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Wang Q, Qin T, Tan H, Ding X, Lin X, Li J, Lin Z, Sun L, Lin H, Chen W. Broadening the genotypic and phenotypic spectrum of MAF in three Chinese Han congenital cataracts families. Am J Med Genet A 2022; 188:2888-2898. [PMID: 36097645 DOI: 10.1002/ajmg.a.62947] [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: 02/21/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 01/31/2023]
Abstract
Pathogenic variants in the v-maf avian musculoaponeurotic fibrosarcoma oncogene homologue (MAF) encoding a transcription factor (from a unique subclass of basic leucine zipper transcription factors) are associated with isolated congenital cataracts (CCs) and Aymé-Gripp syndrome (AYGRPS). We collected detailed disease histories from, and performed comprehensive ophthalmic and systemic examinations in 269 patients with CCs; we then performed whole-exome sequencing. Pathogenicity assessments were evaluated using multiple predictive tools. The clinical validities of the reported gene-disease relationships for MAF genes (MAF-CCs and MAF-AYGRPS) were assessed using the ClinGen gene curation framework. We identified two novel (c.173C>A, p.Thr58Asn and c.947T>C, p. Leu316Pro) variants and one known (c.173C>T, p.Thr58Ile) MAF missense variant in three patients. We described novel phenotypes including cleft palate, macular hypoplasia, and retinal neovascularization in the peripheral avascular area and analyzed the genotype-phenotype correlations. We demonstrated associations of variants in the MAF C-terminal DNA-binding domain with CCs and associations of variants in the N-terminal transactivation domain of MAF with AYGRPS. We thus expand the genotypic and phenotypic spectrum of the MAF gene. The ClinGen gene curation framework results suggested that variants in different domains of MAF are associated with different diseases.
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Affiliation(s)
- Qiwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Tingfeng Qin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | | | - Xiaoyan Ding
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Xiaoshan Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Zhuolin Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Limei Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
| | - Weirong Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Centre, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangdong Provincial Clinical Research Centre for Ocular Diseases, Guangzhou, China
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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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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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Nasreddine G, El Hajj J, Ghassibe-Sabbagh M. Orofacial clefts embryology, classification, epidemiology, and genetics. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2021; 787:108373. [PMID: 34083042 DOI: 10.1016/j.mrrev.2021.108373] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 01/14/2023]
Abstract
Orofacial clefts (OFCs) rank as the second most common congenital birth defect in the United States after Down syndrome and are the most common head and neck congenital malformations. They are classified as cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO). OFCs have significant psychological and socio-economic impact on patients and their families and require a multidisciplinary approach for management and counseling. A complex interaction between genetic and environmental factors contributes to the incidence and clinical presentation of OFCs. In this comprehensive review, the embryology, classification, epidemiology and etiology of clefts are thoroughly discussed and a "state-of-the-art" snapshot of the recent advances in the genetics of OFCs is presented.
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Affiliation(s)
- Ghenwa Nasreddine
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
| | - Joelle El Hajj
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
| | - Michella Ghassibe-Sabbagh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, P.O. Box: 13-5053, Chouran, 1102 2801, Beirut, Lebanon.
