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Awotoye W, Mossey PA, Hetmanski JB, Gowans LJ, Eshete MA, Adeyemo WL, Alade A, Zeng E, Adamson O, James O, Fashina A, Ogunlewe MO, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Oladayo A, Kayali S, Olotu J, Sule V, Hassan M, Pape J, Aladenika ET, Donkor P, Arthur FK, Obiri-Yeboah S, Sabbah DK, Agbenorku P, Ray D, Plange-Rhule G, Oti AA, Albokhari D, Sobreira N, Dunnwald M, Beaty TH, Taub M, Marazita ML, Adeyemo AA, Murray JC, Butali A. Damaging Mutations in AFDN Contribute to Risk of Nonsyndromic Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2024; 61:697-705. [PMID: 36384317 PMCID: PMC10185709 DOI: 10.1177/10556656221135926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel or rare damaging mutations have been implicated in the developmental pathogenesis of nonsyndromic cleft lip with or without cleft palate (nsCL ± P). Thus, we investigated the human genome for high-impact mutations that could explain the risk of nsCL ± P in our cohorts. We conducted next-generation sequencing (NGS) analysis of 130 nsCL ± P case-parent African trios to identify pathogenic variants that contribute to the risk of clefting. We replicated this analysis using whole-exome sequence data from a Brazilian nsCL ± P cohort. Computational analyses were then used to predict the mechanism by which these variants could result in increased risks for nsCL ± P. We discovered damaging mutations within the AFDN gene, a cell adhesion molecule (CAMs) that was previously shown to contribute to cleft palate in mice. These mutations include p.Met1164Ile, p.Thr453Asn, p.Pro1638Ala, p.Arg669Gln, p.Ala1717Val, and p.Arg1596His. We also discovered a novel splicing p.Leu1588Leu mutation in this protein. Computational analysis suggests that these amino acid changes affect the interactions with other cleft-associated genes including nectins (PVRL1, PVRL2, PVRL3, and PVRL4) CDH1, CTNNA1, and CTNND1. This is the first report on the contribution of AFDN to the risk for nsCL ± P in humans. AFDN encodes AFADIN, an important CAM that forms calcium-independent complexes with nectins 1 and 4 (encoded by the genes PVRL1 and PVRL4). This discovery shows the power of NGS analysis of multiethnic cleft samples in combination with a computational approach in the understanding of the pathogenesis of nsCL ± P.
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Affiliation(s)
- Waheed Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lord J.J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A. Eshete
- Addis Ababa University, School Medicine, Surgical Department, Addis Ababa, Ethiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Modupe O Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Thirona Naicker
- Department of Pediatrics, University of KwaZulu-Natal, South Africa
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Aline Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - John Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Emmanuel T. Aladenika
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Fareed K.N. Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel K. Sabbah
- Department of Child Oral Health and Orthodontics, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pius Agbenorku
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gyikua Plange-Rhule
- Department of Child Health, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Acheampong Oti
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniah Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | | | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret Taub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Azeez Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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2
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Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E. Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Mol Genet Genomic Med 2023; 11:e2109. [PMID: 36468602 PMCID: PMC10009911 DOI: 10.1002/mgg3.2109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Sarah L Mehrem
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ariane C Fechtner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Ruth Raff
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.,Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Khalid Aldhorae
- Department of Orthodontics, College of Dentistry, Thamar University, Thamar, Yemen.,Department of Orthodontics, College of Dentistry, University of Ibn al-Nafis for Medical Sciences, Sanaa, Yemen
| | - Bert Braumann
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Teresa Kruse
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | | | - Gerrit Spanier
- Department of Cranio-Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Erlangen-Nürnberg, Erlangen, Germany.,Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,University Hospital Cologne, Cologne, Germany
| | - Tim Becker
- Institute of Community Medicine, University of Greifswald, Greifswald, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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3
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Thieme F, Henschel L, Hammond NL, Ishorst N, Hausen J, Adamson AD, Biedermann A, Bowes J, Zieger HK, Maj C, Kruse T, Buness A, Hoischen A, Gilissen C, Kreusch T, Jäger A, Gölz L, Braumann B, Aldhorae K, Rojas-Martinez A, Krawitz PM, Mangold E, Dixon MJ, Ludwig KU. Extending the allelic spectrum at noncoding risk loci of orofacial clefting. Hum Mutat 2021; 42:1066-1078. [PMID: 34004033 DOI: 10.1002/humu.24219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies (GWAS) have generated unprecedented insights into the genetic etiology of orofacial clefting (OFC). The moderate effect sizes of associated noncoding risk variants and limited access to disease-relevant tissue represent considerable challenges for biological interpretation of genetic findings. As rare variants with stronger effect sizes are likely to also contribute to OFC, an alternative approach to delineate pathogenic mechanisms is to identify private mutations and/or an increased burden of rare variants in associated regions. This report describes a framework for targeted resequencing at selected noncoding risk loci contributing to nonsyndromic cleft lip with/without cleft palate (nsCL/P), the most frequent OFC subtype. Based on GWAS data, we selected three risk loci and identified candidate regulatory regions (CRRs) through the integration of credible SNP information, epigenetic data from relevant cells/tissues, and conservation scores. The CRRs (total 57 kb) were resequenced in a multiethnic study population (1061 patients; 1591 controls), using single-molecule molecular inversion probe technology. Combining evidence from in silico variant annotation, pedigree- and burden analyses, we identified 16 likely deleterious rare variants that represent new candidates for functional studies in nsCL/P. Our framework is scalable and represents a promising approach to the investigation of additional congenital malformations with multifactorial etiology.
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Affiliation(s)
- Frederic Thieme
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Nigel L Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nina Ishorst
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Jonas Hausen
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Antony D Adamson
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Angelika Biedermann
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - Hanna K Zieger
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Carlo Maj
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Teresa Kruse
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Andreas Buness
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany.,Department of Medical Biometry, Informatics, and Epidemiology, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany.,Department of Orthodontics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Bert Braumann
- Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Khalid Aldhorae
- Department of Orthodontics, Thamar University, Thamar, Yemen
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey, Mexico
| | - Peter M Krawitz
- School of Medicine, Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Michael J Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Kerstin U Ludwig
- Institute of Human Genetics, School of Medicine, University Hospital Bonn, University of Bonn, Bonn, Germany
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4
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Nasreddine G, El Hajj J, Ghassibe-Sabbagh M. Orofacial clefts embryology, classification, epidemiology, and genetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2021; 787:108373. [PMID: 34083042 DOI: 10.1016/j.mrrev.2021.108373] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 01/14/2023]
Abstract
Orofacial clefts (OFCs) rank as the second most common congenital birth defect in the United States after Down syndrome and are the most common head and neck congenital malformations. They are classified as cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO). OFCs have significant psychological and socio-economic impact on patients and their families and require a multidisciplinary approach for management and counseling. A complex interaction between genetic and environmental factors contributes to the incidence and clinical presentation of OFCs. In this comprehensive review, the embryology, classification, epidemiology and etiology of clefts are thoroughly discussed and a "state-of-the-art" snapshot of the recent advances in the genetics of OFCs is presented.
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Affiliation(s)
- Ghenwa Nasreddine
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
| | - Joelle El Hajj
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
| | - Michella Ghassibe-Sabbagh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
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5
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Vsevolozhskaya OA, Shi M, Hu F, Zaykin DV. DOT: Gene-set analysis by combining decorrelated association statistics. PLoS Comput Biol 2020; 16:e1007819. [PMID: 32287273 PMCID: PMC7182280 DOI: 10.1371/journal.pcbi.1007819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/24/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Historically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype datasets, including cost of management, difficulties in consolidation of records across research groups, etc. These issues make methods based on SNP-level summary statistics particularly appealing. The most common form of combining statistics is a sum of SNP-level squared scores, possibly weighted, as in burden tests for rare variants. The overall significance of the resulting statistic is evaluated using its distribution under the null hypothesis. Here, we demonstrate that this basic approach can be substantially improved by decorrelating scores prior to their addition, resulting in remarkable power gains in situations that are most commonly encountered in practice; namely, under heterogeneity of effect sizes and diversity between pairwise LD. In these situations, the power of the traditional test, based on the added squared scores, quickly reaches a ceiling, as the number of variants increases. Thus, the traditional approach does not benefit from information potentially contained in any additional SNPs, while our decorrelation by orthogonal transformation (DOT) method yields steady gain in power. We present theoretical and computational analyses of both approaches, and reveal causes behind sometimes dramatic difference in their respective powers. We showcase DOT by analyzing breast cancer and cleft lip data, in which our method strengthened levels of previously reported associations and implied the possibility of multiple new alleles that jointly confer disease risk.
