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Genome Analysis Using Whole-Exome Sequencing of Non-Syndromic Cleft Lip and/or Palate from Malagasy Trios Identifies Variants Associated with Cilium-Related Pathways and Asian Genetic Ancestry. Genes (Basel) 2023; 14:genes14030665. [PMID: 36980938 PMCID: PMC10048728 DOI: 10.3390/genes14030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023] Open
Abstract
Background: Orofacial clefts (OFCs) are common congenital disabilities that can occur as isolated non-syndromic events or as part of Mendelian syndromes. OFC risk factors vary due to differences in regional environmental exposures, genetic variants, and ethnicities. In recent years, significant progress has been made in understanding OFCs, due to advances in sequencing and genotyping technologies. Despite these advances, very little is known about the genetic interplay in the Malagasy population. Methods: Here, we performed high-resolution whole-exome sequencing (WES) on non-syndromic cleft lip with or without palate (nCL/P) trios in the Malagasy population (78 individuals from 26 families (trios)). To integrate the impact of genetic ancestry admixture, we computed both global and local ancestries. Results: Participants demonstrated a high percentage of both African and Asian admixture. We identified damaging variants in primary cilium-mediated pathway genes WNT5B (one family), GPC4 (one family), co-occurrence in MSX1 (five families), WDR11 (one family), and tubulin stabilizer SEPTIN9 (one family). Furthermore, we identified an autosomal homozygous damaging variant in PHGDH (one family) gene that may impact metabiotic activity. Lastly, all variants were predicted to reside on local Asian genetic ancestry admixed alleles. Conclusion: Our results from examining the Malagasy genome provide limited support for the hypothesis that germline variants in primary cilia may be risk factors for nCL/P, and outline the importance of integrating local ancestry components better to understand the multi-ethnic impact on nCL/P.
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Alade A, Awotoye W, Butali A. Genetic and Epigenetic Studies in Nonsyndromic Oral Clefts. Oral Dis 2022; 28:1339-1350. [PMID: 35122708 DOI: 10.1111/odi.14146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The etiology of non-syndromic oral clefts (NSOFC) is complex with genetics, genomics, epigenetics and stochastics factors playing a role. Several approaches have been applied to understand the etiology of non-syndromic oral clefts. These include linkage, candidate gene association studies, genome-wide association studies, whole genome sequencing, copy number variations and epigenetics. In this review we shared these approaches, genes and loci reported in some studies.
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Affiliation(s)
- Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA.,Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.,Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
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Association of ABCA4 Gene Polymorphisms with Cleft Lip with or without Cleft Palate in the Polish Population. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111483. [PMID: 34769998 PMCID: PMC8583664 DOI: 10.3390/ijerph182111483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 12/01/2022]
Abstract
Background: Non-syndromic cleft lip with/without cleft palate (NSCL/P) is a common congenital condition with a complex aetiology reflecting multiple genetic and environmental factors. Single nucleotide polymorphisms (SNPs) in ABCA4 have been associated with NSCL/P in several studies, although there are some inconsistent results. This study aimed to evaluate whether two SNPs in ABCA4, namely rs4147811 and rs560426, are associated with NSCL/P occurrence in the Polish population. Methods: The study included 627 participants: 209 paediatric patients with NSCL/P and 418 healthy newborn controls. DNA was isolated from the saliva of NSCL/P patients and from umbilical cord blood in the controls. Genotyping of rs4147811 and rs560426 was performed using quantitative PCR. Results: The rs4147811 (AG genotype) SNP in ABCA4 was associated with a decreased risk of NSCL/P (odds ratio (OR) 0.57; 95% confidence interval (CI) 0.39–0.84; p = 0.004), whereas the rs560426 (GG genotype) SNP was associated with an increased risk of NSCL/P (OR 2.13; 95% CI 1.31–3.48; p = 0.002). Limitations: This study—based on the correlation between single genetic variants and the occurrence of different phenotypes—might have limited power in detecting relevant, complex inheritance patterns. ORs are often low to moderate when investigating the association of single genes with the risk of a complex trait. Another limitation was the small number of available NSCL/P samples. Conclusions: The results suggest that genetic variations in ABCA4 are important risk markers of NSCL/P in the Polish population. Further investigation in a larger study group is warranted.
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Onah I, Okeke A, Folaranmi N. ORTHODONTIC NEEDS OF PATIENTS WITH CLEFT LIP AND PALATE IN ENUGU, FIVE YEARS POST REPAIR. Ann Ib Postgrad Med 2020; 18:S35-S38. [PMID: 33071694 PMCID: PMC7513380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Orthodontists play an integral role in the management of cleft lip and palate anomaly. This study looks at the frequency of anomalies amenable to orthodontics in patients who have had surgery and the effect of early or late surgical intervention. METHODOLOGY Patients aged 0-5 years with cleft of the lip and/or palate who were operated on by the plastic surgeon at the Good Shepherd Specialist Hospital, Enugu between 1st July 2011 and 30th June 2014, were recalled after a minimum of five years post-surgery and examined to determine the absence or presence of dental anomalies, amenable to orthodontic treatment, which have arisen since surgical repair. Descriptive statistics and t-test were used for data analysis and significance was at 0.05. RESULTS Thirty-one children were operated upon in the period under review. Seventeen had timely (three months or less) lip repair. Seven had timely palate repair (18 months or less). Thirteen patients were successfully recalled, 12 had cleft lip repair while one had cleft palate repair. Repair was timely in 10 (83.3%) of the 12 that had lip repair with a mean frequency of four dental anomalies, while the two (16.7%) that had late repair had a mean frequency of five dental anomalies and this was not statistically significant (P value=0.711). The only isolated cleft palate patient successfully recalled had a late repair. All 13 patients had at least four dental anomalies amenable to orthodontics. Hypoplastic maxilla were the most commonly occurring (eight patients, 61.54%) dental anomaly amenable to orthodontic treatment. None of the patients had a clinically visible supernumerary tooth. Out of 13 patients reviewed, sis were males with a mean frequency of four dental anomalies while seven were females, also with a mean frequency of four dental anomalies. This was not significant (P-value=0.553). CONCLUSION There is need for the long term Orthodontic follow up of cleft lip and palate patients. The orthodontic management of dental anomaly should, therefore, be central in the planning and treatment of patients with cleft lip and palate.
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Affiliation(s)
- I.I. Onah
- Good Shepherd Specialists Hospital, Enugu, Nigeria
| | - A.C. Okeke
- Department of Child Dental Health, University of Nigeria, Enugu, Nigeria
| | - N. Folaranmi
- Department of Child Dental Health, University of Nigeria, Enugu, Nigeria
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Xiao WL, Jia KN, Yu G, Zhao N. Association between forkhead box E1 polymorphisms and risk of non-syndromic cleft lip with or without cleft palate: A meta-analysis. Orthod Craniofac Res 2020; 23:151-159. [PMID: 31944555 DOI: 10.1111/ocr.12366] [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: 09/26/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The purpose of the present work was to investigate the association between forkhead box E1 (FOXE1) and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). MATERIALS AND METHODS Relevant studies were searched in several professional databases up to 31 July 2019. The pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using a fixed-effect model or a random-effect model to analyse the relationship between FOXE1 polymorphisms and NSCL/P. RESULTS A total of four single nucleotide polymorphisms (SNPs), including rs3758249, rs4460498, rs1443434 and rs10217225, were analysed. The overall findings showed that FOXE1 rs4460498 was statistically associated with NSCL/P (including cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO)). Genotypes CC and CT of rs4460498 were significantly more closely correlated with NSCL/P (including CL/P and CPO) than genotype TT (NSCL/P: TT vs CC, OR = 0.630, P = .000; TT vs TC + CC, OR = 0.775, P = .020; CL/P: TT vs CC, OR = 0.664, P = .000; TT vs TC + CC, OR = 0.738, P = .006. CPO: TT vs CC, OR = 0.761, P = .027; TT vs TC + CC, OR = 0.792, P = .045). For rs10217225, only the TT genotype might have contributed to the elevated risk of CL/P (TT vs CC OR = 2.236, P = .000). The other FOXE1 polymorphisms were not associated with NSCLP, CL/P or CPO. CONCLUSION The meta-analysis provided confirmation that the polymorphism of FOXE1 rs10217225 was correlated with an increased risk of CL/P, and the polymorphism of FOXE1 rs4460498 was a protective factor for NSCL/P, including CLP and CPO.
