Saadi I, Oladugba AV, Lachke SA, Amendt BA, Rotimi CN, Marazita ML, Cornell RA, Murray JC, Adeyemo AA. Genomic analyses in African populations identify novel risk loci for cleft palate. Hum Mol Genet 2019; 28:1038-1051. [PMID: 30452639 PMCID: PMC6400042 DOI: 10.1093/hmg/ddy402] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/07/2018] [Accepted: 11/11/2018] [Indexed: 12/13/2022] Open
Abstract
Orofacial clefts are common developmental disorders that pose significant clinical, economical and psychological problems. We conducted genome-wide association analyses for cleft palate only (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub-Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near CTNNA2) and 19 (near SULT2A1). In situ hybridization of Sult2a1 in mice showed expression of SULT2A1 in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously reported 8q24 was the most significant locus for CL/P in our study, and we replicated several previously reported loci including PAX7 and VAX1.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
| | - Peter A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Mekonen A Eshete
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lord J J Gowans
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Tamara D Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Deepti Jain
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Wenjie Yu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Liu Huan
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST, Ministry of Science and Technology) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Cecelia A Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Sarah Nelson
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, David Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - William P Magee
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Kathleen S Magee
- Operation Smile, 3641 Faculty Boulevard, Virginia Beach, VA, USA
| | - Allyn Auslander
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Frederick Brindopke
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Denise M Kay
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa, IA, USA
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rosemary Audu
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chika Onwuamah
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Ganiyu O Oseni
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Arwa Owais
- Department of Pediatric Dentistry, University of Iowa, Iowa, IA, USA
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Peter B Olaitan
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Babatunde S Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ramat O Braimah
- Department of Oral and Maxillofacial Surgery, Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria
| | - Fadekemi O Oginni
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ayodeji O Oladele
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | | | - Jennifer Rhodes
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Rita Shiang
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Peter Donkor
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Peter Twumasi
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Pius Agbenorku
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Olugbenga M Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Afisu A Oladega
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Adegbayi A Adekunle
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Akinwunmi O Erinoso
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Olatunbosun O Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Abosede A Elufowoju
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Oluwanifemi I Ayelomi
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Taiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yohannes Demissie
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Miliard Derebew
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Steve Eliason
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Cynthia Lo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - James Park
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Shaan Desai
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Muiawa Mohammed
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Firke Abate
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lukman O Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Deepti Anand
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Irfaan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas, KS, USA
| | | | - Salil A Lachke
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Brad A Amendt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
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