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Polymorphisms of ATP-Binding Cassette, Sub-Family A, Member 4 (rs560426 and rs481931) and Non-Syndromic Cleft Lip/Palate: A Meta-Analysis. Life (Basel) 2021; 11:life11010058. [PMID: 33467554 PMCID: PMC7830788 DOI: 10.3390/life11010058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/19/2020] [Accepted: 01/07/2021] [Indexed: 12/29/2022] Open
Abstract
Background: A number of genes are associated with the incidence of non-syndromic cleft lip/palate (NSCL/P). Studies have shown a significant association between polymorphisms of ATP-binding cassette, sub-family A, member 4 (ABCA4) with the risk of NSCL/P. The present meta-analysis assessed the association between ABCA4 polymorphisms (rs560426 and rs481931) and the NSCL/P risk by reviewing case-control studies. Methods: Four databases (Scopus; Cochrane Library; Web of Science; and PubMed) were searched for articles published up to June 2020. The Review Manager 5.3 software was used to calculate the crude odds ratio (OR) and 95% confidence interval (CI). Both subgroup analyses for ethnicity and source of controls and a meta-regression related to publication year were conducted. Results: Of 94 retrieved studies, 12 were analyzed in this meta-analysis (2859 NSCL/P patients and 3792 controls for ABCA4 rs560426 polymorphism and 1333 NSCL/P patients and 1884 controls for ABCA4 rs481931 polymorphism). Overall, there was no significant association between both polymorphisms and the risk of NSCL/P. However, subgroup analysis demonstrated that there was a higher risk of NSCL/P for specific models: the allelic model (OR = 1.13; p = 0.03), the homozygote model (OR = 1.53; p = 0.04), and the recessive model (OR = 1.30; p = 0.03) in the Asian ethnicity for the rs560426 polymorphism. Conclusion: The findings confirmed that the NSCL/P risk was significantly associated with the G allele and GG genotype of rs560426 polymorphism but not for rs481931 polymorphism. There were no associations between both polymorphisms (rs560426 and rs481931) and the NSCL/P risk in those of European descent and the mixed ethnicities.
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Li MX, Li Z, Zhang R, Yu Y, Wang LS, Wang Q, Ding Z, Zhang JP, Zhang MR, Xu LC. Effects of small interfering RNA-mediated silencing of susceptibility genes of non-syndromic cleft lip with or without cleft palate on cell proliferation and migration. Int J Pediatr Otorhinolaryngol 2020; 138:110382. [PMID: 33152973 DOI: 10.1016/j.ijporl.2020.110382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Non-syndrome cleft lip with or without cleft palate (NSCL/P) is the most common congenital defect with a complex etiology involving both genetic and environmental factors. Our previous research has identified susceptibility genes of NSCL/P using whole-exome sequencing. The study was to determine the effects of small interfering RNA (siRNA)-mediated silencing of genes on cell proliferation and migration to confirm the roles of the genes in NSCL/P. METHODS We silenced the genes by RNA interference (RNAi) with siRNA in human oral keratinocyte (HOK). We used the Cell Counting Kit-8 (CCK8) assay to determine cell proliferation and the wound healing assay to determine cell migration. RESULTS Migration of HOK was inhibited by RNAi-induced silencing of adenosine triphosphate binding cassette transporter A4 (ABCA4), erythropoietin produces hepatocyte A receptor 3 (EPHA3), alpha-parvin (PARVA), and platelet-derived growth factor C (PDGFC). The change of proliferation was not found. Treated with siRNA-mediated silencing of type IV collagen (COL4A2), eukaryotic translation initiation factor 2B subunit (EIF2B3), fibroblast growth factor receptor 2 (FGFR2), kinesin family member 20B (KIF20B), β-lactamase serine-like protein (LACTB), SEC16 homolog A (SEC16A) and thyroid adenoma target gene (THADA) had no effects on cell proliferation and migration of HOK. CONCLUSIONS We suggest mutations of the four susceptibility genes ABCA4, EPHA3, PARVA and PDGFC are involved in NSCL/P through inhibiting cell migration. The study provides new candidates for future study of NSCL/P.
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Affiliation(s)
- Meng-Xue Li
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Zheng Li
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Rui Zhang
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Yue Yu
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Lu-Shan Wang
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Qi Wang
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Zhen Ding
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Jin-Peng Zhang
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Mei-Rong Zhang
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China
| | - Li-Chun Xu
- Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004, 209 Tong-Shan Road, Xuzhou, Jiangsu, China.