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Affiliation(s)
- Wen-Lin Xiao
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Kai-Ning Jia
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guo Yu
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ning Zhao
- Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao, China
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The Role of Environmental Factors in the Etiology of Nonsyndromic Orofacial Clefts. J Craniofac Surg 2020; 31:113-116. [PMID: 31821209 DOI: 10.1097/scs.0000000000005924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts (NSOFCs) represent the most common congenital anomalies in the head and neck region. Multiple factors contribute to the occurrence of this anomaly. The etiology of NSOFCs in the Ethiopian population has not been investigated prior to this study. AIMS OF THE STUDY To assess the role of maternal environmental factors in the occurrence of NSOFCs in the Ethiopian Population. METHODS The authors used unmatched case control study design and evaluated the role of environmental factors to the occurrence of NSOFCs in the Ethiopian population. The participants were recruited from the same institution (Yekatit 12 Hospital Medical College). The authors studied 760 mothers (359 mothers of children born with NSOFCs and 401 mothers of children born without any congenital anomalies). Univariate and multivariate logistic regression analyses were used to calculate relative risk by odds ratio and 95% confidence interval. RESULTS Mothers who gave history of bronchial asthma and mothers who were admitted for threatened abortion had a higher risk of delivering a child with NSOFCS P value=0.013; AOR=0.194, 95% CI [0.053-0.712], P value <0.001; AOR= 0.179, 95% CI [0.091-0.352] respectively. Higher number of children with NSOFCs were born to mothers who were exposed to diagnostic X-ray investigation during early pregnancy than those who were not exposed P value 0.048; AOR=0.375, 95% CI [0.142-0.990]. CONCLUSION Maternal exposure to diagnostic x-ray, maternal chronic illness like bronchial asthma and threatened abortion were found to be associated with the occurrence of NSOFCS in the studied population.
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Huang L, Liang X, Ou Y, Tang S, He Y. Association between 20q12 rs13041247 polymorphism and risk of nonsyndromic cleft lip with or without cleft palate: a meta-analysis. BMC Oral Health 2020; 20:39. [PMID: 32019513 PMCID: PMC7001214 DOI: 10.1186/s12903-020-1003-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/10/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Previous genome-wide association studies have identified a link between the rs13041247 single nucleotide polymorphisms (SNPs) in the chromosome 20q12 locus and the development of the congenital malformation known as nonsyndromic cleft lip with or without cleft palate (NSCL/P). The present meta-analysis was therefore designed to formally assess the relationship between rs13041247 and NSCL/P. METHODS We searched Embase, Web of Science, PubMed, the China National Knowledge Internet (CNKI), and the China Wanfang database in order to identify relevant published through 25 June 2019. This allowed us to identify 13 studies incorporating 4914 patients and 5981 controls for whom rs13041247 genotyping had been conducted, with STATA 12.0 then being used to conduct a meta-analysis of these pooled results. The I2 statistic was used to compare heterogeneity among studies. RESULTS In total this analysis incorporated 13 case-control studies. No association between the rs13041247 polymorphism and NSCL/P risk was detected in individuals of Asian ethnicity (C vs T: OR = 0.847, 95% CI = 0.702-1.021; CC vs TT: OR = 0.725, 95% CI = 0.494-1.063; CC vs CT: OR = 0.837, 95% CI = 0.657-1.067; CT + TT vs CC: OR = 1.265, 95% CI = 0.951-1.684; CC + CT vs TT: OR = 0.805, 95% CI = 0.630-1.029) or Caucasian ethnicity (C vs T: OR = 0.936, 95% CI = 0.786-1.114; CC vs TT: OR = 0.988, 95% CI = 0.674-1.446; CC vs CT: OR = 1.197, 95% CI = 0.816-1.757; CT + TT vs CC: OR = 0.918, 95% CI = 0.639-1.318; CC + CT vs TT: OR = 0.855, 95% CI = 0.677-1.081). However, an overall analysis of all participants in these studies revealed the rs13041247 C allele, the CT genotype, and the CC + CT model to be linked to a reduced NSCL/P risk (C vs T: OR = 0.897, 95% CI: 0.723-1.114, P = 0.048; CT vs TT: OR = 0.839, 95% CI: 0.734-0.959, P = 0.01; CC + CT vs TT: OR = 0.824, 95% CI: 0.701-0.968, P = 0.019). CONCLUSION These results suggest that the rs13041247 SNP located at the 20q12 chromosomal locus is associated with NSCL/P risk in an overall pooled study population, although this association was not significant in East Asian or Caucasian populations.
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Affiliation(s)
- Liheng Huang
- Department of Anesthesiology, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-sen University, Shantou, Guangdong, China
| | - Xinglong Liang
- Department of Dermatology, Maoming People's Hospital, Maoming, Guangdong, China
| | - Yangzhan Ou
- Department of Plastic Surgery and Burn Center, the Second Affiliated Hospital, Shantou University Medical College, No.69 North Dong Xia Road, Shantou, 515041, Guangdong, China
| | - Shijie Tang
- Department of Plastic Surgery and Burn Center, the Second Affiliated Hospital, Shantou University Medical College, No.69 North Dong Xia Road, Shantou, 515041, Guangdong, China.
| | - Yunpu He
- Department of Plastic Surgery and Burn Center, the Second Affiliated Hospital, Shantou University Medical College, No.69 North Dong Xia Road, Shantou, 515041, Guangdong, China.
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Polymorphic Variants of V-Maf Musculoaponeurotic Fibrosarcoma Oncogene Homolog B (rs13041247 and rs11696257) and Risk of Non-Syndromic Cleft Lip/Palate: Systematic Review and Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16152792. [PMID: 31387249 PMCID: PMC6695977 DOI: 10.3390/ijerph16152792] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 02/06/2023]
Abstract
Background: Non-syndromic cleft lip/palate (NSCL/P) has an etiology, including both genetic and environmental factors. Herein, we evaluated the association of rs13041247 and rs11696257 v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) polymorphisms with the risk of NSCL/P in a meta-analysis. Methods: The PubMed/Medline, Scopus, Cochrane Library, Web of Science, and HuGE Navigator databases were systematically searched to retrieve relevant articles published up to January 2019. The Newcastle–Ottawa scale was applied for quality evaluation of retrieved articles. The 95% confidence interval (CI) and crude odds ratio (OR) were calculated for each study using the Review Manager 5.3 software to show the association between MAFB polymorphisms and risk of NSCL/P. The comprehensive meta-analysis 2.0 software was used to calculate the publication bias. In addition, sensitivity analysis was carried out to show the stability of results. Results: Of 102 articles retrieved from the databases, 10 articles were analyzed in this meta-analysis. Ten articles, including eleven studies reporting rs13041247 MAFB polymorphism, included 3082 NSCL/P patients and 4104 controls. Three studies that reported rs11696257 MAFB polymorphism involved 845 NSCL/P patients and 927 controls. The rs11696257 MAFB polymorphism was not associated with the risk of NSCL/P, but the CC and TC genotypes of rs13041247 polymorphism were associated with the risk of NSCL/P. Nevertheless, the C allele and CC and TC genotypes were associated with a significant decline in the risk of NSCL/P in population-based studies. Conclusions: The results of this meta-analysis demonstrated that the risk of NSCL/P was related to rs13041247 polymorphism, not rs11696257 MAFB polymorphism. Well-designed studies are required to assess the interaction of MAFB and other genes with environmental factors in different ethnic groups.
