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Zawiślak A, Woźniak K, Kawala B, Gupta S, Znamirowska-Bajowska A, Janiszewska-Olszowska J, Lubiński J, Calvo-Guirado JL, Grocholewicz K, Jakubowska A. IRF6 and FGF1 polymorphisms in non-syndromic cleft lip with or without cleft palate in the Polish population. Open Med (Wars) 2023; 18:20230677. [PMID: 37020525 PMCID: PMC10068750 DOI: 10.1515/med-2023-0677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 04/05/2023] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is the most common developmental defect that significantly affects the morphology and function of the stomatognathic system in children. The etiology of these birth defects is multifactorial, and single nucleotide polymorphisms (SNPs) in IRF6 and FGF1 have been associated with NSCL/P. This study aimed to evaluate whether SNPs in IRF6, namely rs2013162, rs642961, rs2235373, and rs34010 in FGF1, are associated with NSCL/P occurrence in the Polish population. The study included 627 participants: 209 children with NSCL/P and 418 healthy controls. DNA was isolated from saliva in the study group and from umbilical cord blood in controls. Genotyping of polymorphisms was performed using quantitative PCR. There was no statistically significant association of IRF6 gene variants with NSCL/P occurrence, although for rs2013162, AA genotype, odds ratio (OR) = 1.16 and for AC genotype, OR = 0.83; for rs642961, AA genotype, OR = 0.84 and for AG genotype, OR = 1.41; and for rs2235373, AA genotype, OR = 0.79 and for AG, OR = 0.85. In the instance of rs34010 polymorphism in FGF1, the presence of the AA genotype was statistically significant in reducing the risk of NSCL/P (OR = 0.31, p = 0.001). Genetic variation in FGF1 is an important risk marker of NSCL/P in the Polish population, which cannot be stated for the polymorphisms in the IRF6 gene.
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Affiliation(s)
- Alicja Zawiślak
- Department of Maxillofacial Orthopaedics and Orthodontics, Institute of Mother and Child, 01-211 Warsaw, Poland
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Krzysztof Woźniak
- Department of Orthodontics, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Beata Kawala
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland
| | - Satish Gupta
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Znamirowska-Bajowska
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland
| | | | - Jan Lubiński
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - José Luis Calvo-Guirado
- Department of Oral Surgery and Implant Dentistry, Faculty of Health Sciences, Universidad Católica de Murcia, UCAM, 30107, Murcia, Spain
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Jakubowska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
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das Neves LT, de Carvalho IMM, Cobourne MT, Gomide MR. Dental anomalies in non-syndromic orofacial clefts: a clinical approach. Oral Dis 2022; 28:1351-1368. [PMID: 35485181 DOI: 10.1111/odi.14226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/28/2022]
Abstract
Orofacial clefts (OC) represent some of the most common congenital malformations and affect multiple structures in the craniofacial region. There are a wide range of morphological OC types within the spectrum of both non-syndromic OC (NSOC) and syndromic OC, including cleft lip (CL); cleft lip and palate (CLP) and cleft palate (CP). Here, we describe the most frequent dental anomalies seen in the permanent dentition of individuals with NSOC, comparing them between the three main cleft types (CL, CLP, CP). We present these findings from the perspective of prevalence relating to each anomaly, as well as the clinical characteristics and potential impact in the rehabilitation process. The investigation of dental anomalies associated with NSOC is important, helping to expand the phenotypic characterization of NSOC, improve initial diagnostics and establish appropriate rehabilitation and counseling.
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Affiliation(s)
- Lucimara Teixeira das Neves
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil.,Bauru School of Dentistry, University of Sao Paulo, Department of Biological Science - FOB/USP), Bauru, Brazil
| | | | - Martyn T Cobourne
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, Guy's Hospital, London, UK.,Department of Orthodontics, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Marcia Ribeiro Gomide
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
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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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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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Li Y, Deng Y, Deng C, Xie L, Yu L, Liu L, Yuan Y, Liu H, Dai L. Association of long interspersed nucleotide element-1 and interferon regulatory factor 6 methylation changes with nonsyndromic cleft lip with or without cleft palate. Oral Dis 2018; 25:215-222. [PMID: 30153397 DOI: 10.1111/odi.12965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/09/2018] [Accepted: 07/04/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To examine the possible associations between methylation changes in the promoter regions of long interspersed nucleotide element-1 (LINE-1) and interferon regulatory factor 6 gene (IRF6) and nonsyndromic cleft lip with or without cleft palate (NSCL/P). METHODS A case-control investigation was performed to compare 37 infants affected by NSCL/Ps with 60 babies without cleft malformations. Their genomic DNA samples were obtained, and the LINE-1 and IRF6 methylation levels were measured by using Sequenom MassArray. Unconditional logistic regression was adopted to estimate the odds ratio. RESULTS Infants with NSCL/Ps had a higher methylation level at LINE-1 and IRF6 promoter regions than controls. High levels of LINE-1 (≥64.07%) and IRF6 (≥6.46%) methylation were associated with an increased risk of NSCL/P (LINE-1, OR = 2.63, 95% CI: 1.07-6.57; IRF6, OR = 4.73, 95% CI: 2.10-13.07), and the associations remained to be significant after adjusting for potential confounders. Similar associations were also found for cleft lip only, cleft lip, and palate. CONCLUSION Our study suggested that aberrant methylation of LINE-1 and IRF6 might contribute to the development of NSCL/Ps. Further studies are needed to replicate the findings.