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Liang X, Huang L, Ou Y, He Y, Tang S. Association between MAFB rs17820943 and rs6072081 polymorphism and risk of nonsyndromic cleft lip with or without cleft palate: a meta-analysis. Br J Oral Maxillofac Surg 2020; 58:1065-1072. [PMID: 32646788 DOI: 10.1016/j.bjoms.2020.05.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 05/20/2020] [Indexed: 02/05/2023]
Abstract
While there have been previous studies examining the relation between the rs17820943 and rs6072081 polymorphisms in the v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) gene and rates of nonsyndromic cleft lip with or without cleft palate (NSCL/P), at present the results of these studies have been inconsistent. This meta-analysis therefore aimed to conduct a more robust assessment of the association between the MAFB rs17820943 and rs6072081 polymorphisms and NSCL/P risk. The Embase, Web of Science, PubMed, the China National Knowledge Internet (CNKI), and Wanfang databases were systematically searched to identify relevant studies. In total, five studies incorporating 2769 patients and 2885 controls were identified assessing the rs17820943 polymorphism and three studies incorporating 1242 patients and 1310 controls assessing the rs6072081 polymorphism were identified. This analysis revealed the MAFB rs17820943 and rs6072081 polymorphisms to be linked to a significantly reduced NSCL/P risk (rs17820943: C vs T: OR=0.76, 95% CI=0.70-0.82; CC vs CT: OR=0.75, 95% CI=0.67-0.85; CC vs TT: OR=0.58, 95% CI=0.49-0.67; CC+CT vs TT: OR=0.67, 95% CI=0.59-0.77; CT+TT vs CC: OR=1.43, 95% CI=1.28-1.60; rs6072081: A vs G: OR=0.77, 95%CI=0.68-0.86; AA vs AG: OR=0.76, 95%CI=0.64-0.90; AA vs GG: OR=0.58, 95%CI=0.45-0.74; AA+AG vs GG: OR=0.68, 95%CI=0.54-0.84; AG+GG vs AA: OR=1.40, 95% CI=1.19-1.65). The results of the present meta-analysis indicate that in an East Asian population, for both rs17820943 and rs6072081 were associated with NSCL/P.
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Affiliation(s)
- X Liang
- Department of Dermatology, Maoming People's Hospital, Maoming, Guangdong, 525000, China.
| | - L Huang
- Department of Anesthesiology, Shantou Central Hospital, Shantou, Guangdong, 515041, China.
| | - Y Ou
- Department of Plastic Surgery and Burn Center, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - Y He
- Department of Plastic Surgery and Burn Center, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - S Tang
- Department of Plastic Surgery and Burn Center, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, 515041, China.
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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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Wu-Chou YH, Chen KTP, Lu YC, Lin YT, Chang HF, Lo LJ. The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts. Cleft Palate Craniofac J 2020; 57:671-677. [PMID: 31950859 DOI: 10.1177/1055665619899764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE Nonsyndromic oral clefts are common birth defect with complex etiology. In the present study, we attempt to further validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. DESIGN We performed allelic transmission disequilibrium test analysis, on 10 eligible single nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test. PARTICIPANTS The study sample consisted of 334 case-parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. RESULTS We found only the SNP rs560426 within the ABCA4 gene showed strong association with NSCPO (P = .03498; Permuted P = .05382). No association between other 9 selected SNPs in ABCA4-ARHGAP29 region and the risk of nonsyndromic oral clefts was found. For the haplotype analyses, we found only haplotype T-C (rs570926 and rs3789431) in ABCA4 block 2 showed significant association with nonsyndromic NSCL/P in these Taiwanese trios. CONCLUSIONS We used a family-based analysis in 334 Taiwanese case-parent trios to validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. This study provides a new evidence for an association between the intron variant rs560426 within ABCA4 and nonsyndromic cleft palate which may contribute their regulatory role in craniofacial development.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ting Philip Chen
- Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Chieh Lu
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yin-Ting Lin
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsien-Fang Chang
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lun-Jou Lo
- Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Dental and Craniofacial Science, Chang Gung University, Taoyuan, Taiwan
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10
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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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11
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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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12
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Kan S, Zhu G, Du Y, Fan L, Yang F, Lou S, Li D, Ma L, Pan Y. Non-syndromic cleft lip with or without palate-susceptible SNPs is associated with hyperdontia. Oral Dis 2019; 25:1751-1758. [PMID: 31233659 DOI: 10.1111/odi.13149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Non-syndromic supernumerary teeth (NSST) or hyperdontia may share common genetic determinants with non-syndromic cleft lip with or without palate (NSCL/P). The aim of this study was to test the associations between five genome-wide-associated NSCL/P-susceptible single nucleotide polymorphisms (SNPs) (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) and the occurrence of NSST. MATERIALS AND METHODS A total of 163 cases and 326 controls were recruited and their genomic DNA was extracted from blood samples. Five NSCL/P-susceptible SNPs (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) were genotyped by TaqMan method. Odds ratio (OR) and 95% confidence interval (CI) were used to estimate the associations between the SNPs and the risk of NSST by PLINK software. RESULTS Rs4791774 (A > G) and rs13041247 (T > C) were associated with risk of NSST (rs4791774: Padd = 0.011, OR, 95% CI = 0.62, 0.43-0.90; rs13041247: Phomo = 0.031, OR, 95% CI = 1.79, 1.05-3.05) and one supernumerary tooth (rs4791774: Pdom = 0.009, OR, 95% CI = 0.56, 0.36-0.87; rs13041247: Phomo = 0.034, OR, 95% CI = 1.82, 1.05-3.15). Rs4791774 (A > G) was also showed association with risk of upper arch supernumerary teeth only (Padd = 0.010, OR, 95% CI = 0.60, 0.41-0.89). CONCLUSION Non-syndromic cleft lip with or without palate-susceptible loci rs4791774 (A > G) and rs13041247 (T > C) were associated with the risk of supernumerary teeth.
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Affiliation(s)
- Shiyi Kan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yifei Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Oral-maxillary surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Fan Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yongchu 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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13
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Ge X, Hong JW, Shen JY, Li Z, Zhang R, Wang Q, Ding Z, Chen G, Xu LC. Investigation of candidate genes of non-syndromic cleft lip with or without cleft palate, using both case-control and family-based association studies. Medicine (Baltimore) 2019; 98:e16170. [PMID: 31261547 PMCID: PMC6617431 DOI: 10.1097/md.0000000000016170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE Non-syndromic cleft of the lip and/or palate (NSCL/P) is one of the most common polygenic diseases. In this study, both case-control and family-based association study were used to confirm whether the Single Nucleotide Polymorphisms (SNPs) were associated with NSCL/P. METHODS A total of 37 nuclear families and 189 controls were recruited, whose blood DNA was extracted and subjected to genotyping of SNPs of 27 candidate genes by polymerase chain reaction-improved multiple ligase detection reaction technology (PCR-iMLDR). Case-control statistical analysis was performed using the SPSS 19.0. Haplotype Relative Risk (HRR), transmission disequilibrium test (TDT), and Family-Based Association Test (FBAT) were used to test for over-transmission of the target alleles in case-parent trios. The gene-gene interactions on NSCL/P were analyzed by Unphased-3.1.4. RESULTS In case-control statistical analysis, only C14orf49 chr14_95932477 had statistically significant on genotype model (P = .03) and allele model (P = .03). Seven SNPs had statistically significant on TDT. None of 26 alleles has association with NSCL/P on FBAT. Some SNPs had haplotype-haplotype interactions and genotype-genotype interactions. CONCLUSION C14orf49 chr14_95932477 was significantly different between cases and controls on genotype model and allele model by case-control design. Seven SNPs were significantly different on HRR. Four SNPs were significantly different on TDT.