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Affiliation(s)
- Olga A. Vsevolozhskaya
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Min Shi
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Fengjiao Hu
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Dmitri V. Zaykin
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
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6
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van Rooij IALM, Ludwig KU, Welzenbach J, Ishorst N, Thonissen M, Galesloot TE, Ongkosuwito E, Bergé SJ, Aldhorae K, Rojas-Martinez A, Kiemeney LALM, Vermeesch JR, Brunner H, Roeleveld N, Devriendt K, Dormaar T, Hens G, Knapp M, Carels C, Mangold E. Non-Syndromic Cleft Lip with or without Cleft Palate: Genome-Wide Association Study in Europeans Identifies a Suggestive Risk Locus at 16p12.1 and Supports SH3PXD2A as a Clefting Susceptibility Gene. Genes (Basel) 2019; 10:genes10121023. [PMID: 31817908 PMCID: PMC6947597 DOI: 10.3390/genes10121023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 01/16/2023] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) ranks among the most common human congenital malformations, and has a multifactorial background in which both exogenous and genetic risk factors act in concert. The present report describes a genome-wide association study (GWAS) involving a total of 285 nsCL/P patients and 1212 controls from the Netherlands and Belgium. Twenty of the 40 previously reported nsC/LP susceptibility loci were replicated, which underlined the validity of this sample. SNV-based analysis of the data identified an as yet unreported suggestive locus at chromosome 16p12.1 (p-value of the lead SNV: 4.17 × 10-7). This association was replicated in two of three patient/control replication series (Central European and Yemeni). Gene analysis of the GWAS data prioritized SH3PXD2A at chromosome 10q24.33 as a candidate gene for nsCL/P. To date, support for this gene as a cleft gene has been restricted to data from zebrafish and a knockout mouse model. The present GWAS was the first to implicate SH3PXD2A in non-syndromic cleft formation in humans. In summary, although performed in a relatively small sample, the present GWAS generated novel insights into nsCL/P etiology.
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Affiliation(s)
- Iris ALM van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Michelle Thonissen
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Edwin Ongkosuwito
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Stefaan J Bergé
- Department of Oral and Maxillofacial Surgery, Radboud university medical center, 6500 HB Nijmegen, The Netherlands;
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen;
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, School of Medicine, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey 64460, Mexico;
| | - Lambertus ALM Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
- Department of Urology, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | | | - Han Brunner
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Department of Clinical Genetics, and GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium;
| | - Titiaan Dormaar
- Department of Imaging and Pathology, KU Leuven, 3000 Leuven, Belgium;
- Oral and Maxillofacial Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Greet Hens
- Department of Neurosciences, Experimental Otorhinolaryngology, KU Leuven, 3000 Leuven, Belgium;
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany;
| | - Carine Carels
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium (C.C.)
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Orthodontics, University Hospitals KU Leuven, 3000 Leuven, Belgium
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
- Correspondence: ; Tel.: +49-228-28751008
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7
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Huang L, Jia Z, Shi Y, Du Q, Shi J, Wang Z, Mou Y, Wang Q, Zhang B, Wang Q, Ma S, Lin H, Duan S, Yin B, Lin Y, Wang Y, Jiang D, Hao F, Zhang L, Wang H, Jiang S, Xu H, Yang C, Li C, Li J, Shi B, Yang Z. Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLoS Genet 2019; 15:e1008357. [PMID: 31609978 PMCID: PMC6812857 DOI: 10.1371/journal.pgen.1008357] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 10/24/2019] [Accepted: 08/07/2019] [Indexed: 02/05/2023] Open
Abstract
Nonsyndromic orofacial cleft (NSOFC) is a severe birth defect that occurs early in embryonic development and includes the subtypes cleft palate only (CPO), cleft lip only (CLO) and cleft lip with cleft palate (CLP). Given a lack of specific genetic factor analysis for CPO and CLO, the present study aimed to dissect the landscape of genetic factors underlying the pathogenesis of these two subtypes using 6,986 cases and 10,165 controls. By combining a genome-wide association study (GWAS) for specific subtypes of CPO and CLO, as well as functional gene network and ontology pathway analysis, we identified 18 genes/loci that surpassed genome-wide significance (P < 5 × 10−8) responsible for NSOFC, including nine for CPO, seven for CLO, two for both conditions and four that contribute to the CLP subtype. Among these 18 genes/loci, 14 are novel and identified in this study and 12 contain developmental transcription factors (TFs), suggesting that TFs are the key factors for the pathogenesis of NSOFC subtypes. Interestingly, we observed an opposite effect of the genetic variants in the IRF6 gene for CPO and CLO. Moreover, the gene expression dosage effect of IRF6 with two different alleles at the same single-nucleotide polymorphism (SNP) plays important roles in driving CPO or CLO. In addition, PAX9 is a key TF for CPO. Our findings define subtypes of NSOFC using genetic factors and their functional ontologies and provide a clue to improve their diagnosis and treatment in the future. Although GWAS have discovered 43 genes/loci associated with NSOFC, most previous studies used mixed samples of CL/P subtypes rather than CPO or CLO separately. Our findings define the CPO and CLO subtypes using genetic factors and their functional ontologies based on CPO and CLO GWAS data. In this study, we identified 18 genes/loci that contribute to CPO, CLO or CLP. Fourteen of them are novel and identified, and 12 contain developmental transcription factors (TFs), suggesting that TFs are the key factors for the pathogenesis of NSOFC subtypes. We observed an opposite effect in the strongest associated locus IRF6 for CPO and CLO; this information was omitted by previous CL/P GWAS. Furthermore, we reveal that the gene expression dosage of IRF6 plays important roles in driving CPO or CLO. In addition, we found that PAX9 is a strong genetic factor for CPO. These results suggest that transcription factors are the key genetic reason for the pathogenesis of NSOFC subtypes.
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Affiliation(s)
- Lulin Huang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Shi
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Qin Du
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, United States of America
| | - Ziyan Wang
- Department of basic medicine, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yandong Mou
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Qingwei Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Bihe Zhang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shi Ma
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - He Lin
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shijun Duan
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yansong Lin
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yiru Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dan Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Fang Hao
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Haixin Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Suyuan Jiang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Huijuan Xu
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Chengwei Yang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenghao Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jingtao Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhenglin Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
- Department of basic medicine, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- * E-mail:
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8
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Böhmer AC, Gölz L, Kreusch T, Kramer FJ, Pötzsch B, Nöthen MM, Jäger A, Mangold E, Knapp M, Ludwig KU. Investigation of dominant and recessive inheritance models in genome-wide association studies data of nonsyndromic cleft lip with or without cleft palate. Birth Defects Res 2017; 110:336-341. [PMID: 29134786 DOI: 10.1002/bdr2.1144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is one of the most common congenital malformation worldwide, and its etiology involves both genetic and environmental factors. Recent genome-wide and targeted genetic studies of nsCL/P have identified numerous genetic risk loci, under the hypothesis of a multiplicative mode of inheritance. The present study investigated whether novel nsCL/P risk loci could be identified by analyzing dominant/recessive genetic effects in single nucleotide polymorphism (SNP) data from genome-wide association studies. For this purpose, a genome-wide investigation of dominant/recessive common SNP effects was performed in our previously published meta-analysis data set. Twenty-four loci were identified as candidate regions. In a subsequent association analysis in an independent study cohort of 224 nsCL/P patients and 986 controls of European descent, none of the loci could be replicated. Therefore, our strategy of identifying novel loci by applying different genetic models did not yield any novel findings, suggesting that recessive/dominant common variation only make a limited contribution to nsCL/P in Europeans. However, we cannot rule out that such effects are present at some of the loci that have previously been identified, or are present in different populations.
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Affiliation(s)
- Anne C Böhmer
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Thomas Kreusch
- Department of Oral and Maxillofacial Surgery, Head and Neck Centre, Asklepios Klinik Nord, Heidberg, Hamburg, Germany
| | - Franz-Josef Kramer
- Department of Oral and Maxillofacial Surgery, University of Göttingen, Göttingen, Germany
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University of Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Andreas Jäger
- Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Department of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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9
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Masotti C, Brito L, Nica A, Ludwig K, Nunes K, Savastano C, Malcher C, Ferreira S, Kobayashi G, Bueno D, Alonso N, Franco D, Rojas-Martinez A, dos Santos S, Galante P, Meyer D, Hünemeier T, Mangold E, Dermitzakis E, Passos-Bueno M. MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach. J Dent Res 2017; 97:33-40. [DOI: 10.1177/0022034517735805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.
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Affiliation(s)
- C. Masotti
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - L.A. Brito
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - A.C. Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - K. Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C.P. Savastano
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C. Malcher
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - S.G. Ferreira
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - G.S. Kobayashi
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - D.F. Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - N. Alonso
- Department of Plastic Surgery, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - D. Franco
- Department of Plastic Surgery, Hospital Clementino Braga Filho, Federal University of Rio de Janeiro Medical School, Rio de Janeiro, RJ, Brazil
| | - A. Rojas-Martinez
- Department of Biochemistry and Molecular Medicine, School of Medicine, and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - S.E. dos Santos
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - P.A. Galante
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - D. Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - T. Hünemeier
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - E. Mangold
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - E.T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - M.R. Passos-Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
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10
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Dodhia S, Celis K, Aylward A, Cai Y, Fontana ME, Trespalacios A, Hoffman DC, Alfonso HO, Eisig SB, Su GH, Chung WK, Haddad J. ACSS2 gene variant associated with cleft lip and palate in two independent Hispanic populations. Laryngoscope 2017; 127:E336-E339. [PMID: 28543373 DOI: 10.1002/lary.26637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 03/16/2017] [Accepted: 03/28/2017] [Indexed: 01/08/2023]
Abstract
OBJECTIVES/HYPOTHESIS A candidate variant (p.Val496Ala) of the ACSS2 gene (T > C missense, rs59088485 variant at chr20: bp37 33509608) was previously found to consistently segregate with nonsyndromic cleft lip and/or palate (NSCLP) in three Honduran families. Objectives of this study were 1) to investigate the frequency of this ACSS2 variant in Honduran unrelated NSCLP patients and unrelated unaffected controls and 2) to investigate the frequency of this variant in Colombian unrelated affected NSCLP patients and unrelated unaffected controls. STUDY DESIGN Case-control studies. METHODS Sanger sequencing of 99 unrelated Honduran NSCLP patients and 215 unrelated unaffected controls for the p.Val496Ala ACSS2 variant was used to determine the carrier frequency in NSCLP patients and controls. Sanger sequencing of 230 unrelated Colombian NSCLP patients and 146 unrelated unaffected controls for the p.Val496Ala ACSS2 variant was used to determine the carrier frequency in NSCLP patients and controls. RESULTS In the Honduran population, the odds ratio of having NSCLP among carriers of the p.Val496Ala ACSS2 variant was 4.0 (P = .03), with a carrier frequency of seven of 99 (7.1%) in unrelated affected and four of 215 (1.9%) in unrelated unaffected individuals. In the Colombian population, the odds ratio of having NSCLP among carriers of the p.Val496Ala ACSS2 variant was 2.6 (P = .04), with a carrier frequency of 23 of 230 (10.0%) in unrelated affected and six of 146 (4.1%) in unrelated unaffected individuals. CONCLUSIONS These findings support the role of ACSS2 in NSCLP in two independent Hispanic populations from Honduras and Colombia. LEVEL OF EVIDENCE NA Laryngoscope, 127:E336-E339, 2017.