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Fournier BP, Bruneau MH, Toupenay S, Kerner S, Berdal A, Cormier-Daire V, Hadj-Rabia S, Coudert AE, de La Dure-Molla M. Patterns of Dental Agenesis Highlight the Nature of the Causative Mutated Genes. J Dent Res 2018; 97:1306-1316. [PMID: 29879364 DOI: 10.1177/0022034518777460] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The most common outcome of defective dental morphogenesis in human patients is dental agenesis (absence of teeth). This may affect either the primary or permanent dentition and can range from 5 or fewer missing teeth (hypodontia), 6 or more (oligodontia), to complete absence of teeth (anodontia). Both isolated and syndromic dental agenesis have been reported to be associated with a large number of mutated genes. The aim of this review was to analyze the dental phenotypes of syndromic and nonsyndromic dental agenesis linked to gene mutations. A systematic review of the literature focusing on genes ( MSX1, PAX9, AXIN2, PITX2, WNT10A, NEMO, EDA, EDAR, EDARADD, GREMLIN2, LTBP3, LRP6, and SMOC2) known to be involved in dental agenesis was performed and included 101 articles. A meta-analysis was performed using the dental phenotypes of 522 patients. The total number and type of missing teeth were analyzed for each mutated gene. The percentages of missing teeth for each gene were compared to determine correlations between genotypes and phenotypes. Third molar agenesis was included in the clinical phenotype assessment. The findings show that isolated dental agenesis exists as part of a spectrum of syndromes for all the identified genes except PAX9 and that the pattern of dental agenesis can be useful in clinical diagnosis to identify (or narrow) the causative gene mutations. While third molar agenesis was the most frequent type of dental agenesis, affecting 70% of patients, it was described in only 30% of patients with EDA gene mutations. This study shows that the pattern of dental agenesis gives information about the mutated gene and could guide molecular diagnosis for geneticists.
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Affiliation(s)
- B P Fournier
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,2 Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Hôpital Rothschild, AP-HP, Paris, France.,3 Centre de Recherche des Cordeliers, INSERM UMRS 1138, Laboratoire de Physiopathologie Orale Moléculaire, Université Pierre et Marie Curie-Paris, Université Paris-Descartes, Paris, France
| | - M H Bruneau
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France
| | - S Toupenay
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,2 Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Hôpital Rothschild, AP-HP, Paris, France
| | - S Kerner
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,2 Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Hôpital Rothschild, AP-HP, Paris, France.,4 Département de Parodontologie; Hôpital Rothschild, AP-HP, Paris, France
| | - A Berdal
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,2 Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Hôpital Rothschild, AP-HP, Paris, France.,3 Centre de Recherche des Cordeliers, INSERM UMRS 1138, Laboratoire de Physiopathologie Orale Moléculaire, Université Pierre et Marie Curie-Paris, Université Paris-Descartes, Paris, France
| | - V Cormier-Daire
- 5 INSERM UMR1163, Institut IMAGINE, Hôpital Necker-Enfants Malades, Paris, France.,6 Département de Génétique, Centre de Référence pour les Dysplasies Osseuses.,7 Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - S Hadj-Rabia
- 7 Université Paris Descartes-Sorbonne Paris Cité, Paris, France.,8 Département de Dermatologie; Centre national de référence des Maladies Génétiques à Expression Cutanée (MAGEC), Hôpital Universitaire Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - A E Coudert
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,3 Centre de Recherche des Cordeliers, INSERM UMRS 1138, Laboratoire de Physiopathologie Orale Moléculaire, Université Pierre et Marie Curie-Paris, Université Paris-Descartes, Paris, France
| | - M de La Dure-Molla
- 1 Université Paris-Diderot, UFR d'Odontologie, Paris, France.,2 Centre de Référence des Maladies Rares Orales et Dentaires, O-Rares, Hôpital Rothschild, AP-HP, Paris, France.,4 Département de Parodontologie; Hôpital Rothschild, AP-HP, Paris, France
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Kumari P, Singh SK, Raman R. TGFβ3, MSX1, and MMP3 as Candidates for NSCL±P in an Indian Population. Cleft Palate Craniofac J 2018; 56:363-372. [PMID: 29738289 DOI: 10.1177/1055665618775727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To evaluate the association of transforming growth factor β3 ( TGFβ3), muscle segment homeobox 1 ( MSX1), Metalloproteinases 3 ( MMP3), and MMP9 genes as candidates for nonsyndromic cleft lip and/or palate in an Indian population. DESIGN Case-control association study, mutational screening, and functional evaluation of obtained mutations. SETTING Mutational screening of the developmental genes, TGFβ3 and MSX1, along with functional evaluation and association of promoter region SNPs-one each in MMP3 and MMP9. PATIENTS, PARTICIPANTS Two hundred forty five NSCL±P cases from G. S. Memorial Plastic Surgery Hospital and Trauma Center, Varanasi and 201 healthy controls without a family history of congenital malformations from nearby schools, primary health centers, and the university hospital. MAIN OUTCOME MEASURE(S) Sequencing, SSCP, and PCR-RFLP were used for candidate gene screening. MatInspector and electrophoretic mobility shift assay (EMSA) were used to check the differential transcription factor binding of the variants at promoter region. Luciferase assay was used to test the transcriptional potential of the variant, and evaluation of the alternative splice site was carried out using exon-trapping experiment. RESULTS Metalloproteinases3 -1171 5A/6A was associated with NSCL±P, whereas MMP9 -1562 C/T did not show association. A rare variant in the promoter region of TGFβ3 (rs117462711) creates a differential binding site, confirmed by EMSA. Luciferase assay showed 3.7-fold increased expression level in mutant construct. A synonymous change in MSX1 (rs34165410) showed association with NSCL±P, which may create an alternative splice site or lead to low codon usage. Exon-trapping experiment failed to confirm alternative splicing, indicating low codon usage frequency of the mutant affecting the gene function. CONCLUSIONS TGFβ3, MSX1, and MMP3 are candidates for NSCL±P.
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Affiliation(s)
- Priyanka Kumari
- 1 Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Subodh Kumar Singh
- 2 G. S. Memorial Plastic Surgery Hospital and Trauma Center, Varanasi, Uttar Pradesh, India
| | - Rajiva Raman
- 1 Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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Adeyemo AA, Amodu OK, Ekure EE, Omotade OO. Medical genetics and genomic medicine in Nigeria. Mol Genet Genomic Med 2018; 6:314-321. [PMID: 29871027 PMCID: PMC6014475 DOI: 10.1002/mgg3.419] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 12/11/2022] Open
Abstract
Medical genetics and genomic medicine in Nigeria.