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14
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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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15
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Peng HH, Chang NC, Chen KT, Lu JJ, Chang PY, Chang SC, Wu-Chou YH, Chou YT, Phang W, Cheng PJ. Nonsynonymous variants in MYH9 and ABCA4 are the most frequent risk loci associated with nonsyndromic orofacial cleft in Taiwanese population. BMC MEDICAL GENETICS 2016; 17:59. [PMID: 27527345 PMCID: PMC4986225 DOI: 10.1186/s12881-016-0322-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 06/10/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Nonsyndromic orofacial cleft is a common birth defect with a complex etiology, including multiple genetic and environmental risk factors. Recent whole genome analyses suggested associations between nonsyndromic orofacial cleft and up to 18 genetic risk loci (ABCA4, BMP4, CRISPLD2, GSTT1, FGF8, FGFR2, FOXE1, IRF6, MAFB, MSX1, MTHFR, MYH9, PDGFC, PVRL1, SUMO1, TGFA, TGFB3, and VAX1), each of which confers a different relative risk in different populations. We evaluate the nonsynonymous variants in these 18 genetic risk loci in nonsyndromic orofacial clefts and normal controls to clarify the specific variants in Taiwanese population. METHODS We evaluated these 18 genetic risk loci in 103 cases of nonsyndromic orofacial clefts and 100 normal controls using a next-generation sequencing (NGS) customized panel and manipulated a whole-exon targeted-sequencing study based on the NGS system of an Ion Torrent Personal Genome Machine (IT-PGM). IT-PGM data processing, including alignment with the human genome build 19 reference genome (hg19), base calling, trimming of barcoded adapter sequences, and filtering of poor signal reads, was performed using the IT platform-specific pipeline software Torrent Suite, version 4.2, with the plug-in "variant caller" program. Further advanced annotation was facilitated by uploading the exported VCF file from Variant Caller to the commercial software package Ion Reporter; the free online annotation software Vanno and Mutation Taster. Benign or tolerated amino acid changes were excluded after analysis using sorting intolerant from tolerant and polymorphism phenotyping. Sanger sequencing was used to validate the significant variants identified by NGS. Furthermore, each variant was confirmed in asymptomatic controls using the Sequenom MassARRAY (San Diego, CA, USA). RESULTS We identified totally 22 types of nonsynonymous variants specific in nonsyndromic orofacial clefts, including 19 single nucleotide variants, 2 deletions, and 1 duplication in 10 studied genes(ABCA4, MYH9, MTHFR, CRISPLD2, FGF8, PVRL1, FOXE1, VAX1, FGFR2, and IRF6). Nonsynonymous variants in MYH9 and ABCA4, which were detected in 6 and 5 individuals, respectively, were identified to be the most frequent risk loci in nonsyndromic orofacial clefts in the Taiwanese population. CONCLUSIONS Nonsynonymous variants in MYH9 and ABCA4 were identified to be the most frequent risk loci in nonsyndromic orofacial clefts in the Taiwanese population. These findings in our study have provided additional information regarding specific variants associated with nonsyndromic orofacial clefts in different population and demonstrate the power of our customized NGS panel, which is clinically useful for the simultaneous detection of multiple genes associated with nonsyndromic orofacial clefts.
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Affiliation(s)
- Hsiu-Huei Peng
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Nai-Chung Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Kuo-Ting Chen
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Plastic and Reconstructive surgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yah-Huei Wu-Chou
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yi-Ting Chou
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wanni Phang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Po-Jen Cheng
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan. .,Chang Gung University College of Medicine, Taoyuan, Taiwan.
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16
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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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17
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Yin X, Zhang H, Zhu Z, Wang H, Du Y, Li S, Zhang Z, Fan W, Pan Y. FOXE1 polymorphisms and non-syndromic orofacial cleft susceptibility in a Chinese Han population. Oral Dis 2016; 22:274-9. [PMID: 26728781 DOI: 10.1111/odi.12435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVE FOXE1 plays an important role in craniofacial development. The aim of this study was to investigate associations between genetic variants of FOXE1 and risk of non-syndromic orofacial clefts in a Chinese population. MATERIALS AND METHODS Three potentially functional SNPs of FOXE1 (rs3758250 and rs907577 in the 5' upstream and rs7043516 in the 3'-UTR) were selected and their associations with non-syndromic orofacial cleft susceptibility were investigated in a case-control study from a Chinese population (602 cases and 605 controls). Genotyping was performed with double ligation and multiplex fluorescence PCR. Associations between the SNPs and risk of non-syndromic orofacial clefts and its subgroups were estimated from unconditional logistic regression analysis. Luciferase reporter assay was conducted to assess SNP function. RESULTS Overall, we did not find any of the individual SNP or haplotype was associated with NSOC susceptibility. Nevertheless, in stratified analysis, we found rs7043516, locating in the 3'-UTR of FOXE1, was associated with risk of cleft lip only. Further in vitro luciferase assay indicated that this SNP could contribute to differential binding ability with miRNA. CONCLUSIONS Taken together, this study showed that rs7043516 may be considered as a potentially susceptible marker of cleft lip only among Chinese Han populations.