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Affiliation(s)
- Sonam Dodhia
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, New York, U.S.A
| | - Katrina Celis
- John P. Hussman Institute for Genomics, University of Miami, Miami, Florida, U.S.A
| | - Alana Aylward
- Department of Otolaryngology-Head and Neck Surgery, University of Utah, Salt Lake City, Utah, U.S.A
| | - Yi Cai
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, New York, U.S.A
| | - Maria E Fontana
- College of Dental Medicine, Columbia University, New York, New York, U.S.A
| | - Alberto Trespalacios
- Department of Plastic Surgery, Hernando Moncaleano University Hospital, Neiva, Huila, Colombia
| | - David C Hoffman
- Department of Oral and Maxillofacial Surgery, Staten Island University Hospital, Staten Island, New York, U.S.A
| | - Henry Ostos Alfonso
- Laboratory of Genomic Medicine, South Colombian University, Neiva, Huila, Colombia
| | - Sidney B Eisig
- Department of Craniofacial Surgery, Columbia University Medical Center, New York, New York, U.S.A
| | - Gloria H Su
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, New York, U.S.A.,Pathology and Cell Biology, Columbia University Medical Center, New York, New York, U.S.A
| | - Wendy K Chung
- Pediatrics, Columbia University Medical Center, New York, New York, U.S.A.,Medicine, Columbia University Medical Center, New York, New York, U.S.A
| | - Joseph Haddad
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, New York, U.S.A
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11
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Guo Q, Li D, Meng X, Liu T, Shi J, Hao Y, Jiao X, Lv K, Hu T, Song T. Association between PAX7 and NTN1 gene polymorphisms and nonsyndromic orofacial clefts in a northern Chinese population. Medicine (Baltimore) 2017; 96:e6724. [PMID: 28489749 PMCID: PMC5428583 DOI: 10.1097/md.0000000000006724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts (NSOC) are the most common orofacial congenital defect with a complex etiology. Genome-wide association studies have identified paired box protein 7 (PAX7) and netrin-1 (NTN1) as candidate susceptibility genes for NSOC in both European and Asian populations. Here, possible associations between single-nucleotide polymorphisms (SNPs) in or near PAX7 and NTN1 were investigated in relation to risk of NSOC in a northern Chinese population. METHODS A total of 602 individuals with NSOC and 510 controls were recruited from northern China. Polymerase chain reaction-ligation detection reactions were used to analyze 4 SNPs (rs742071, rs6659735, rs766325, and rs4920520) of PAX7 and 2 SNPs (rs9904526 and rs9788972) of NTN1. Investigations of polymorphisms and risk of NSOC were conducted by using the PLINK software. RESULTS NTN1 rs9788972 AG was found to be associated with an increased risk of NSOC compared to the GG homozygous genotype (OR = 1.43, 95% CI = 1.11-1.86, P = .006). When the multifactor dimensionality reduction method was applied, NTN1 rs9788972 still exhibited an increased risk for NSOC (P = .008). In contrast, SNPs in PAX7 were not associated with any increased risk of NSOC. CONCLUSION NTN1 rs9788972 is identified as a risk locus for NSOC susceptibility in a northern Chinese population.
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Affiliation(s)
- Qiang Guo
- Scientific Research Management Office, The First Affiliated Hospital, Harbin Medical University, Nangang District, Harbin, China
| | | | | | | | - Jinna Shi
- Scientific Research Management Office, The First Affiliated Hospital, Harbin Medical University, Nangang District, Harbin, China
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12
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Salagovic J, Klimcakova L, Zabavnikova M, Behunova J, Hudakova T, Fedeles J, Molnarova A, Podracka L. Polymorphisms at 1q32, 8q24, and 17q22 loci are associated with nonsyndromic cleft lip with or without cleft palate risk in the Slovak population. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:152-157. [PMID: 28422192 DOI: 10.5507/bp.2017.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is the most common orofacial birth defect with an aetiology involving both genetic and environmental factors. Genome-wide association studies (GWAS) have identified several genomic susceptibility regions for nsCL/P. In the present study, the three well established single nucleotide polymorphisms (SNPs) identified by GWAS (rs987525 at 8q24, rs7078160 at 10q25, and rs227731 at 17q22 loci) and one SNP identified by candidate gene study (rs642961 in IRF6 gene at 1q32 locus) were analysed for an association with nsCL/P in Slovak population. METHODS Nucleotide variants were genotyped in 165 nsCL/P patients and 326 unaffected controls. All variants of interest were genotyped using high-resolution melting analysis after real-time PCR. RESULTS We found significant differences between patient and control groups with respect to the allele and genotype frequencies for the SNPs at the 1q32, 8q24, and 17q22 loci. SNP at the 10q25 locus showed a trend toward association with nsCL/P risk. CONCLUSIONS The results suggest that SNPs at the 1q32, 8q24 and 17q22 loci may contribute to the nsCL/P risk in Slovak population.
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Affiliation(s)
- Jan Salagovic
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Lucia Klimcakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Marianna Zabavnikova
- Department of Plastic, Reconstructive and Aesthetic Surgery, LP University Hospital, Kosice, Slovak Republic
| | - Jana Behunova
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,Institut fur Medizinische Genetik, Medizinische Universitat Wien, Austria
| | - Terezia Hudakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Jozef Fedeles
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Agata Molnarova
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Ludmila Podracka
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,1st Department of Paediatrics, Faculty of Medicine, Comenius University and Children's University Hospital, Bratislava, Slovak Republic
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13
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Li D, Liu T, Meng X, Guo Q, Shi J, Hao Y, Jiao X, Lv K, Song T. Polymorphic variants in VAX1 and the risk of nonsyndromic cleft lip with or without cleft palate in a population from northern China. Medicine (Baltimore) 2017; 96:e6550. [PMID: 28383424 PMCID: PMC5411208 DOI: 10.1097/md.0000000000006550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common craniofacial birth defects, and the etiology of NSCL/P involves both genetic and environmental factors. Genome-wide association study (GWAS) identified a novel susceptibility locus of ventral anterior homeobox 1 (VAX1) in patients with NSCL/P. However, the association of single nucleotide polymorphisms (SNPs) of VAX1 with NSCL/P is inconclusive due to the differences in the racial and ethnic populations. The aim of this study was to replicate the association between VAX1 and NSCL/P in a northern Chinese Han population. METHODS Our study included 186 patients with NSCL/P and 223 healthy individuals from northern China. Five SNPs (rs4752028, rs10787760, rs7078160, rs6585429, and rs1871345) on VAX1 were genotyped using the SNaPshot method. RESULTS Recessive genetic model analysis revealed that homozygous genotype CC of VAX1 rs4752028 was associated with an increased risk of NSCL/P (odds ratio = 1.89, 95% confidence interval = 1.12-3.19, P = 0.017), but the results were not significant after the Bonferroni correction for multiple comparisons. The allele and genotype frequencies of rs10787760, rs7078160, rs6585429, and rs1871345 and the allele frequencies of rs4752028 showed no significant differences between cases and controls. Haplotype and SNP-SNP interaction analyses did not detect any significant association of VAX1 with the occurrence of NSCL/P. CONCLUSION VAX1 rs4752028 was weakly associated with NSCL/P development in the studied northern Chinese Han population.
