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Phan HDB, Phuong LH, Vu HA. Association of Single-Nucleotide Polymorphisms of MAFB Gene with Nonsyndromic Cleft Lip with or without Cleft Palate in Kinh Vietnamese Patients. Indian J Plast Surg 2022; 55:70-74. [PMID: 35444740 PMCID: PMC9015842 DOI: 10.1055/s-0041-1733809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background
Cleft lip with or without palate (CL/P) is the most common orofacial birth defect. Single-nucleotide polymorphisms (SNPs) in
MAFB
gene (V-Maf avian musculoaponeurotic fibrosarcoma oncogene homolog B) were identified as susceptible to this defect in a genome-wide association study. To further evaluate its role in this birth defect, we conducted this study with the aim of identifying allele frequencies, genotype frequencies, and association of SNPs rs13041247, rs6065259, and rs6072081 of
MAFB
gene with nonsyndromic cleft lip/palate (NCL/P) in Kinh Vietnamese patients.
Methods
We performed case–control study involved 79 patients with NCL/P and 77 healthy controls. DNAs were extracted from participants' saliva and tetra-amplification refractory mutation system polymerase chain reaction (tetra-ARMS PCR) was used for genotyping SNPs.
Results
SNPs of
MAFB
gene were genotyped using the Tetra-ARMS PCR method. We found that genotype CT of rs13041247 was associated with an increased risk of NCL/P in Kinh Vietnamese (odds ratio
TCTT
[OR
TC/TT
] = 1.63, 95% confidence interval [CI] = 0.83–3.19,
p
= 0.17). The G allele genotypes of SNP rs6072081 increase high risk for the malformation, statistically significant result (OR
GG/AA
= 7.06, 95% CI = 2.13–23.42,
p
< 0.001). There is no clear association between rs6065259 and CL/P (OR
AA/GG
= 0.75, 95% CI = 0.22–2.50,
p
= 0.32; OR
AG/GG
= 1.53, 95% CI = 0.79–2.97,
p
= 0.32). When the patients were divided into the phenotypic subgroups, there was a similar significant trend between the patients and controls for all SNPs.
Conclusions
Our study provides further evidence of role of
MAFB
gene variations with NCL/P defect in Kinh Vietnamese.
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Affiliation(s)
- Hoanh Duy Ba Phan
- Department of Oral and Maxillofacial Surgery, University Medical Center, Ho Chi Minh City, Vietnam
| | - Lam Hoai Phuong
- Department of Oral and Maxillofacial Surgery, University Medical Center, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
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2
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Abstract
Orofacial clefts (OFCs) are the most common congenital birth defects in humans and immediately recognized at birth. The etiology remains complex and poorly understood and seems to result from multiple genetic and environmental factors along with gene-environment interactions. It can be classified into syndromic (30%) and nonsyndromic (70%) clefts. Nonsyndromic OFCs include clefts without any additional physical or cognitive deficits. Recently, various genetic approaches, such as genome-wide association studies (GWAS), candidate gene association studies, and linkage analysis, have identified multiple genes involved in the etiology of OFCs. This article provides an insight into the multiple genes involved in the etiology of OFCs. Identification of specific genetic causes of clefts helps in a better understanding of the molecular pathogenesis of OFC. In the near future, it helps to provide a more accurate diagnosis, genetic counseling, personalized medicine for better clinical care, and prevention of OFCs.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth CS
- Department of Orthodontics & Dentofacial Orthopedics, DAPM R.V. Dental College, Bangalore, Karnataka, India
| | - Narasimha Murthy Srinath
- Department of Oral & Maxillofacial Surgery, Krishnadevaraya College of Dental Sciences, Bangalore, Karnataka, India
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3
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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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4
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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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He Y, Huang L, Zheng Y, Chen J, Tang S. Association of single nucleotide polymorphisms at 20q12 with nonsyndromic cleft lip with or without cleft palate in a Southern Chinese Han cohort. Mol Genet Genomic Med 2020; 8:e1028. [PMID: 31713353 PMCID: PMC6978266 DOI: 10.1002/mgg3.1028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/18/2019] [Accepted: 10/16/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation in the world. Both environment and genetics are involved with the etiology of the disease. Genome-wide association studies have identified two single nucleotide polymorphisms (SNPs) at chromosome 20q12 to be associated with NSCL/P. The current study aimed