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Affiliation(s)
- X Yin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - H Zhang
- Xuzhou First People's Hospital, Xuzhou, China
| | - Z Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - H Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Y Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - S Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Z Zhang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - W Fan
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
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18
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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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do Rego Borges A, Sá J, Hoshi R, Viena CS, Mariano LC, de Castro Veiga P, Medrado AP, Machado RA, de Aquino SN, Messetti AC, Spritz RA, Coletta RD, Reis SRA. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry. Am J Med Genet A 2015. [DOI: 10.1002/ajmg.a.37181] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea do Rego Borges
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Jamile Sá
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Ryuichi Hoshi
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Camila Sane Viena
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Lorena C. Mariano
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Patricia de Castro Veiga
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Alena Peixoto Medrado
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | | | - Ana Camila Messetti
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program; University of Colorado School of Medicine; Aurora Colorado
| | - Ricardo D. Coletta
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Silvia R. A. Reis
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
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A polymorphic marker associated with non-syndromic cleft lip with or without cleft palate in a population in Heilongjiang Province, northern China. Arch Oral Biol 2014; 60:357-61. [PMID: 25499508 DOI: 10.1016/j.archoralbio.2014.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 09/24/2014] [Accepted: 11/16/2014] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To further assess the roles of the ABCA4 (ATP-binding cassette, sub-family A, member 4) gene in NSCL/P, we investigated two tag SNPs in ABCA4 (rs481931 and rs560426) in a northern Chinese Han population where the prevalence of NSCL/P is high. MATERIALS AND METHODS The two SNPs were examined for association with NSCL/P in 344 patients and 324 healthy controls. Peripheral blood samples were acquired at study enrollment, and DNA samples were extracted. SNPs were genotyped using a mini-sequencing (SNAPSHOT) method. RESULTS We observed a significant correlation between the ABCA4 SNP rs560426 and NSCL/P (p=0.0041) but no evidence of association between rs481931 and NSCL/P. The G/G genotype at the rs560426 SNP in ABCA4 gene had an odd ratios of 2.39 (95%CI: 1.38-4.14, p=0.0041) compared with the A/A genotype, and a similar significance was noted in the CL/P subgroup (ORA/G=1.60, 95%CI: 1.09-2.34, ORG/G=2.96, 95%CI: 1.63-5.37 and ORG/G+A/G=1.80, 95%CI: 1.25-2.60, p=0.0007). CONCLUSIONS Our study provides further evidence regarding the roles of genetic markers in ABCA4 in NSCL/P development in this northern Chinese Han population. G allele of rs560426 may be a risk factor for developing NSCL/P.
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Mi N, Hao Y, Jiao X, Zheng X, Song T, Shi J, Dong C. Association study of single nucleotide polymorphisms of MAFB with non-syndromic cleft lip with or without cleft palate in a population in Heilongjiang Province, northern China. Br J Oral Maxillofac Surg 2014; 52:746-50. [PMID: 24972815 DOI: 10.1016/j.bjoms.2014.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP) is a common complex birth defect. MAFB (v-maf musculoaponeurotic fibrosarcoma oncogene homolog B) is a new gene that may be involved in susceptibility to cleft lip with or without cleft palate (CL/P). To further assess its role in NSCLP, we investigated 3 identified single nucleotide polymorphisms in MAFB (rs13041247, rs6065259, and rs11696257) and examined them for association with NSCLP in 344 patients and 324 healthy controls in a northern Chinese Han population with a high incidence of the syndrome. Peripheral blood samples were taken when patients enrolled in the study and DNA samples were extracted from the blood. The 3 single nucleotide polymorphisms were genotyped using a mini-sequencing method (Snapshot(®) Multiplex System for SNP genotyping, Life Technologies Ltd, Paisley, UK). We found that rs6065259 was the most important single nucleotide polymorphism in MAFB (OR6065259-AA=0.45; 95% CI: 0.28 to 0.71; p=0.0027), followed by rs13041247; however, no association was found between rs11696257 and NSCLP. Our study provides further evidence regarding the role of MAFB variations in the development of NSCLP in this northern Chinese Han population.