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Affiliation(s)
| | | | | | - Qiang Guo
- Scientific Research Management Office, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jinna Shi
- Scientific Research Management Office, The First Affiliated Hospital, Harbin Medical University, Harbin, China
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14
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Wang F, Jiang Y, Yang S, Liu Q, Lin J, Zhang H. Associations between the NOGGIN rs227731 polymorphism and NSCL/P risk may be associated with ethnicities: A meta-analysis. Birth Defects Res 2017; 109:445-451. [PMID: 28398705 DOI: 10.1002/bdra.23612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/15/2016] [Accepted: 12/01/2016] [Indexed: 11/06/2022]
Abstract
BACKGROUND The aim of this study was to evaluate the association between the noggin rs227731 polymorphism on chromosome 17q22 and risk of nonsyndromic cleft lip with or without palate (NSCL/P). METHODS Three online databases were searched, including Embase, PubMed, and Chinese National Knowledge Infrastructure. The strength of the associations was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs). We also made a subgroup analysis to explore sources of heterogeneity. RESULTS Nine comparisons from seven studies were included in this meta-analysis. We used five genetic models and found that the noggin rs227731 polymorphism may increase NSCL/P risk in Caucasians: C versus A: OR = 1.43, 95% CI, 1.30-1.58; CC versus AA: OR = 2.00, 95% CI, 1.59-2.52; CA versus AA: OR = 1.50, 95% CI, 1.27-1.77; CC+CA versus AA: OR = 1.64, 95% CI, 1.40-1.92; CC versus CA+AA: OR = 1.56, 95% CI, 1.30-1.87. However, for the Chinese population, no significant association between the rs227731 polymorphism and NSCL/P risk was found: C vs. A: OR = 1.04, 95% CI, 0.81-1.33; CC vs. AA: OR = 1.01, 95% CI, 0.52-1.95; CA vs. AA: OR = 1.03, 95% CI, 0.75-1.40; CC+CA vs. AA: OR = 1.04, 95% CI, 0.76-1.43; CC vs. CA+AA: OR = 1.01, 95% CI, 0.56-1.81. CONCLUSION Our meta-analysis suggested that the rs227731 polymorphism may increase NSCL/P risk in Caucasians and may have no significant association in the Chinese population. Effects of individual and environmental risk factors and of gene-environment interactions may play a different role in Caucasians than in the Chinese population. More relevant case-control studies are required to obtain more precise results. Birth Defects Research 109:445-451, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Feilong Wang
- Department of Pediatric Dentistry, the Affiliated Stomatology Hospital, Chongqing Medical University, China
| | - Ying Jiang
- Department of Pediatric Dentistry, the Affiliated Stomatology Hospital, Chongqing Medical University, China
| | - Sheng Yang
- Department of Pediatric Dentistry, the Affiliated Stomatology Hospital, Chongqing Medical University, China
| | - Qin Liu
- Department of Social Medicine and Management, Chongqing Medical University, China
| | - Juhong Lin
- Department of Pediatric Dentistry, the Affiliated Stomatology Hospital, Chongqing Medical University, China
| | - Hongmei Zhang
- Department of Pediatric Dentistry, the Affiliated Stomatology Hospital, Chongqing Medical University, China
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15
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Wattanawong K, Rattanasiri S, McEvoy M, Attia J, Thakkinstian A. Association between IRF6 and 8q24 polymorphisms and nonsyndromic cleft lip with or without cleft palate: Systematic review and meta-analysis. ACTA ACUST UNITED AC 2016; 106:773-88. [PMID: 27511269 PMCID: PMC5095821 DOI: 10.1002/bdra.23540] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/07/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND We conducted a systematic review and meta-analysis of interferon regulatory factor 6 and 8q24 polymorphisms with nonsyndromic cleft lip with/without cleft palate (NSCL/P). METHODS Data extraction was independently performed by two reviewers. Genotypic effects of four polymorphisms from 31 studies were pooled separately by ethnicity using a mixed-effect logit model with accounting for heterogeneity. RESULTS For rs2235371, AA and GA carried, respectively, 51% (95% confidence interval [CI], 37%-61%) and 42% (95% CI, 32%-50%) lower risks of NSCL/P than GG genotypes in Asians, but these genotypes were not significant in Caucasians. For rs2013162, only AA was significant, that is, carried 0.65 (95% CI, 0.52-0.82) times lower odds than CC in Caucasians but not for Asians. For rs642961, AA and GA genotypes, respectively, carried 2.47 (95% CI, 1.41-4.35) and 1.40 (95% CI, 1.12-1.75) times higher odds in Asian, and 2.03 (95% CI, 1.52-2.71) and 1.58 (95% CI, 1.37-1.82) times higher odds in Caucasians compare with GG genotypes. For rs987525, AA and CA genotypes carried 2.27 (95% CI, 1.43-3.60) and 1.34 (95% CI, 1.02-1.77) times higher odds in Asian, and 5.25 (95% CI, 3.98-6.91) and 2.13 (95% CI-1.82, 2.49) times higher odds in Caucasians, and 1.42 (95% CI, 1.10-1.82) and 1.28 (95% CI, 1.09-1.50) times higher odds in mixed ethnicities compared with CC genotypes. These variant effects remained significant based on applying Bonferroni corrected-thresholds, except in the mixed ethnicity. CONCLUSION We show robust variant effects in NSCL/P. Considering them with other genes and risk factors might be useful to improve prediction of NSCL/P occurrence. Birth Defects Research (Part A) 106:773-788, 2016. © 2016 The Authors Birth Defects Research Part A: Clinical and Molecular Teratology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kachin Wattanawong
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sasivimol Rattanasiri
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Mark McEvoy
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - John Attia
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - Ammarin Thakkinstian
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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16
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Velázquez-Aragón JA, Alcántara-Ortigoza MA, Estandia-Ortega B, Reyna-Fabián ME, Méndez-Adame CD, González-Del Angel A. Gene Interactions Provide Evidence for Signaling Pathways Involved in Cleft Lip/Palate in Humans. J Dent Res 2016; 95:1257-64. [PMID: 27154735 DOI: 10.1177/0022034516647034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect that has a complex etiology. Genome-wide association studies have recently identified new loci associated with NSCL/P, but these loci have not been analyzed in a Mexican Mestizo population. A complex etiology implies the presence of genetic interactions, but there is little available information regarding this in NSCL/P, and no signaling pathway has been clearly implicated in humans. Here, we analyzed the associations of 24 single nucleotide polymorphisms (SNPs) with NSCL/P in a Mexican Mestizo population (133 cases, 263 controls). The multifactorial dimensionality reduction method was used to examine gene-gene and gene-folic acid consumption interactions for the 24 SNPs analyzed in this study and for 2 additional SNPs that had previously been genotyped in the same study population. Six SNPs located in paired box 7, ventral anterior homeobox 1, sprouty RTK signaling antagonist 2, bone morphogenetic protein 4, and tropomyosin 1 genes were associated with higher risks of NSCL/P (P = 0.0001 to 0.04); 2 SNPs, 1 each in netrin 1 and V-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B, were associated with a lower risk of NSCL/P (P = 0.013 to 0.03); and 2 SNPs, 1 each in ATP binding cassette subfamily A member 4 (ABCA4) and noggin, showed associations with NSCL/P that approached the threshold of significance (P = 0.056 to 0.07). In addition, 6 gene-gene interactions (P = 0.0001 to 0.001) and an ABCA4-folic acid consumption interaction (P < 0.0001) were identified. On the basis of these results, combined with those of previous association studies in the literature and biological characterizations of murine models, we propose an interaction network in which interferon regulatory factor 6 plays a central role in the etiology of NSCL/P.
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Affiliation(s)
- J A Velázquez-Aragón
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - M A Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - B Estandia-Ortega
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - M E Reyna-Fabián
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - C D Méndez-Adame
- Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - A González-Del Angel
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
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17
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Ludwig KU, Ahmed ST, Böhmer AC, Sangani NB, Varghese S, Klamt J, Schuenke H, Gültepe P, Hofmann A, Rubini M, Aldhorae KA, Steegers-Theunissen RP, Rojas-Martinez A, Reiter R, Borck G, Knapp M, Nakatomi M, Graf D, Mangold E, Peters H. Meta-analysis Reveals Genome-Wide Significance at 15q13 for Nonsyndromic Clefting of Both the Lip and the Palate, and Functional Analyses Implicate GREM1 As a Plausible Causative Gene. PLoS Genet 2016; 12:e1005914. [PMID: 26968009 PMCID: PMC4788144 DOI: 10.1371/journal.pgen.1005914] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/15/2016] [Indexed: 12/22/2022] Open
Abstract
Nonsyndromic orofacial clefts are common birth defects with multifactorial etiology. The most common type is cleft lip, which occurs with or without cleft palate (nsCLP and nsCLO, respectively). Although genetic components play an important role in nsCLP, the genetic factors that predispose to palate involvement are largely unknown. In this study, we carried out a meta-analysis on genetic and clinical data from three large cohorts and identified strong association between a region on chromosome 15q13 and nsCLP (P = 8.13×10−14 for rs1258763; relative risk (RR): 1.46, 95% confidence interval (CI): 1.32–1.61)) but not nsCLO (P = 0.27; RR: 1.09 (0.94–1.27)). The 5 kb region of strongest association maps downstream of Gremlin-1 (GREM1), which encodes a secreted antagonist of the BMP4 pathway. We show during mouse embryogenesis, Grem1 is expressed in the developing lip and soft palate but not in the hard palate. This is consistent with genotype-phenotype correlations between rs1258763 and a specific nsCLP subphenotype, since a more than two-fold increase in risk was observed in patients displaying clefts of both the lip and soft palate but who had an intact hard palate (RR: 3.76, CI: 1.47–9.61, Pdiff<0.05). While we did not find lip or palate defects in Grem1-deficient mice, wild type embryonic palatal shelves developed divergent shapes when cultured in the presence of ectopic Grem1 protein (P = 0.0014). The present study identified a non-coding region at 15q13 as the second, genome-wide significant locus specific for nsCLP, after 13q31. Moreover, our data suggest that the closely located GREM1 gene contributes to a rare clinical nsCLP entity. This entity specifically involves abnormalities of the lip and soft palate, which develop at different time-points and in separate anatomical regions. Clefts of the lip and palate are common birth defects, and require long-term multidisciplinary management. Their etiology involves genetic factors and environmental influences and/or a combination of both, however, these interactions are poorly defined. Moreover, although clefts of the lip may or may not involve the palate, the determinants predisposing to specific subphenotypes are largely unknown. Here we demonstrate that variations in the non-coding region near the GREM1 gene show a highly significant association with a particular phenotype in which cleft lip and cleft palate co-occur (nsCLP; P = 8.13×10−14). Our data suggest that the risk is even higher for patients who have a cleft lip and a cleft of the soft palate, but not of the hard palate. Interestingly, this subphenotype corresponds to the expression of the mouse Grem1 gene, which is found in the developing lip and soft palate but not in the hard palate. While Grem1-deficient mice display no lip or palate defects, we demonstrate that ectopic Grem1 protein alters palatal shelve morphogenesis. Together, our results identify a region near GREM1 as the second, genome-wide significant risk locus for nsCLP, and suggest that deregulated GREM1 expression during craniofacial development may contribute to this common birth defect.