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Affiliation(s)
- Adebowale A. Adeyemo
- National Human Genome Research InstituteNational Institutes of HealthBethesdaMaryland
| | - Olukemi K. Amodu
- Institute of Child HealthCollege of MedicineUniversity of IbadanIbadanNigeria
| | - Ekanem E. Ekure
- Department of PaediatricsCollege of MedicineUniversity of LagosLagosNigeria
| | - Olayemi O. Omotade
- Institute of Child HealthCollege of MedicineUniversity of IbadanIbadanNigeria
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12
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Gowans LJJ, Oseni G, Mossey PA, Adeyemo WL, Eshete MA, Busch TD, Donkor P, Obiri-Yeboah S, Plange-Rhule G, Oti AA, Owais A, Olaitan PB, Aregbesola BS, Oginni FO, Bello SA, Audu R, Onwuamah C, Agbenorku P, Ogunlewe MO, Abdur-Rahman LO, Marazita ML, Adeyemo AA, Murray JC, Butali A. Novel GREM1 Variations in Sub-Saharan African Patients With Cleft Lip and/or Cleft Palate. Cleft Palate Craniofac J 2018; 55:736-742. [PMID: 29489415 DOI: 10.1177/1055665618754948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Cleft lip and/or cleft palate (CL/P) are congenital anomalies of the face and have multifactorial etiology, with both environmental and genetic risk factors playing crucial roles. Though at least 40 loci have attained genomewide significant association with nonsyndromic CL/P, these loci largely reside in noncoding regions of the human genome, and subsequent resequencing studies of neighboring candidate genes have revealed only a limited number of etiologic coding variants. The present study was conducted to identify etiologic coding variants in GREM1, a locus that has been shown to be largely associated with cleft of both lip and soft palate. PATIENTS AND METHOD We resequenced DNA from 397 sub-Saharan Africans with CL/P and 192 controls using Sanger sequencing. Following analyses of the sequence data, we observed 2 novel coding variants in GREM1. These variants were not found in the 192 African controls and have never been previously reported in any public genetic variant database that includes more than 5000 combined African and African American controls or from the CL/P literature. RESULTS The novel variants include p.Pro164Ser in an individual with soft palate cleft only and p.Gly61Asp in an individual with bilateral cleft lip and palate. The proband with the p.Gly61Asp GREM1 variant is a van der Woude (VWS) case who also has an etiologic variant in IRF6 gene. CONCLUSION Our study demonstrated that there is low number of etiologic coding variants in GREM1, confirming earlier suggestions that variants in regulatory elements may largely account for the association between this locus and CL/P.
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Affiliation(s)
- Lord Jephthah Joojo Gowans
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ganiyu Oseni
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Peter A Mossey
- 3 Department of Orthodontics, University of Dundee, Dundee, United Kingdom
| | - Wasiu Lanre Adeyemo
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Mekonen A Eshete
- 5 Addis Ababa University, School of Public Health, Addis Ababa, Ethiopia
| | - Tamara D Busch
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gyikua Plange-Rhule
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander A Oti
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Arwa Owais
- 7 Department of Pediatric Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter B Olaitan
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Babatunde S Aregbesola
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Fadekemi O Oginni
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Rosemary Audu
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Chika Onwuamah
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Pius Agbenorku
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mobolanle O Ogunlewe
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Lukman O Abdur-Rahman
- 11 Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - Mary L Marazita
- 12 Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.,13 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- 14 National Human Genome Research Institute, Bethesda, MD, USA
| | - Jeffrey C Murray
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- 15 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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13
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Assis Machado R, de Toledo IP, Martelli-Júnior H, Reis SR, Neves Silva Guerra E, Coletta RD. Potential genetic markers for nonsyndromic oral clefts in the Brazilian population: A systematic review and meta-analysis. Birth Defects Res 2018; 110:827-839. [DOI: 10.1002/bdr2.1208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
| | - Isabela Porto de Toledo
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | | | | | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
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14
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Trindade-Suedam IK, Kostrisch LMV, Pimenta LAF, Negrato CA, Franzolin SB, Trindade AS. Diabetes mellitus and drug abuse during pregnancy and the risk for orofacial clefts and related abnormalities. Rev Lat Am Enfermagem 2017; 24:e2701. [PMID: 27508899 PMCID: PMC4990026 DOI: 10.1590/1518-8345.0815.2701] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/18/2015] [Indexed: 11/23/2022] Open
Abstract
Objective: to assessed the prevalence of diabetes mellitus (DM) and drug abuse in mothers of
children with orofacial clefts (OFC). Methods: 325 women who had children (0-3y) with clefts were interviewed. Data regarding
type of diabetes, use of legal/illegal drugs during pregnancy, waist girth and
fasting blood sugar at the first prenatal consult were collected. Results: twenty seven percent of the women had DM, out of these, 89% had gestational DM,
5,5% type 1 DM and 5,5% type 2 DM. The prevalence of DM in mothers of children
with OFC was 27%, it is significantly higher than the average Brazilian population
which is 7.6% (p<0.01) (OR=4.5, 95%CI=3.5-5.8). Regarding drug abuse during
pregnancy, 32% of the mothers used drugs and a significant positive correlation
was observed between drug abuse and the occurrence of clefts and other
craniofacial anomalies (p=0.028) (OR=2.87; 95%CI=1.1-7.4). Conclusions: DM and drug abuse during pregnancy increases the risk for OFC and related
anomalies and early diagnosis of DM and prevention of drug abuse, especially in
pregnant women, should be emphasized.
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Affiliation(s)
- Ivy Kiemle Trindade-Suedam
- PhD, Associate Professor, Faculdade de Odontologia de Bauru, Universidade de São Paulo, Bauru, SP, Brazil
| | - Lília Maria von Kostrisch
- RN, Hospital de Messejana Dr. José Alberto Studart Gomes, Secretaria de Municipal de Saúde de Fortaleza, Fortaleza, CE, Brazil. Doctoral student, Hospital de Reabilitação de Anomalias Craniofaciais, Universidade de São Paulo, Bauru, SP, Brazil
| | - Luiz André Freire Pimenta
- Clinical Professor, School of Dentistry, University of North Carolina, Chapel Hill, NC, United States
| | | | | | - Alceu Sergio Trindade
- PhD, Full Professor, Faculdade de Odontologia de Bauru, Universidade de São Paulo, Bauru, SP, Brazil
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15
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Haddaji Mastouri M, De Coster P, Zaghabani A, Jammali F, Raouahi N, Ben Salem A, Saad A, Coucke P, H'mida Ben Brahim D. Genetic study of non-syndromic tooth agenesis through the screening of paired box 9, msh homeobox 1, axin 2, and Wnt family member 10A genes: a case-series. Eur J Oral Sci 2017; 126:24-32. [PMID: 29114927 DOI: 10.1111/eos.12391] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 02/04/2023]
Abstract
Non-syndromic tooth agenesis (NSTA) is the most common developmental anomaly in humans. Several studies have been conducted on dental agenesis and numerous genes have been identified. However, the pathogenic mechanisms responsible for NSTA are not clearly understood. We studied a group of 28 patients with sporadic NSTA and nine patients with a family history of tooth agenesis. We focused on four genes - paired box 9 (PAX9), Wnt family member 10A (WNT10A), msh homeobox 1 (MSX1), and axin 2 (AXIN2) - using direct Sanger sequencing of the exons and intron-exon boundaries. The most prevalent variants identified in PAX9 and AXIN2 genes were analyzed using the chi-square test. The sequencing results revealed a number of variants in the AXIN2 gene, including one novel missense mutation in one patient with agenesis of a single second premolar. We also identified one variant in the AXIN2 gene as being a putative risk factor for tooth agenesis. Only one missense mutation was identified in the WNT10A gene and this mutation was found in two patients. Interestingly, WNT10A is reported as the most prevalent gene mutated in the European population with NSTA.
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Affiliation(s)
- Marwa Haddaji Mastouri
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
| | - Peter De Coster
- Department of Restorative Dentistry, Endodontology and Oral Biology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | | | - Frej Jammali
- Department of Orthodontics, Farhat Hached University Hospital, Sousse, Tunisia
| | - Nabiha Raouahi
- Department of Orthodontics, Farhat Hached University Hospital, Sousse, Tunisia
| | | | - Ali Saad
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
| | - Paul Coucke
- Center for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Dorra H'mida Ben Brahim
- Department of Human Cytogenetics, Molecular Genetics and Reproductive Biology, Farhat Hached University Hospital, Sousse, Tunisia
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16
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Adeyemo WL, Butali A. Genetics and genomics etiology of nonsyndromic orofacial clefts. Mol Genet Genomic Med 2017; 5:3-7. [PMID: 28116324 PMCID: PMC5241211 DOI: 10.1002/mgg3.272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Orofacial clefts (OFC) are complex birth defects. Studies using contemporary genomic techniques, bioinformatics, and statistical analyses have led to appreciable advances in identifying the causes of syndromic forms of clefts. This commentary gives an overview of the important cleft gene discoveries found using various genomic methods and tools.