to explore the association of the two SNPs at 20q12 with NSCL/P and different subtypes in a Southern Chinese Han cohort. METHODS A total of 430 NSCL/P patients and 451 controls were recruited in the current study. Two SNPs including rs17820943 and rs6072081 at 20q12 were genotyped in the study cohort using Taqman SNP genotyping analysis. Chi-Square test was used to compare allele and genotype frequencies of NSCL/P patients and control group. RESULTS Case-control analysis showed that the allele and genotype of rs17820943 and rs6072081 were significantly associated with NSCL/P (p < .01). Comparison between subtypes of NSCL/P and controls showed that frequencies of the G allele and GG genotype of rs6072081 (p = 4.52 × 10-4 and p = .001 respectively), and those of the T allele and TT genotype of rs17820943 (p = 6.7 × 10-5 and p = 1.71 × 10-4 respectively) were decreased in cleft lip and palate (CLP). No significant association of the two SNPs with cleft lip only (CLO) and cleft palate only (CPO) was found (p > .05). CONCLUSION These results showed that rs17820943 and rs6072081 at 20q12 were associated with NSCL/P, especially with the CLP subtype in a Southern Chinese Han cohort.
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Affiliation(s)
- Yunpu He
- Department of Plastic Surgery and Burn CenterThe Second Affiliated HospitalShantou University Medical CollegeShantouGuangdongChina
| | - Liheng Huang
- Department of AnesthesiologyShantou Central HospitalShantouGuangdongChina
| | - Yuqian Zheng
- Joint Shantou International Eye Center of Shantou UniversityChinese University of Hong KongShantouGuangdongChina
| | - Jian‐Huan Chen
- Joint Shantou International Eye Center of Shantou UniversityChinese University of Hong KongShantouGuangdongChina
- Laboratory of Genomic and Precision MedicineWuxi School of MedicineJiangnan UniversityWuxiJiangsuChina
| | - Shijie Tang
- Department of Plastic Surgery and Burn CenterThe Second Affiliated HospitalShantou University Medical CollegeShantouGuangdongChina
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6
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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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7
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Yin X, Ma L, Li Y, Xu M, Wang W, Wang H, Yuan H, Du Y, Li S, Ma J, Jiang H, Wang L, Zhang W, Pan Y. Genetic variants of 20q12 contributed to non-syndromic orofacial clefts susceptibility. Oral Dis 2016; 23:50-54. [PMID: 27537108 DOI: 10.1111/odi.12570] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/29/2016] [Accepted: 08/14/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Previous genomewide association studies (GWAS) identified a region near MAFB at chr20q12 associated with non-syndromic orofacial clefts (NSOC) susceptibility. However, whether other SNPs in this area could independently contribute to non-syndromic orofacial clefts in Chinese populations remained obscure. MATERIALS AND METHODS We selected 24 SNPs based on a haplotype-tagging SNP strategy and evaluated their associations with risk of non-syndromic orofacial clefts in a large-scale two-stage case-control study with 1278 cases and 1295 controls. Genotyping was performed with Sequenom and TaqMan assay. Associations between the SNPs and risk of non-syndromic orofacial clefts were estimated from unconditional logistic regression analyses. RESULTS Overall, six SNPs were found to be the susceptible factors of non-syndromic orofacial clefts. The most significant and independent SNP was rs6129653 (additive model of P value = 1.4E-06). In subgroup analysis, its significant associations with cleft lip only (CLO) and cleft lip and palate (CLP) were observed. Furthermore, in silico bioinformatics analysis indicated that rs6129653 was located in the transcriptionally active region and associated with MAFB expression in human brain tissues. CONCLUSIONS Rs6129653 was an independent locus of non-syndromic orofacial clefts among Chinese populations possibly due to its potential of distal transcriptional regulation of MAFB expression.
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Affiliation(s)
- X Yin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Y Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - M Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - W Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - H Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - H Yuan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Y Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - S Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - J Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - H Jiang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - L Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - W Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
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