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Affiliation(s)
- Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
- * E-mail: (KUL); (HP)
| | - Syeda Tasnim Ahmed
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Anne C. Böhmer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Nasim Bahram Sangani
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Sheryil Varghese
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Johanna Klamt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Hannah Schuenke
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Pinar Gültepe
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Italy
| | | | - Regine P. Steegers-Theunissen
- Department of Obstetrics and Gynaecology, ErasmusMC, Rotterdam, Netherlands
- Department of Epidemiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Augusto Rojas-Martinez
- Department of Biochemistry and Molecular Medicine, School of Medicine, and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Rudolf Reiter
- Department of Otolaryngology—Head and Neck Surgery, Section of Phoniatrics and Pedaudiology, University of Ulm, Ulm, Germany
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | | | - Daniel Graf
- Orofacial Development and Regeneration, Institute of Oral Biology, Center for Dental Medicine, University of Zurich, Zurich, Switzerland
- Departments of Dentistry and Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | | | - Heiko Peters
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
- * E-mail: (KUL); (HP)
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18
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A multicentric association study between 39 genes and nonsyndromic cleft lip and palate in a Brazilian population. J Craniomaxillofac Surg 2016; 44:16-20. [DOI: 10.1016/j.jcms.2015.07.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 07/02/2015] [Accepted: 07/27/2015] [Indexed: 12/20/2022] Open
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19
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Cura F, Böhmer AC, Klamt J, Schünke H, Scapoli L, Martinelli M, Carinci F, Nöthen MM, Knapp M, Ludwig KU, Mangold E. Replication analysis of 15 susceptibility loci for nonsyndromic cleft lip with or without cleft palate in an italian population. ACTA ACUST UNITED AC 2015; 106:81-7. [DOI: 10.1002/bdra.23454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/30/2015] [Accepted: 08/13/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Francesca Cura
- Department of Experimental; Diagnostic and Specialty Medicine, University of Bologna; Bologna Italy
| | - Anne C. Böhmer
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
| | - Johanna Klamt
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
| | - Hannah Schünke
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
| | - Luca Scapoli
- Department of Experimental; Diagnostic and Specialty Medicine, University of Bologna; Bologna Italy
| | - Marcella Martinelli
- Department of Experimental; Diagnostic and Specialty Medicine, University of Bologna; Bologna Italy
| | - Francesco Carinci
- Department of Morphology; Surgery and Experimental Medicine, University of Ferrara; Ferrara Italy
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn; Bonn Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center, University of Bonn; Bonn Germany
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20
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do Rego Borges A, Sá J, Hoshi R, Viena CS, Mariano LC, de Castro Veiga P, Medrado AP, Machado RA, de Aquino SN, Messetti AC, Spritz RA, Coletta RD, Reis SRA. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry. Am J Med Genet A 2015. [DOI: 10.1002/ajmg.a.37181] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea do Rego Borges
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Jamile Sá
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Ryuichi Hoshi
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Camila Sane Viena
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Lorena C. Mariano
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Patricia de Castro Veiga
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Alena Peixoto Medrado
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | | | - Ana Camila Messetti
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program; University of Colorado School of Medicine; Aurora Colorado
| | - Ricardo D. Coletta
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Silvia R. A. Reis
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
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21
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Is a polymorphism in 10q25 associated with non-syndromic cleft lip with or without cleft palate? A meta-analysis based on limited evidence. Br J Oral Maxillofac Surg 2015; 53:8-12. [DOI: 10.1016/j.bjoms.2014.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 08/26/2014] [Indexed: 11/23/2022]
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22
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A rare interstitial duplication of 8q22.1-8q24.3 associated with syndromic bilateral cleft lip/palate. Case Rep Dent 2014; 2014:730375. [PMID: 25506438 PMCID: PMC4260438 DOI: 10.1155/2014/730375] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022] Open
Abstract
We present a rare case of 8q interstitial duplication derived from maternal balanced translocations in a patient with bilateral cleft lip and palate in syndromic form associated with other congenital malformations. G-banding cytogenetic analysis revealed a chromosomal abnormality in the form of the karyotype 46,XX der(22)t(8;22)(q22.1;p11.1)mat. Chromosome microarray analysis evidenced a 49 Mb duplicated segment of chromosome 8q with no pathogenic imbalances on chromosome 22. Two siblings also carry the balanced translocation. We have compared this case with other “pure” trisomies of 8q patients reported in the literature and with genome wide association studies recently published. This work highlights the involvement of chromosome 8q in orofacial clefts.
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Watkins SE, Meyer RE, Strauss RP, Aylsworth AS. Classification, epidemiology, and genetics of orofacial clefts. Clin Plast Surg 2014; 41:149-63. [PMID: 24607185 DOI: 10.1016/j.cps.2013.12.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Orofacial clefts (OFCs) include a broad range of facial conditions that differ in cause and disease burden. In the published literature, there is substantial ambiguity in both terminology and classification of OFCs. This article discusses the terminology and classification of OFCs and the epidemiology of OFCs. Demographic, environmental, and genetic risk factors for OFCs are described, including suggestions for family counseling. This article enables clinicians to counsel families regarding the occurrence and recurrence of OFCs. Although much of the information is detailed, it is intended to be accessible to all health professionals for use in their clinical practices.
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Affiliation(s)
- Stephanie E Watkins
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, 1700 Martin Luther King Jr Boulevard, Chapel Hill, NC, USA.
| | - Robert E Meyer
- Birth Defects Monitoring Program, Division of Public Health, North Carolina Department of Health and Human Services, State Center for Health Statistics, 222 North Dawson Street, Cotton Building, Raleigh, NC 27603, USA
| | - Ronald P Strauss
- UNC Center for AIDS Research, UNC School of Dentistry, UNC School of Medicine, University of North Carolina at Chapel Hill, 104 South Building, CB# 3000, Chapel Hill, NC 27599-3000, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, CB# 7487, UNC Campus, Chapel Hill, NC 27599-7487, USA
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Butali A, Mossey P, Adeyemo WL, Eshete M, Gaines LAL, Braimah RO, Aregbesola BS, Rigdon J, Emeka C, Olutayo J, Ogunlewe O, Ladeinde A, Abate F, Hailu T, Mohammed I, Gravem P, Deribew M, Gesses M, Adeyemo A, Marazita M, Murray J. Rare functional variants in genome-wide association identified candidate genes for nonsyndromic clefts in the African population. Am J Med Genet A 2014; 164A:2567-71. [PMID: 25081408 PMCID: PMC4169286 DOI: 10.1002/ajmg.a.36691] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/23/2014] [Indexed: 01/27/2023]
Abstract
Nonsyndromic clefts of the lip and palate (NSCLP) are complex genetic traits. Together, they are classified as one of the most common birth defects with a prevalence of 1/700 live births. Genome-wide association studies (GWAS) for nonsyndromic cleft lip with or without cleft palate (NSCL[P]) revealed significant association for common single nucleotide polymorphisms near genes involved in craniofacial development i.e., MAFB, PAX7, VAX1, ARHGAP29 (ABCA4 locus), and IRF6. Sequencing of protein coding regions of the NSCL(P) GWAS candidate genes or adjacent genes suggest a role for rare functional variants. Replication studies in the African population did not observe any significant association with the GWAS candidate genes. On the other hand, the role of rare functional variants in GWAS candidate genes has not been evaluated in the African population. We obtained saliva samples from case triads in Nigeria and Ethiopia for Sanger sequencing of the GWAS candidate genes (MAFB, PAX7, VAX1, ARHGAP29, and IRF6) in order to identify rare functional variants. A total of 220 African samples (140 Nigerians and 80 Ethiopians) were sequenced and we found the following new rare variants- p.His165Asn in the MAFB gene, p.Asp428Asn in the PAX7, a splice-site variant that creates a new donor splice-site in PAX7. We also found three previously reported missense variants p.Gly466Ser in PAX7; p.Leu913Ser and Arg955His in ARHGAP29. No de novo mutations were found. Future genome-wide association and sequencing studies should be conducted using samples from Africa in order to identify new molecular genetic factors that contribute to the etiology of NSCLP.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA. U.S.A
| | | | | | | | | | | | | | - Jennifer Rigdon
- Department of Pediatrics, University of Iowa, Iowa City, IA, U.S.A
| | | | | | | | | | - Fikre Abate
- Addis Ababa University, Addis Ababa, Ethiopia
| | - Taye Hailu
- Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Paul Gravem
- Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Mary Marazita
- University of Pittsburgh, Pittsburgh Pennsylvania, U.S.A
| | - Jeffrey Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, U.S.A
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de Aquino SN, Messetti AC, Hoshi R, Borges A, Viena CS, Reis SRA, Oliveira Swerts MS, Graner E, Martelli-Júnior H, Coletta RD. Analysis of susceptibility polymorphisms for nonsyndromic cleft lip with or without cleft palate in the Brazilian population. ACTA ACUST UNITED AC 2014; 100:36-42. [PMID: 24446087 DOI: 10.1002/bdra.23204] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 09/16/2013] [Accepted: 10/04/2013] [Indexed: 11/06/2022]
Abstract
BACKGROUND Although genome-wide association studies have identified several susceptibility loci for nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations around the world, the role of most loci is unknown in the highly heterogeneous Brazilian population. METHODS To determine the association of 7 markers that showed genome-wide significant association in Brazilians with NSCL/P, we conducted a structured association study conditioned upon the individual ancestry proportions to evaluate markers at 1p36 (rs742071), 2p21 (rs7590268), 3p11.1 (rs7632427), 8q21.3 (rs12543318), 13q31.1 (rs8001641), 15q22.2 (rs1873147), and 17q22 (rs227731) in 505 patients with NSCL/P and 594 healthy controls recruited from 2 different geographical regions of Brazil. The polymorphisms were genotyped by TaqMan 5'-exonuclease allelic discrimination assay, and each sample was independently typed for 40 biallelic short insertion/deletion markers to characterize the genomic ancestry. RESULTS After Bonferroni correction for multiple tests, significant associations with NSCL/P were observed for rs742071, rs1873147, and rs227731. However, the frequency of the risk alleles varied between the geographical regions, according to the proportions of European and African genomic ancestry. The group enriched by European ancestry showed significant association with rs227731 (p = 0.001), whereas the group with high African ancestry was significantly associated with rs1873147 polymorphism (p = 0.005). The significant association with rs742071 was only detected in the combined sample (p = 0.005). CONCLUSION The findings of the present study revealed the associations of 1p36 (rs742071), 15q22 (rs1873147), and 17p22 (rs227731) with NSCL/P in the Brazilian population, and further confirmed that the genetic heterogeneity of NSCL/P may be related to the different ethnic background of the affected individuals.