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Affiliation(s)
- Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery College of Medicine University of Lagos Surulere Nigeria
| | - Azeez Butali
- Department of Oral Pathology, Radiology and MedicineCollege of DentistryUniversity of IowaIowa CityIowa; Iowa Institute of Oral Health ResearchCollege of DentistryUniversity of IowaIowa CityIowa
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17
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Ibarra-Arce A, Albavera-Giles T, Zavaleta-Villa B, Ortiz de Zárate-Alarcón G, Flores-Peña L, Sierra-Romero MDC, Romero-Valdovinos M, Olivo-Díaz A. MSX1 gene polymorphisms in Mexican patients with non-syndromic cleft lip/palate. Int J Pediatr Otorhinolaryngol 2016; 90:119-124. [PMID: 27729116 DOI: 10.1016/j.ijporl.2016.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/07/2016] [Accepted: 09/09/2016] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Non-syndromic cleft lip/palate malformation (CL/P) is one of the most common birth defects in humans and has a complex etiology involving genetic and environmental factors. Mutations in the MSX1 gene are critical during craniofacial development. The purpose of this study was to investigate the contribution of MSX1 gene polymorphisms to the risk of developing CL/P in a sample of Mexican patients. METHODS The sample consisted of 282 subjects (69 cases and 213 relatives). Four single-nucleotide polymorphisms (SNP1, P147Q, SNP5 and P278S) were tested for association with CL/P in triad and case-pseudo-control analyses. Polymorphism typing was performed by restriction fragment length polymorphism and dot-blot techniques. Allele and genotype frequencies were calculated between patients and pseudo-controls and compared using the Chi square test with Yates correction. Odds ratios and 95% confidence intervals were obtained using SPSS software (v19). Triad analysis was also performed using the program HAPLIN (v5.3). RESULTS In the cases and pseudo-controls, an association was found between CL/P and the SNP1-G allele (P = 0.031) and the SNP1-G/G genotype (P = 0.032), a polymorphism located near MSX1. Triad analysis showed a tendency toward CL/P susceptibility for the genotype SNP1-G/G (P = 0.075) and an association between CL/P and the haplotype GCTC (P = 0.037). No associated haplotype was found in the cases and pseudo-controls. Two partial haplotypes, GT (SNP1-SNP5) (P = 0.032) and GC (SNP1-P278S) (P = 0.033), were associated with susceptibility in the heterozygous and homozygous types, respectively. In contrast, haplotype AT (SNP1-SNP5) was associated with protection (P = 0.012) in the homozygous type. CONCLUSIONS The results of this study suggest an association between CL/P susceptibility and SNP1, located near the MSX1 gene, in the Mexican population.
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Affiliation(s)
- Aurora Ibarra-Arce
- Genetics Division, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Tania Albavera-Giles
- Department of Molecular Biology and Histocompatibility, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Beatriz Zavaleta-Villa
- Department of Molecular Biology and Histocompatibility, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | | | - Laura Flores-Peña
- Genetics Division, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | | | - Mirza Romero-Valdovinos
- Department of Molecular Biology and Histocompatibility, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Angélica Olivo-Díaz
- Department of Molecular Biology and Histocompatibility, General Hospital "Dr. Manuel Gea Gonzalez", Mexico City, Mexico.
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18
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Gowans LJJ, Adeyemo WL, Eshete M, Mossey PA, Busch T, Aregbesola B, Donkor P, Arthur FKN, Bello SA, Martinez A, Li M, Augustine-Akpan EA, Deressa W, Twumasi P, Olutayo J, Deribew M, Agbenorku P, Oti AA, Braimah R, Plange-Rhule G, Gesses M, Obiri-Yeboah S, Oseni GO, Olaitan PB, Abdur-Rahman L, Abate F, Hailu T, Gravem P, Ogunlewe MO, Buxó CJ, Marazita ML, Adeyemo AA, Murray JC, Butali A. Association Studies and Direct DNA Sequencing Implicate Genetic Susceptibility Loci in the Etiology of Nonsyndromic Orofacial Clefts in Sub-Saharan African Populations. J Dent Res 2016; 95:1245-56. [PMID: 27369588 DOI: 10.1177/0022034516657003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Orofacial clefts (OFCs) are congenital dysmorphologies of the human face and oral cavity, with a global incidence of 1 per 700 live births. These anomalies exhibit a multifactorial pattern of inheritance, with genetic and environmental factors both playing crucial roles. Many loci have been implicated in the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations of Asian and European ancestries, through genome-wide association studies and candidate gene studies. However, few populations of African descent have been studied to date. Here, the authors show evidence of an association of some loci with NSCL/P and nonsyndromic cleft palate only (NSCPO) in cohorts from Africa (Ghana, Ethiopia, and Nigeria). The authors genotyped 48 single-nucleotide polymorphisms that were selected from previous genome-wide association studies and candidate gene studies. These markers were successfully genotyped on 701 NSCL/P and 163 NSCPO cases, 1,070 unaffected relatives, and 1,078 unrelated controls. The authors also directly sequenced 7 genes in 184 nonsyndromic OFC (NSOFC) cases and 96 controls from Ghana. Population-specific associations were observed in the case-control analyses of the subpopulations, with West African subpopulations (Ghana and Nigeria) showing a similar pattern of associations. In meta-analyses of the case-control cohort, PAX7 (rs742071, P = 5.10 × 10(-3)), 8q24 (rs987525, P = 1.22 × 10(-3)), and VAX1 (rs7078160, P = 0.04) were nominally associated with NSCL/P, and MSX1 (rs115200552, P = 0.01), TULP4 (rs651333, P = 0.04), CRISPLD2 (rs4783099, P = 0.02), and NOG1 (rs17760296, P = 0.04) were nominally associated with NSCPO. Moreover, 7 loci exhibited evidence of threshold overtransmission in NSOFC cases through the transmission disequilibrium test and through analyses of the family-based association for disease traits. Through DNA sequencing, the authors also identified 2 novel, rare, potentially pathogenic variants (p.Asn323Asp and p.Lys426IlefsTer6) in ARHGAP29 In conclusion, the authors have shown evidence for the association of many loci with NSCL/P and NSCPO. To the best of this knowledge, this study is the first to demonstrate any of these association signals in any African population.