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Affiliation(s)
- Na Mi
- The Department of Oral Maxillofacial Surgery, College of Stomatology, Harbin Medical University, Harbin, China.
| | - Yanru Hao
- The Department of Oral Maxillofacial Surgery, College of Stomatology, Harbin Medical University, Harbin, China.
| | - Xiaohui Jiao
- The Department of Oral Maxillofacial Surgery, College of Stomatology, Harbin Medical University, Harbin, China.
| | - Xudong Zheng
- The medical department, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Tao Song
- The Department of Oral Maxillofacial Surgery, College of Stomatology, Harbin Medical University, Harbin, China.
| | - Jinna Shi
- The Department of Periodontology, The First Affiliated Hospital, Harbin Medical University, Harbin, China.
| | - Chen Dong
- The Department of Oral Maxillofacial Surgery, College of Stomatology, Harbin Medical University, Harbin, China.
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Leslie EJ, Marazita ML. Genetics of cleft lip and cleft palate. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:246-58. [PMID: 24124047 DOI: 10.1002/ajmg.c.31381] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.
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Bagordakis E, Paranaiba LMR, Brito LA, de Aquino SN, Messetti AC, Martelli-Junior H, Swerts MSO, Graner E, Passos-Bueno MR, Coletta RD. Polymorphisms at regions 1p22.1 (rs560426) and 8q24 (rs1530300) are risk markers for nonsyndromic cleft lip and/or palate in the Brazilian population. Am J Med Genet A 2013; 161A:1177-80. [PMID: 23532876 DOI: 10.1002/ajmg.a.35830] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 12/02/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Elizabete Bagordakis
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
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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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Huang E, Cheng H, Xu M, Shu S, Tang S. Association between single-nucleotide polymorphisms on chromosome 1p22 and 20q12 and nonsyndromic cleft lip with or without cleft palate: new data in Han Chinese and meta-analysis. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2012; 94:469-76. [PMID: 22522387 DOI: 10.1002/bdra.23013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 03/04/2012] [Accepted: 03/07/2012] [Indexed: 02/05/2023]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation associated with genetic and environmental risk factors. A recent genome-wide association study identified two novel susceptibility loci on chromosomes 1p22 and 20q12; however, conflicting results, especially for 1p22, have been reported in Han Chinese population. The aims of this study were to replicate this association with risk of NSCL/P in the southern Han Chinese population and to discern the effect of these loci by a meta-analysis. METHODS To this end, 305 patients with NSCL/P, 356 phenotypically normal controls, and an additional 176 case-parent trios were recruited. Four of the previously associated single nucleotide polymorphisms (SNPs) were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Furthermore, two published datasets were combined with the present results to determine the precise roles of the loci. RESULTS SNPs (rs6072081, rs13041247, and rs6102085) on 20q12 were found to be strongly associated with NSCL/P (Bonferroni-corrected and χ(2) test; p values < 0.05). Subsequent analysis of the case-parent trio provided similar results. However, neither the association study nor the trio analysis supported a causative role for SNP rs560426 on 1p22 in NSCL/P susceptibility. Stratified meta- analysis combining Chinese samples supported our findings. CONCLUSIONS This cross-validation study confirmed the previous findings that SNPs in 20q12 are associated with NSCL/P in Han Chinese population. We further conclude that rs560426 on 1p22 might not have a major influence on susceptibility to NSCL/P in southern Han Chinese, but future studies with other Han Chinese populations are needed.
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Affiliation(s)
- Enmin Huang
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, People's Republic of China
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