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Affiliation(s)
- Sibele Nascimento de Aquino
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
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Letra A, Maili L, Mulliken JB, Buchanan E, Blanton SH, Hecht JT. Further evidence suggesting a role for variation in ARHGAP29 variants in nonsyndromic cleft lip/palate. ACTA ACUST UNITED AC 2014; 100:679-85. [PMID: 25163644 DOI: 10.1002/bdra.23286] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 06/25/2014] [Indexed: 01/05/2023]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect of complex etiology. Several genes have been implicated in the etiology of NSCL/P, although only a few have been replicated across datasets. METHODS ARHGAP29 was suggested as a candidate gene for NSCL/P as it is located in close proximity to ABCA4 (1p22), a gene previously identified in a genome-wide association study of NSCL/P. RESULTS Rare, potentially damaging, coding variants in ARHGAP29 were found in NSCL/P cases, and its expression was detected during murine craniofacial development. In this study, we investigated whether variations in ARHGAP29 were associated with NSCL/P in our family based dataset. Five single-nucleotide polymorphisms (SNPs) flanking and within ARHGAP29 were genotyped in our NSCL/P datasets consisting of simplex and multiplex families of non-Hispanic white (NHW, primarily European) and Hispanic ethnicities. Results showed strong association of three ARHGAP29 SNPs with NSCL/P in the NHW families. Two intronic SNPs (rs1541098 and rs3789688) showed strong association with NSCL/P in all NHW families (p = 0.0005 and p = 0.0002, respectively), and simplex NHW families (p = 0.003 for both SNPs). A SNP in the 3' untranslated region (rs1576593) also showed strong association with NSCL/P in all NHW families (p = 0.002), and the multiplex subset (p = 0.002). ARHGAP29 SNP haplotypes were also associated with NSCL/P. Evidence of gene-gene interaction was found between ARHGAP29 and additional cleft susceptibility genes. CONCLUSION This study further supports ARHGAP29 as a candidate gene for human NSCL/P in families of Caucasian descent.
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Affiliation(s)
- Ariadne Letra
- Department of Endodontics, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas; Craniofacial Research Center, University of Texas Health Science Center at Houston School of Dentistry, Houston, Texas
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27
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Genetics of cleft lip and/or cleft palate: Association with other common anomalies. Eur J Med Genet 2014; 57:381-93. [DOI: 10.1016/j.ejmg.2014.04.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/03/2014] [Indexed: 12/16/2022]
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Aldhorae KA, Böhmer AC, Ludwig KU, Esmail AHA, Al-Hebshi NN, Lippke B, Gölz L, Nöthen MM, Daratsianos N, Knapp M, Jäger A, Mangold E. Nonsyndromic cleft lip with or without cleft palate in arab populations: Genetic analysis of 15 risk loci in a novel case-control sample recruited in Yemen. ACTA ACUST UNITED AC 2014; 100:307-13. [DOI: 10.1002/bdra.23221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/17/2013] [Accepted: 01/13/2014] [Indexed: 12/16/2022]
Affiliation(s)
| | - Anne C. Böhmer
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics Life and Brain Center; University of Bonn; Bonn Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics Life and Brain Center; University of Bonn; Bonn Germany
| | | | - Nezar Noor Al-Hebshi
- Molecular Research Laboratory Faculty of Medical Sciences; University of Science and Technology; Sana'a Yemen
| | - Bärbel Lippke
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics Life and Brain Center; University of Bonn; Bonn Germany
| | - Lina Gölz
- Department of Orthodontics; University of Bonn; Bonn Germany
| | - Markus M. Nöthen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics Life and Brain Center; University of Bonn; Bonn Germany
| | | | - Michael Knapp
- Institute of Medical Biometry Informatics and Epidemiology; University of Bonn; Bonn Germany
| | - Andreas Jäger
- Department of Orthodontics; University of Bonn; Bonn Germany
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Ludwig KU, Böhmer AC, Rubini M, Mossey PA, Herms S, Nowak S, Reutter H, Alblas MA, Lippke B, Barth S, Paredes-Zenteno M, Muñoz-Jimenez SG, Ortiz-Lopez R, Kreusch T, Hemprich A, Martini M, Braumann B, Jäger A, Pötzsch B, Molloy A, Peterlin B, Hoffmann P, Nöthen MM, Rojas-Martinez A, Knapp M, Steegers-Theunissen RP, Mangold E. Strong association of variants around FOXE1 and orofacial clefting. J Dent Res 2014; 93:376-81. [PMID: 24563486 DOI: 10.1177/0022034514523987] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Nonsyndromic orofacial clefting (nsOFC) is a common, complex congenital disorder. The most frequent forms are nonsyndromic cleft lip with or without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO). Although they are generally considered distinct entities, a recent study has implicated a region around the FOXE1 gene in both nsCL/P and nsCPO. To investigate this hypothesis, we analyzed the 2 most strongly associated markers (rs3758249 and rs4460498) in 2 independent samples of differing ethnicities: Central European (949 nsCL/P cases, 155 nsCPO cases, 1163 controls) and Mayan Mesoamerican (156 nsCL/P cases, 10 nsCPO cases, 338 controls). While highly significant associations for both single-nucleotide polymorphisms were obtained in nsCL/P (rs4460498: p Europe = 6.50 × 10(-06), p Mayan = .0151; rs3758249: p Europe = 2.41 × 10(-05), p Mayan = .0299), no association was found in nsCPO (p > .05). Genotyping of rs4460498 in 472 independent European trios revealed significant associations for nsCL/P (p = .016) and nsCPO (p = .043). A meta-analysis of all data revealed a genomewide significant result for nsCL/P (p = 1.31 × 10(-08)), which became more significant when nsCPO cases were added (p nsOFC = 1.56 × 10(-09)). These results strongly support the FOXE1 locus as a risk factor for nsOFC. With the data of the initial study, there is now considerable evidence that this locus is the first conclusive risk factor shared between nsCL/P and nsCPO.
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Affiliation(s)
- K U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
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30
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Ludwig KU, Wahle P, Reutter H, Paredes-Zenteno M, Muñoz-Jimenez SG, Ortiz-Lopez R, Böhmer AC, Tessmann P, Nowak S, Nöthen MM, Knapp M, Rojas-Martinez A, Mangold E. Evaluating eight newly identified susceptibility loci for nonsyndromic cleft lip with or without cleft palate in a Mesoamerican population. ACTA ACUST UNITED AC 2013; 100:43-7. [DOI: 10.1002/bdra.23209] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/30/2013] [Accepted: 10/31/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Kerstin U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - Philipp Wahle
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - Heiko Reutter
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Neonatology; Children's Hospital, University of Bonn; Bonn Germany
| | | | | | - Rocio Ortiz-Lopez
- Department of Biochemistry and Molecular Medicine; School of Medicine; Universidad Autonoma de Nuevo Leon; Monterrey Mexico
- Centro de Investigación y Desarrollo en Ciencias de la Salud; Universidad Autónoma de Nuevo León; Monterrey Mexico
| | - Anne C. Böhmer
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - Peter Tessmann
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - Stefanie Nowak
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Markus M. Nöthen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center, University of Bonn; Bonn Germany
| | - Michael Knapp
- Institute of Medical Biometry; Informatics and Epidemiology, University of Bonn; Bonn Germany
| | - Augusto Rojas-Martinez
- Department of Biochemistry and Molecular Medicine; School of Medicine; Universidad Autonoma de Nuevo Leon; Monterrey Mexico
- Centro de Investigación y Desarrollo en Ciencias de la Salud; Universidad Autónoma de Nuevo León; Monterrey Mexico
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Lu Y, Liu Q, Xu W, Li Z, Jiang M, Li X, Zhao N, Liu W, Sui Y, Ma C, Feng W, Han W, Li J. TGFA and IRF6 contribute to the risk of nonsyndromic cleft lip with or without cleft palate in northeast China. PLoS One 2013; 8:e70754. [PMID: 23940636 PMCID: PMC3735505 DOI: 10.1371/journal.pone.0070754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/23/2013] [Indexed: 11/19/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) are common birth defects with a complex etiology. Multiple interacting loci and possible environmental factors influence the risk of NSCL/P. 12 single nucleotide polymorphisms (SNPs) in 7 candidate genes were tested using an allele-specific primer extension for case-control and case-parent analyses in northeast China in 236 unrelated patients, 185 mothers and 154 fathers, including 128 complete trios, and 400 control individuals. TGFA and IRF6 genes showed a significant association with NSCL/P. In IRF6, statistical evidence of an association between rs2235371 (p = 0.003), rs2013162 (p<0.0001) and NSCL/P was observed in case-control analyses. Family based association tests (FBATs) showed over-transmission of the C allele at the rs2235371 polymorphism (p = 0.007). In TGFA, associations between rs3771494, rs3771523 (G3822A), rs11466285 (T3851C) and NSCL/P were observed in case-control and FBAT analyses. Associations between other genes (BCL3, TGFB3, MTHFR, PVRL1 and SUMO1) and NSCL/P were not detected.