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Affiliation(s)
- L J J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Pediatrics, University of Iowa, Iowa City, IA, USA Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W L Adeyemo
- College of Medicine, University of Lagos, Lagos, Nigeria
| | - M Eshete
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P A Mossey
- Department of Orthodontics, University of Dundee, Dundee, Scotland
| | - T Busch
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - B Aregbesola
- Obafemi Awolowo University Teaching Hospital, Ile-Ife, Nigeria
| | - P Donkor
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - F K N Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - S A Bello
- Department of Oral and Maxillofacial Surgery, State House Hospital, Abuja, Nigeria
| | - A Martinez
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - E A Augustine-Akpan
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
| | - W Deressa
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P Twumasi
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - J Olutayo
- College of Medicine, University of Lagos, Lagos, Nigeria
| | - M Deribew
- Addis Ababa University, Addis Ababa, Ethiopia
| | - P Agbenorku
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - A A Oti
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - R Braimah
- Obafemi Awolowo University Teaching Hospital, Ile-Ife, Nigeria
| | - G Plange-Rhule
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - M Gesses
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - S Obiri-Yeboah
- Cleft Clinic, Komfo Anokye Teaching Hospital, Kumasi, Ghana Department of Surgery, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - G O Oseni
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - P B Olaitan
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - L Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - F Abate
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - T Hailu
- Yekatit 12 Hospital Medical College, Addis Ababa, Ethiopia
| | - P Gravem
- Haukeland University Hospital Bergen, Bergen, Norway
| | - M O Ogunlewe
- Department of Burns and Plastic Surgery, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, Nigeria
| | - C J Buxó
- School of Dental Medicine, University of Puerto Rico Medical Science Campus, San Juan, Puerto Rico
| | - M L Marazita
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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19
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Luan F, Sun F, Xu C, Zhang H. WITHDRAWN: The MSX1 gene polymorphisms rs12532 and rs1001179 confer an increased risk of non syndromic orofacial clefts. J Craniomaxillofac Surg 2016:S1010-5182(16)00029-9. [PMID: 27038504 DOI: 10.1016/j.jcms.2016.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 01/05/2016] [Accepted: 01/26/2016] [Indexed: 11/21/2022] Open
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Fang Luan
- Department of Plastic Surgery, Zibo Central Hospital, Zibo 255036, PR China.
| | - Fengling Sun
- Department of Plastic Surgery, Zibo Central Hospital, Zibo 255036, PR China
| | - Chao Xu
- Department of Plastic Surgery, Zibo Central Hospital, Zibo 255036, PR China
| | - Haixia Zhang
- Department of Plastic Surgery, Zibo Central Hospital, Zibo 255036, PR China
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20
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Babu Gurramkonda V, Hussain Syed A, Murthy J, Chaubey G, Bhaskar Lakkakula VKS. Polymorphic variants near 1p22 and 20q11.2 loci and the risk of non-syndromic cleft lip and palate in South Indian population. Int J Pediatr Otorhinolaryngol 2015; 79:2389-93. [PMID: 26586245 DOI: 10.1016/j.ijporl.2015.10.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/29/2022]
Abstract
BACKGROUND Recent genome-wide association studies (GWAS) have reported multiple genetic risk loci for non-syndromic orofacial clefts (NSOFCs) in many populations. However, the contribution of these loci to NSOFC in India, which comprises one-fifth of the global population, is completely lacking. Our aim was to replicate the association of the SNPs located on 1p22 chromosomal loci (rs540026, rs481931) and 20q11.2 (rs13041247, rs11696257) in the aetiology of NSOFCs, in South Indian populations. METHODS The SNPs were genotyped by using KBiosciences KASPar SNP genotyping chemistry in 173 cases and 176 controls for NSOFCs in South India. To estimate the association between these SNPs and NSOFCs, chi-square test was adopted. Odds ratios (OR) with 95% confidence intervals (CI) were also calculated in order to assess the risk. RESULTS Single nucleotide polymorphisms located at chromosomal region 1p22 are not found to be associated with cleft lip with or without non-syndromic cleft palate (NSCL/P) and non-syndromic cleft palate only (NSCPO) at either the genotype or allele levels. Further, there is no LD observed between these variants. The polymorphic variants near 20q11.2 (rs13041247, rs11696257) are in complete linkage disequilibrium (LD) and are significantly associated with only NSCL/P in genotypic (p=0.013) and allelic models (p=0.029). In the genotypic model significance persisted even after Bonferroni correction (p<0.016). CONCLUSION These results suggest that 20q11.2 SNPs could play a contributory role in the pathophysiology and risk of NSCL/P, while the variations in 1p22 do not underlie the pathophysiology of NSOFCs in South Indian populations.
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Affiliation(s)
| | - Altaf Hussain Syed
- Department of Plastic Surgery, Sri Ramachandra University, Chennai, India
| | - Jyotsna Murthy
- Department of Plastic Surgery, Sri Ramachandra University, Chennai, India
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Machado RA, Messetti AC, de Aquino SN, Martelli-Júnior H, Swerts MSO, de Almeida Reis SR, Moreira HSB, Persuhn DC, Coletta RD. Association Between Genes Involved in Craniofacial Development and Nonsyndromic Cleft Lip and/or Palate in the Brazilian Population. Cleft Palate Craniofac J 2015; 53:550-6. [PMID: 26402724 DOI: 10.1597/15-107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To determine the association of single-nucleotide polymorphisms (SNPs) in genes related to craniofacial development, which were previously identified as susceptibility signals for nonsyndromic oral clefts, in Brazilians with nonsyndromic cleft lip and/or palate (NSCL/P). DESIGN The SNPs rs748044 (TNP1), rs1106514 (MSX1), rs28372960, rs15251 and rs2569062 (TCOF1), rs7829058 (FGFR1), rs1793949 (COL2A1), rs11653738 (WNT3), and rs242082 (TIMP3) were assessed in a family-based transmission disequilibrium test (TDT) and a structured case-control analysis based on the individual ancestry proportions. SETTING The SNPs were initially analyzed by TDT, and polymorphisms showing a trend toward excess transmission were subsequently studied in an independent case-control sample. PARTICIPANTS The study sample consisted of 189 case-parent trios of nonsyndromic cleft lip with or without cleft palate (NSCL±P), 107 case-parent trios of nonsyndromic cleft palate (NSCP), 318 isolated samples of NSCL±P, 189 isolated samples of NSCP, and 599 healthy controls. MAIN OUTCOME MEASURE Association of alleles with NSCL/P pathogenesis. RESULTS Preferential transmission of SNPs rs28372960 and rs7829058 in NSCL±P trios and rs11653738 in NSCP trios (P = .04) were observed, although the structured case-control analysis did not confirm these associations. The haplotype T-C-C formed by TCOF1 SNPs rs28372960, rs15251, and rs2569062 was more frequently transmitted from healthy parents to NSCL±P offspring, but the P value (P = .01) did not withstand Bonferroni correction for multiple tests. CONCLUSIONS With the modest associations, our results do not support the hypothesis that TNP1, MSX1, TCOF1, FGFR1, COL2A1, WNT3, and TIMP3 variants are risk factors for nonsyndromic oral clefts in the Brazilian population.
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Yu Q, He S, Zeng N, Ma J, Zhang B, Shi B, Jia Z. BMP7 Gene involved in nonsyndromic orofacial clefts in Western Han Chinese. Med Oral Patol Oral Cir Bucal 2015; 20:e298-304. [PMID: 25662552 PMCID: PMC4464917 DOI: 10.4317/medoral.20335] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/25/2014] [Indexed: 02/05/2023] Open
Abstract
Background Nonsyndromic orofacial clefts (NSOCs) are the most common craniofacial birth defects with complex etiology in which multiple genes and environmental exposures are involved. Bone morphogenetic protein 7 (BMP7), as a member of the transforming growth factor-beta (TGF-beta) superfamily, has been shown to play crucial roles in palate and other orofacial ectodermal appendages development in animal models. Material and Methods This study was designed to investigate the possible associations between BMP7 gene and the NSOCs (221 case-parent trios) in Western Han Chinese. Five tagSNPs at BMP7, rs12438, rs6099486, rs6127973, rs230188 and rs6025469 were picked and tried to cover the entire gene. In order to identify the contribution of BMP7 gene to the etiology of NSOCs, we performed several statistical analysis from different aspects including transmission disequilibrium test (TDT), pairwise linkage disequilibrium (LD), parent-of-origin effect and Chi-squared/Fisher’s exact tests. Results Rs6127973 G allele and G/G homozygotes were over-transmitted for both NSOCs (P=0.005 and P=0.011, respectively) and NSCL/P (P=0.0061 and P=0.011, respectively), rs6127973 G allele was also paternally over-transmitted for both NSOCs (P=0.0061) and NSCL/P (P=0.011). Conclusions This study suggested that rs6127973 may be a risk factor of being NSOCs and confirmed the role of BMP7 gene in orofacial deformity from Western Han Chinese, which will also supply scientific evidence for future research and genetic counseling. Key words:
Single nucleotide polymorphisms, nonsyndromic orofacial clefts, BMP7.