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Affiliation(s)
- Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Qiang Liu
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Wei Xu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Zengjian Li
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Miao Jiang
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Xuefu Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Ning Zhao
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wei Liu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Yu Sui
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Chao Ma
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wenhua Feng
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Weitian Han
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
| | - Jianxin Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
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Butali A, Suzuki S, Cooper ME, Mansilla AM, Cuenco K, Leslie EJ, Suzuki Y, Niimi T, Yamamoto M, Ayanga G, Erkhembaatar T, Furukawa H, Fujiwawa K, Imura H, Petrin AL, Natsume N, Beaty TH, Marazita ML, Murray JC. Replication of genome wide association identified candidate genes confirm the role of common and rare variants in PAX7 and VAX1 in the etiology of nonsyndromic CL(P). Am J Med Genet A 2013; 161A:965-72. [PMID: 23463464 DOI: 10.1002/ajmg.a.35749] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 10/11/2012] [Indexed: 11/08/2022]
Abstract
Following recent genome wide association studies (GWAS), significant genetic associations have been identified for several genes with nonsyndromic cleft lip with or without cleft palate (CL(P)). To replicate two of these GWAS signals, we investigated the role of common and rare variants in the PAX7 and VAX1 genes. TaqMan genotyping was carried out for SNPs in VAX1 and PAX7 and transmission disequilibrium test (TDT) was performed to test for linkage and association in each population. Direct sequencing in and around the PAX7 and VAX1 genes in 1,326 individuals of European and Asian ancestry was done. The TDT analysis showed strong associations with markers in VAX1 (rs7078160, P = 2.7E-06 and rs475202, P = 0.0002) in a combined sample of Mongolian and Japanese CL(P) case-parent triads. Analyses using parent-of-origin effects showed significant excess transmission of the minor allele from both parents with the effect in the mothers (P = 6.5E-05, OR (transmission) = 1.91) more striking than in the fathers (P = 0.004, OR (transmission) = 1.67) for VAX1 marker rs7078160 in the combined Mongolian and Japanese samples when all cleft types were combined. The rs6659735 trinucleotide marker in PAX7 was significantly associated with all the US cleft groups combined (P = 0.007 in all clefts and P = 0.02 in CL(P)). Eight rare missense mutations found in PAX7 and two rare missense mutations in VAX1. Our study replicated previous GWAS findings for markers in VAX1 in the Asian population, and identified rare variants in PAX7 and VAX1 that may contribute to the etiology of CL(P). Determining the role of rare variants clearly warrants further investigation.
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Affiliation(s)
- Azeez Butali
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242-1181, USA
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Velázquez-Aragón JA, Alcántara-Ortigoza MA, Estandia-Ortega B, Reyna-Fabián ME, Cruz-Fuentes C, Villagómez S, González-del Angel A. Association of interactions among the IRF6 gene, the 8q24 region, and maternal folic acid intake with non-syndromic cleft lip/palate in Mexican Mestizos. Am J Med Genet A 2012; 158A:3207-10. [PMID: 23169698 DOI: 10.1002/ajmg.a.35641] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 08/05/2012] [Indexed: 11/09/2022]
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Wang M, Pan Y, Zhang Z, Wang L. Three polymorphisms inIRF6and 8q24 are associated with nonsyndromic cleft lip with or without cleft palate: Evidence from 20 studies. Am J Med Genet A 2012; 158A:3080-6. [DOI: 10.1002/ajmg.a.35634] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 07/25/2012] [Indexed: 11/09/2022]
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Cardoso ML, Bezerra JF, Oliveira GHM, Soares CD, Oliveira SR, de Souza KSC, da Silva HPV, Silbiger VN, Luchessi AD, Fajardo CM, Hirata RDC, Almeida MG, Hirata MH, Rezende AA. MSX1 gene polymorphisms in non-syndromic cleft lip and/or palate. Oral Dis 2012; 19:507-12. [PMID: 23130753 DOI: 10.1111/odi.12033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 09/13/2012] [Accepted: 09/28/2012] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The aim of this study was to investigate the contribution of 6 polymorphic variants of the MSX1 gene in non-syndromic cleft lip and/or palate (NSCL/P). METHODS Three hundred and fifty-eight individuals (158 NSCL/P cases and 200 controls) were genotyped by TaqMan allelic discrimination using predesigned SNP assays. Statistical analyses were conducted using the software spss 15.0 and the r statistical suite. Haplotype block structure and haplotype frequencies were determined using the Haploview. A P-value of 0.05 and confidence interval of 95% were used for all of statistical tests. RESULTS The patients with non-syndromic cleft lip and/or palate were characterized by similar distribution of MSX1 genotypes and allele in comparison to subjects without oral clefts (P > 0.05). Two haplotype blocks were constructed with polymorphisms of MSX1 gene and haplotypes formed showed a similar frequency in patients with and without oral clefts. CONCLUSIONS The present study provides no evidence that MSX1 polymorphisms (rs3775261, rs1042484, rs12532, rs6446693, rs4464513 and rs1907998) play a major role in NSCL/P.
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Affiliation(s)
- M L Cardoso
- Department of Clinical and Toxicological Analysis, School of Pharmaceutical Sciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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Genetics and management of the patient with orofacial cleft. PLASTIC SURGERY INTERNATIONAL 2012; 2012:782821. [PMID: 23213504 PMCID: PMC3503281 DOI: 10.1155/2012/782821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/01/2012] [Indexed: 01/24/2023]
Abstract
Cleft lip or palate (CL/P) is a common facial defect present in 1 : 700 live births and results in substantial burden to patients. There are more than 500 CL/P syndromes described, the causes of which may be single-gene mutations, chromosomopathies, and exposure to teratogens. Part of the most prevalent syndromic CL/P has known etiology. Nonsyndromic CL/P, on the other hand, is a complex disorder, whose etiology is still poorly understood. Recent genome-wide association studies have contributed to the elucidation of the genetic causes, by raising reproducible susceptibility genetic variants; their etiopathogenic roles, however, are difficult to predict, as in the case of the chromosomal region 8q24, the most corroborated locus predisposing to nonsyndromic CL/P. Knowing the genetic causes of CL/P will directly impact the genetic counseling, by estimating precise recurrence risks, and the patient management, since the patient, followup may be partially influenced by their genetic background. This paper focuses on the genetic causes of important syndromic CL/P forms (van der Woude syndrome, 22q11 deletion syndrome, and Robin sequence-associated syndromes) and depicts the recent findings in nonsyndromic CL/P research, addressing issues in the conduct of the geneticist.
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Hikida M, Tsuda M, Watanabe A, Kinoshita A, Akita S, Hirano A, Uchiyama T, Yoshiura KI. No Evidence of Association between 8q24 and Susceptibility to Nonsyndromic Cleft Lip with or without Palate in Japanese Population. Cleft Palate Craniofac J 2012; 49:714-7. [DOI: 10.1597/10-242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective Recent genome-wide association studies identified susceptibility loci for nonsyndromic cleft lip with or without cleft palate (NSCL±P) on 8q24.21, 10q25.3, 13q31.1, 15q13.3, 17q22, and 18q22 in populations of European origin. The purpose of this study was to determine, using DNA samples, whether 8q24.21 was a susceptibility locus for the development of NSCL±P in Japanese patients. Methods We used DNA from 167 Japanese NSCL±P patients (45 cleft lip without cleft palate and 122 cleft lip with cleft palate patients) and 190 Japanese unaffected control individuals. We performed an association study using 13 single nucleotide polymorphisms (SNPs) selected on the 8q24.21 locus. Genotyping of each SNP was carried out by direct sequencing of genomic DNA. Additionally, a haplotype block was constructed using the selected SNPs. Results The 13 selected SNPs were successfully genotyped in 357 individuals. The p values obtained were not low enough to indicate a significant association between the haplotypes and the development of NSCL±P in this population. Conclusions Our results suggest that the 8q24.21 locus is not associated with susceptibility to NSCL±P in Japanese patients and provide further evidence that ethnicity is a strong factor in determining susceptibility loci, albeit using a limited number of samples. Further studies are needed to identify regions involved in the development of NSCL±P in the Japanese population.