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Affiliation(s)
- Qiongqiong Yu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, 3rd Section, Renmin Nan Road, Chengdu, China, 610041
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James A, Oluwatosin B, Njideka G, Babafemi, Benjamin OG, Olufemi D, Leo R, Folorunso I, Phylis, Olusina O. CLEFT PALATE IN HIV-EXPOSED NEWBORNS OF MOTHERS ON HIGHLY ACTIVE ANTIRETROVIRAL THERAPY. ORAL SURGERY 2014; 7:102-106. [PMID: 25653715 PMCID: PMC4313880 DOI: 10.1111/ors.12117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/02/2014] [Indexed: 11/30/2022]
Abstract
AIMS Cleft lip/palate, though rare, is the commonest head and neck congenital malformation. Both genetic and environmental factors have been implicated in the aetiopathogenesis but the role of in-utero exposure to human immunodeficiency virus (HIV) and highly active antiretroviral therapy (HAART) is still being investigated. This short communication reports the occurrence of cleft palate in three newborns exposed in-utero to HIV and HAART. MATERIAL AND METHODS This is a case series of HIV-exposed newborns observed to have cleft palate among a larger cohort of HIV-exposed and unexposed newborns in a study evaluating the effect of HIV infection and HAART on newborn hearing. The Risk Ratio (RR) was calculated to detect a potential association between in-utero exposure to Efavirenz containing ART and cleft palate. RESULTS Three HIV-exposed newborns with cleft palate were identified during hearing screening performed on 126 HIV-exposed and 121 HIV unexposed newborns. Two had exposure to tenofovir+lamivudine+efavirenz (TDF+3TC+EFV) while the third had exposure to zidovudine+lamivudine+nevirapine (ZDV+3TC+NVP) during the first trimester. There was no statistically significant association between presence of cleft palate and exposure to an EFV containing HAART regimen (p=0.07, RR=10.95 [0.94-126.84]). CONCLUSIONS This communication highlights the possible aetiologic role of HAART in cleft palate, the need for further prospective follow-up studies and establishment of antiretroviral pregnancy, birth and neonatal registries.
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Affiliation(s)
- Ayotunde James
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Nigeria
| | | | - Georgina Njideka
- Department of Virology, College of Medicine, University of Ibadan, Nigeria ; MEDICAL EDUCATION PARTNERSHIP IN NIGERIA ; PRESIDENT'S EMERGENCY PLAN FOR AIDS RELIEF - AIDS PREVENTION INITIATIVE NIGERIA (PEPFAR-APIN PLUS)
| | - Babafemi
- Center for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | | | - David Olufemi
- Department of Virology, College of Medicine, University of Ibadan, Nigeria ; MEDICAL EDUCATION PARTNERSHIP IN NIGERIA ; PRESIDENT'S EMERGENCY PLAN FOR AIDS RELIEF - AIDS PREVENTION INITIATIVE NIGERIA (PEPFAR-APIN PLUS)
| | - Robert Leo
- Center for Global Health, Feinberg School of Medicine, Northwestern University, Chicago, USA
| | - Isaac Folorunso
- Department of Obstetrics and Gynaecology, College of Medicine, University of Ibadan, Nigeria ; MEDICAL EDUCATION PARTNERSHIP IN NIGERIA ; PRESIDENT'S EMERGENCY PLAN FOR AIDS RELIEF - AIDS PREVENTION INITIATIVE NIGERIA (PEPFAR-APIN PLUS)
| | - Phylis
- Department of Immunology & Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Olusegun Olusina
- Department of Paediatrics, College of Medicine, University of Ibadan, Nigeria ; MEDICAL EDUCATION PARTNERSHIP IN NIGERIA ; PRESIDENT'S EMERGENCY PLAN FOR AIDS RELIEF - AIDS PREVENTION INITIATIVE NIGERIA (PEPFAR-APIN PLUS)
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Joint testing of genotypic and gene-environment interaction identified novel association for BMP4 with non-syndromic CL/P in an Asian population using data from an International Cleft Consortium. PLoS One 2014; 9:e109038. [PMID: 25303326 PMCID: PMC4193821 DOI: 10.1371/journal.pone.0109038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/28/2014] [Indexed: 11/23/2022] Open
Abstract
Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common disorder with complex etiology. The Bone Morphogenetic Protein 4 gene (BMP4) has been considered a prime candidate gene with evidence accumulated from animal experimental studies, human linkage studies, as well as candidate gene association studies. The aim of the current study is to test for linkage and association between BMP4 and NSCL/P that could be missed in genome-wide association studies (GWAS) when genotypic (G) main effects alone were considered. Methodology/Principal Findings We performed the analysis considering G and interactions with multiple maternal environmental exposures using additive conditional logistic regression models in 895 Asian and 681 European complete NSCL/P trios. Single nucleotide polymorphisms (SNPs) that passed the quality control criteria among 122 genotyped and 25 imputed single nucleotide variants in and around the gene were used in analysis. Selected maternal environmental exposures during 3 months prior to and through the first trimester of pregnancy included any personal tobacco smoking, any environmental tobacco smoke in home, work place or any nearby places, any alcohol consumption and any use of multivitamin supplements. A novel significant association held for rs7156227 among Asian NSCL/P and non-syndromic cleft lip and palate (NSCLP) trios after Bonferroni correction which was not seen when G main effects alone were considered in either allelic or genotypic transmission disequilibrium tests. Odds ratios for carrying one copy of the minor allele without maternal exposure to any of the four environmental exposures were 0.58 (95%CI = 0.44, 0.75) and 0.54 (95%CI = 0.40, 0.73) for Asian NSCL/P and NSCLP trios, respectively. The Bonferroni P values corrected for the total number of 117 tested SNPs were 0.0051 (asymptotic P = 4.39*10−5) and 0.0065 (asymptotic P = 5.54*10−5), accordingly. In European trios, no significant association was seen for any SNPs after Bonferroni corrections for the total number of 120 tested SNPs. Conclusions/Significance Our findings add evidence from GWAS to support the role of BMP4 in susceptibility to NSCL/P originally identified in linkage and candidate gene association studies.
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Butali A, Mossey P, Adeyemo W, Eshete M, Gaines L, Braimah R, Aregbesola B, 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 DOI: 10.1002/ajmg.a.36691] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [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
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26
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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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27
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Song T, Wu D, Wang Y, Li H, Yin N, Zhao Z. SNPs and interaction analyses of IRF6, MSX1 and PAX9 genes in patients with non‑syndromic cleft lip with or without palate. Mol Med Rep 2013; 8:1228-34. [PMID: 23921572 DOI: 10.3892/mmr.2013.1617] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 07/23/2013] [Indexed: 11/06/2022] Open
Abstract
Non‑syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital deformity, often associated with missing or deformed teeth. The genes interferon regulatory factor 6 (IRF6), muscle segment homeobox 1 (MSX1) and paired box gene 9 (PAX9) are important for the development of the maxillofacial region and dentition. The aim of this study was to explore how genetic variations in IRF6, MSX1 and PAX9, as well as gene‑gene interactions, are associated with NSCL/P. We investigated 9 IRF6 tag single nucleotide polymorphisms (SNPs), 2 MSX1 tag SNPs and 8 PAX9 tag SNPs selected from HapMap data from the Chinese population. The SNPs were examined for associations with NSCL/P in 204 patients and 226 controls. The results demonstrated a significant association between NSCL/P and rs2073485, rs2235371, rs2236909 and rs861020 in the IRF6 gene, and haplotype analysis supported these findings. A marginally significant difference was observed in the NSCL/P group for rs17176643 in the PAX9 gene compared to the control group. The results of gene‑gene interaction analyses also indicated that the combination of rs2073485, rs2235371 or rs2236909 in IRF6 and rs17176643 in PAX9, increased the risk of NSCL/P. Thus, our study provided additional understanding of IRF6 variations in patients with NSCL/P and suggested that interactions between the IRF6 and PAX9 genes are potentially important for susceptibility to NSCL/P.