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Affiliation(s)
- Masanori Hikida
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Chiba, Japan
| | - Masayoshi Tsuda
- Department of Plastic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Watanabe
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Chiba, Japan
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Sadanori Akita
- Department of Plastic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akiyoshi Hirano
- Department of Plastic Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Uchiyama
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Chiba, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Nasser E, Mangold E, Tradowsky DC, Fier H, Becker J, Boehmer AC, Herberz R, Fricker N, Barth S, Wahle P, Nowak S, Reutter H, Reich RH, Lauster C, Braumann B, Kreusch T, Hemprich A, Pötzsch B, Hoffmann P, Kramer FJ, Knapp M, Lange C, Nöthen MM, Ludwig KU. Resequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate. ACTA ACUST UNITED AC 2012; 94:925-33. [PMID: 23081944 DOI: 10.1002/bdra.23078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/16/2012] [Accepted: 08/02/2012] [Indexed: 11/11/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common of all congenital anomalies, and has a multifactorial etiology involving both environmental and genetic factors. Recent genome-wide association studies (GWAS) identified strong association between a locus on chromosome 10q25.3 and NSCL/P in European samples. One gene at 10q25.3, the ventral anterior homeobox 1 (VAX1) gene, is considered a strong candidate gene for craniofacial malformations. The purpose of the present study was to provide further evidence that VAX1 is the causal gene at the 10q25.3 locus through identification of an excess of rare mutations in patients with NSCL/P. METHODS The 5'UTR, complete coding regions, and adjacent splice sites of the two known VAX1 isoforms were sequenced in 384 patients with NSCL/P and 384 controls of Central European descent. Observed variants were investigated with respect to familial cosegregation or de novo occurrence, and in silico analyses were performed to identify putative effects on the transcript or protein level. RESULTS Eighteen single-base variants were found, 15 of them rare and previously unreported. In the long VAX1 isoform, predicted functionally relevant variants were observed more often in NSCL/P cases, although this difference was not significant (p = 0.17). Analysis of family members demonstrated incomplete cosegregation in most pedigrees. CONCLUSION Our data do not support the hypothesis that highly penetrant rare variants in VAX1 are a cause of NSCL/P. To determine whether VAX1 is the causative gene at 10q25.3 further research, in particular into the biologic function of its long isoform, is warranted. Birth Defects Research (Part A), 2012.
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Affiliation(s)
- Entessar Nasser
- Institute of Human Genetics, University of Bonn, Bonn, Germany; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
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Abstract
Orofacial clefts (OFCs)--primarily cleft lip and cleft palate--are among the most common birth defects in all populations worldwide, and have notable population, ethnicity, and gender differences in birth prevalence. Interest in these birth defects goes back centuries, as does formal scientific interest; scientists often used OFCs as examples or evidence during paradigm shifts in human genetics, and have also used virtually every new method of human genetic analysis to deepen our understanding of OFC. This review traces the evolution of human genetic investigations of OFC, highlights the specific insights gained about OFC through the years, and culminates in a review of recent key OFC genetic findings resulting from the powerful tools of the genomics era. Notably, OFC represents a major success for genome-wide approaches, and the field is poised for further breakthroughs in the near future.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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40
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Murray T, Taub MA, Ruczinski I, Scott AF, Hetmanski JB, Schwender H, Patel P, Zhang TX, Munger RG, Wilcox AJ, Ye X, Wang H, Wu T, Wu-Chou YH, Shi B, Jee SH, Chong S, Yeow V, Murray JC, Marazita ML, Beaty TH. Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and Europeans. Genet Epidemiol 2012; 36:392-9. [PMID: 22508319 PMCID: PMC3615645 DOI: 10.1002/gepi.21633] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 12/31/2022]
Abstract
In a recent genome-wide association study (GWAS) from an international consortium, evidence of linkage and association in chr8q24 was much stronger among nonsyndromic cleft lip/palate (CL/P) case-parent trios of European ancestry than among trios of Asian ancestry. We examined marker information content and haplotype diversity across 13 recruitment sites (from Europe, United States, and Asia) separately, and conducted principal components analysis (PCA) on parents. As expected, PCA revealed large genetic distances between Europeans and Asians, and a north-south cline from Korea to Singapore in Asia, with Filipino parents forming a somewhat distinct Southeast Asian cluster. Hierarchical clustering of SNP heterozygosity revealed two major clades consistent with PCA results. All genotyped SNPs giving P < 10(-6) in the allelic transmission disequilibrium test (TDT) showed higher heterozygosity in Europeans than Asians. On average, European ancestry parents had higher haplotype diversity than Asians. Imputing additional variants across chr8q24 increased the strength of statistical evidence among Europeans and also revealed a significant signal among Asians (although it did not reach genome-wide significance). Tests for SNP-population interaction were negative, indicating the lack of strong signal for 8q24 in families of Asian ancestry was not due to any distinct genetic effect, but could simply reflect low power due to lower allele frequencies in Asians.
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Affiliation(s)
- Tanda Murray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
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Xu MY, Deng XL, Tata LJ, Han H, Chen XH, Liu TY, Chen QS, Yao XW, Tang SJ. Case-control and family-based association studies of novel susceptibility locus 8q24 in nonsyndromic cleft lip with or without cleft palate in a Southern Han Chinese population located in Guangdong Province. DNA Cell Biol 2012; 31:700-5. [PMID: 22044123 DOI: 10.1089/dna.2011.1383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common congenital malformations and a susceptibility locus on chromosome 8q24 has been replicated as a genetic risk factor for NSCL/P in patients of European and Asian descent. However, given considerable variations in allele frequencies across geographical regions studied, the aim of this study was to investigate the association of rs987525 located at 8q24 with NSCL/P only among the southern Han Chinese population from Guangdong province. We recruited 216 NSCL/P cases, their parents, and 200 controls to conduct case-control analysis and family-based association studies. Genotyping of rs987525 was carried out by the matrix assisted laser desorption ionization-time of flight mass spectrometry method. Case-control analysis showed allele and genotype distributions for rs987525 were not significantly associated with the risk of NSCL/P in our study population. Similar results were found when all cases were stratified into cleft lip only and cleft lip with cleft palate. A transmission disequilibrium test showed no statistically significant transmission of A nor C alleles and family-based association test (FBAT) analysis provided no evidence of NSCL/P risk with single markers. These results do not provide evidence for an association between rs987525 at 8q24 and the risk of NSCL/P in the southern Han Chinese population from Guangdong province.
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Affiliation(s)
- Ming Yan Xu
- Cleft Lip and Palate Treatment Centre, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
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Mangold E, Ludwig KU, Nöthen MM. Breakthroughs in the genetics of orofacial clefting. Trends Mol Med 2011; 17:725-33. [PMID: 21885341 DOI: 10.1016/j.molmed.2011.07.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 01/03/2023]
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43
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Mostowska A, Hozyasz KK, Wojcicka K, Biedziak B, Jagodzinski PP. Polymorphic variants at 10q25.3 and 17q22 loci and the risk of non-syndromic cleft lip and palate in the polish population. ACTA ACUST UNITED AC 2011; 94:42-6. [DOI: 10.1002/bdra.22862] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 08/23/2011] [Indexed: 11/12/2022]
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Pan Y, Zhang W, Du Y, Tong N, Han Y, Zhang H, Wang M, Ma J, Wan L, Wang L. Different roles of two novel susceptibility loci for nonsyndromic orofacial clefts in a Chinese Han population. Am J Med Genet A 2011; 155A:2180-5. [DOI: 10.1002/ajmg.a.34170] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Accepted: 05/22/2011] [Indexed: 11/09/2022]
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Shen X, Liu RM, Yang L, Wu H, Li PQ, Liang YL, Xie XD, Yao T, Zhang TT, Yu M. The CRISPLD2 gene is involved in cleft lip and/or cleft palate in a Chinese population. ACTA ACUST UNITED AC 2011; 91:918-24. [PMID: 21800413 DOI: 10.1002/bdra.20840] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 04/18/2011] [Accepted: 04/28/2011] [Indexed: 11/06/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip and/or cleft palate (NSCLP) are common congenital anomalies in humans, the etiologies of which are complex and associated with both genetic and environmental factors. Previous data suggested single nucleotide polymorphisms (SNPs) of rs1546124, rs4783099, and rs16974880 of the CRISPLD2 gene were associated with an increased risk of NSCLP; however, subsequent studies have yielded conflicting results. This study aims to evaluate the associations of the aforementioned polymorphisms with NSCLP in a Northwestern Chinese population. METHODS Three CRISPLD2 SNPs were genotyped in a case-control study (n = 907), including 444 NSCLP patients and 463 healthy individuals, using polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC). RESULTS The genotype and allele frequencies of rs1546124 (odds ratio [OR], 2.30; 95% confidence interval [CI], 1.58-3.34; p = 1 × 10(-5) ) and rs4783099 (OR, 0.73; 95% CI, 0.54-1.00; p = 0.05) were different in NSCLP patients compared with controls. Furthermore, the CC genotype at rs1546124 was associated with increased risk for cleft lip with or without cleft palate (CL/P; OR, 2.11; 95% CI, 1.41-3.15; p(correct) = 1.5 × 10(-4) ) and for cleft palate only (CPO; OR, 2.93; 95% CI, 1.69-5.07; p(correct) = 5.4 × 10(-4) ), whereas the T allele of rs4783099 was associated with decreased risk for CPO. Further gender stratification showed that the statistical association of these two loci is mainly in the male patients, and not in female patients. CONCLUSION Our results suggest that the CRISPLD2 gene contributes to the etiology of NSCLP in the Northwestern Chinese population. SNP rs1546124 is significantly related to NSCLP, associated with both CL/P and CPO groups, and SNP rs4783099 is significantly associated with CPO.
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Affiliation(s)
- Xi Shen
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, China
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Hozyasz KK. The search for risk factors that contribute to the etiology of non-syndromic cleft lip with or without cleft palate (CL/P) in the Polish population. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s0031-3939(10)70562-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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