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Affiliation(s)
- Tao Song
- Center of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shijingshan, Beijing 100144, P.R. China
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Souza LT, Kowalski TW, Collares MVM, Félix TM. MSX1 gene and nonsyndromic oral clefts in a Southern Brazilian population. Braz J Med Biol Res 2013; 46:555-8. [PMID: 23903689 PMCID: PMC3859340 DOI: 10.1590/1414-431x20133054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/02/2013] [Indexed: 11/22/2022] Open
Abstract
Nonsyndromic oral clefts (NSOC) are the most common craniofacial birth defects in
humans. The etiology of NSOC is complex, involving both genetic and
environmental factors. Several genes that play a role in cellular proliferation,
differentiation, and apoptosis have been associated with clefting. For example,
variations in the homeobox gene family member MSX1, including a
CA repeat located within its single intron, may play a role in clefting. The aim
of this study was to investigate the association between MSX1
CA repeat polymorphism and NSOC in a Southern Brazilian population using a
case-parent triad design. We studied 182 nuclear families with NSOC recruited
from the Hospital de Clínicas de Porto Alegre in Southern Brazil. The
polymorphic region was amplified by the polymerase chain reaction and analyzed
by using an automated sequencer. Among the 182 families studied, four different
alleles were observed, at frequencies of 0.057 (175 bp), 0.169 (173 bp), 0.096
(171 bp) and 0.67 (169 bp). A transmission disequilibrium test with a
family-based association test (FBAT) software program was used for analysis.
FBAT analysis showed overtransmission of the 169 bp allele in NSOC (P=0.0005).
These results suggest that the CA repeat polymorphism of the
MSX1 gene may play a role in risk of NSOC in populations
from Southern Brazil.
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Affiliation(s)
- L T Souza
- Laborato´ rio de Medicina Genoˆ mica, Centro de Pesquisa Experimental, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brasil
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29
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Butali A, Adeyemo WL, Mossey PA, Olasoji HO, Onah II, Adebola A, Efunkoya, Akintububo A, James O, Adeosun OO, Ogunlewe MO, Ladeinde AL, Mofikoya BO, Adeyemi MO, Ekhaguere OA, Emeka C, Awoyale TA, The Nigeriacran Collaboration. Prevalence of orofacial clefts in Nigeria. Cleft Palate Craniofac J 2013; 51:320-5. [PMID: 23557093 DOI: 10.1597/12-135] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Orofacial clefts are the most common malformations of the head and neck. In Africa, orofacial clefts are underascertained, with little or no surveillance system in most parts for clefts and other birth defects. A Nigerian craniofacial anomalies study, NigeriaCRAN, was established in 2006 to support cleft research specifically for epidemiological studies, treatment outcomes, and studies into etiology and prevention. We pooled data from seven of the largest Smile Train treatment centers in the six geopolitical zones in Nigeria. Data from September 2006 to June 2011 were analyzed and clefts compared between sides and genders using the Fisher exact test. A total of 2197 cases were identified during the study period, with an estimated prevalence rate of 0.5 per 1000. Of the total number of orofacial clefts, 54.4% occur in males and 45.6% in females. There was a significant difference (P = .0001) between unilateral left clefts and unilateral right clefts, and there was a significant difference (P = .0001) between bilateral clefts and clefts on either the left or right side. A significant gender difference (P = .03) was also observed for cleft palate, with more females than males. A total of 103 (4.7%) associated anomalies were identified. There were nine syndromic cleft cases, and 10.4% of the total number of individuals with clefts have an affected relative. The significant difference between unilateral clefts and the gender differences in the proportion of cleft palate only are consistent with the literature. The present study emphasizes the need for birth defects registries in developing countries in order to estimate the exact prevalence of birth defects including orofacial clefts.
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Antunes LS, Küchler EC, Tannure PN, Costa MC, Gouvêa CVD, Olej B, Granjeiro JM. BMP4 Polymorphism is Associated With Nonsyndromic Oral Cleft in a Brazilian Population. Cleft Palate Craniofac J 2012; 50:633-8. [PMID: 23237431 DOI: 10.1597/12-048] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Objective : To evaluate the association of the polymorphisms in the TGFB3 gene (rs2268626) and the BMP4 gene (rs17563) with nonsyndromic oral clefts. Design : A hospital-based case-control study was conducted with nonsyndromic oral clefts cases and unaffected controls. Cleft type and tooth agenesis data were collected by clinical examination and confirmed through medical records. Risk factors were obtained through a questionnaire. Genotyping of the selected polymorphisms for TGFB3 and BMP4 were carried out by real-time polymerase chain reaction using the Taqman assay method from a genomic DNA isolated from buccal epithelial cells of all individuals. Setting : The case group was ascertained through a public reference hospital of oral cleft rehabilitation in Rio de Janeiro, Brazil. The noncleft group consisted of unrelated subjects, with no history of oral cleft in the family, recruited at the Dental Clinic at the Federal University of Rio de Janeiro, Brazil. Participants : A total of 833 unrelated individuals (450 control individuals and 383 cases with nonsyndromic oral clefts). Results : No significant association in relation to genotype or allele distributions for TGFB3 polymorphism was found between oral cleft subgroups and the control group. For BMP4, there were significant differences in the genotype frequencies between the oral cleft and control groups (P = .0007). Regarding cleft type, there were statistically significant differences between the cleft lip and control groups (P = .00009). Conclusion : Our findings provide preliminary evidence suggesting that the risk of nonsyndromic oral clefts may be influenced by variation in the BMP4 gene.
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Fontoura C, Silva RM, Granjeiro JM, Letra A. Further evidence of association of the ABCA4 gene with cleft lip/palate. Eur J Oral Sci 2012; 120:553-7. [PMID: 23167473 DOI: 10.1111/eos.12001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2012] [Indexed: 11/27/2022]
Abstract
Non-syndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex etiology. Numerous genes and environmental factors, and their interactions, are thought to play a role in the susceptibility to CL/P. A recent genome-wide association study with several populations revealed markers in/near transcription factor vmaf musculoaponeurtoic fibrosarcoma oncogene homolog B (MAFB) and ATP-binding cassette sub-family A member 4 (ABCA4) genes as new susceptibility loci for CL/P. We hypothesized that these genes could also contribute to CL/P in a Brazilian population, and hence we evaluated if the associated single-nucleotide polymorphisms (SNPs) in MAFB (rs13041247 and rs11696257) and ABCA4 (rs560426 and rs481931) were associated with CL/P in our case-control data set. We genotyped 812 Caucasian individuals (400 cases and 412 controls) from Brazil. Allele frequencies were compared for cases and controls as well as for cleft subgroups and controls. ABCA4 rs540426 showed strong associations with CL/P, unilateral and right CL/P, and bilateral CL/P, whereas the SNP rs481931 showed borderline associations with CL/P and bilateral CL/P . No association was found for MAFB. Our results support a potential role for ABCA4 in the etiology of CL/P in individuals from Brazil.
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Affiliation(s)
- Clarissa Fontoura
- Department of Cell and Molecular Biology, Fluminense Federal University, Niteroi, RJ, Brazil
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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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