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Affiliation(s)
- Yanhua Li
- Obstetric and Gynecologic Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Deng
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Changfei Deng
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Liang Xie
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Yu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lijun Liu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yumei Yuan
- Hengyang Women and Children Hospital, Hengyang, China
| | - Hanmin Liu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Dai
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
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Zhang BH, Huang N, Shi JY, Shi B, Jia ZL. Homozygote C/C at rs12543318 was risk factor for non-syndromic cleft lip only from Western Han Chinese population. J Oral Pathol Med 2018; 47:620-626. [PMID: 29683526 DOI: 10.1111/jop.12719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 02/05/2023]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a complex disorder, and it results from both of the genetic modifiers and environmental factors, with genetic modifiers contributes to it more than environmental factors. GWASs made great progress in identifying the candidate genes for NSCL/P, but the findings need to be replicated in other populations. In this study, we selected eleven SNPs from recent GWASs and GWAS meta-analysis to investigate their associations among 308 NSCL/P trios (134 non-syndromic cleft lip only (NSCLO) trios and 174 non-syndromic cleft lip with cleft palate (NSCLP) trios) from Han Chinese population. All SNPs were genotyped using SNPscan method and analyzed the data with FBAT, PLINK, and R package. Allelic TDT analysis showed that allele A at rs12543318 was associated with NSCLO trios (P = .0032, OR = 0.57, 95% CI: 0.39-0.83), and parent-of-origin effect analysis indicated that allele A at rs12543318 was significantly maternally undertransmitted among NSCLO (P = .0046), which implied the potential influence of genomic imprinting; global TDT further confirmed this association. Individual genotypic TDT showed homozygote C/C at rs12543318 was overtransmitted among NSCLO (Z = 3.79, P = .00015) and NSCL/P groups (Z = 3.83, P = .00013), which indicated that it could increase the risk to have cleft babies. Our findings indicated that rs12543318 was associated with NSCLO from Western Han Chinese population, which will give new scientific evidence for later researches in the etiology of NSOCs.
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Affiliation(s)
- Bi-He Zhang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ning Huang
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases, Department of Cleft Lip and Palate, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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7
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Maternal active smoking and risk of oral clefts: a meta-analysis. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 122:680-690. [PMID: 27727103 DOI: 10.1016/j.oooo.2016.08.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/20/2016] [Accepted: 08/08/2016] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To assess the association between maternal active cigarette smoking and the risk of oral clefts in the offspring. STUDY DESIGN Oral clefts are divided into three subgroups: total clefts, cleft lip with or without cleft palate (CL ± P), and cleft palate only (CP). Data from studies on different levels of smoking were gathered to examine the dose-response effect. RESULTS The present meta-analysis included 29 case-control and cohort studies through Cochrane, PubMed, and Ovid Medline searches. A modest but statistically significant association was found between maternal active smoking and CL ± P (odds ratio [OR] 1.368; 95% confidence interval [CI] 1.259-1.486) as well as CP (OR 1.241; 95% CI 1.117-1.378). Half the studies showed positive dose-response effect for each subgroup (test for linear trend, P < .05). CONCLUSIONS There is a moderate risk for having a child with a CL ± P or CP in women who smoke during pregnancy. We could not confirm whether there was a positive dose-response effect between maternal smoking and clefts.
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Blanton SH, Burt A, Garcia E, Mulliken JB, Stal S, Hecht JT. Ethnic heterogeneity of IRF6 AP-2a binding site promoter SNP association with nonsyndromic cleft lip and palate. Cleft Palate Craniofac J 2014; 47:574-7. [PMID: 21039277 DOI: 10.1597/09-153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE The goal of this study was to confirm the reported association between a noncoding SNP (rs642961) in IRF6 and nonsyndromic cleft lip and palate. DESIGN, SETTING, AND PARTICIPANTS Two SNPs in IRF6 (rs2235371 and rs64296) were genotyped in Hispanic and non-Hispanic white multiplex (122) and simplex (308) nonsyndromic cleft lip and palate families. Linkage and family-based association analyses were performed on the individual SNPs as well as the 2-SNP haplotype. RESULTS Only modest evidence was found for an association with rs642961 and the 2-SNP haplotype. In contrast, strong evidence was found for the association with rs2235371; this was most evident in the non-Hispanic white simplex families. CONCLUSIONS Although it is confirmed that variation in IRF6 is associated with nonsyndromic cleft lip and palate, the results do not support the reported association with SNP rs64296. Importantly, the association varies between ethnic groups. This finding underscores the need for evaluating additional variations in IRF6 across multiple populations to better determine its role in nonsyndromic cleft lip and palate.
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Affiliation(s)
- Susan H Blanton
- University of Miami, Miller School of Medicine, Miami, Florida, USA
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Lin Y, Shu S, Tang S. A case-control study of environmental exposures for nonsyndromic cleft of the lip and/or palate in eastern Guangdong, China. Int J Pediatr Otorhinolaryngol 2014; 78:544-50. [PMID: 24485177 DOI: 10.1016/j.ijporl.2014.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/30/2013] [Accepted: 01/04/2014] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To study the relationship between environmental factors and nonsyndromic cleft of the lip and/or palate (NSCLP) in eastern Guangdong for the prevention of NSCLP. METHODS A 1:1 retrospective case-control study was carried out. Data from 479 children with NSCLP who accepted comprehensive care in our center were recruited as cases from April 2010 to April 2013. An equal number of controls were recruited from pediatrics during the same period. Then we conducted face-to-face interviews with both parents using a structural questionnaire to identify the relationship between NSCLP and environmental risk factors. RESULTS Univariate Chi-square analysis identified 23 factors (P<0.05) as being significantly related to NSCLP. Stepwise multiple logistic regression analyses demonstrated that there were 16 factors significantly associated with this disease. Being male (OR=0.609), parental childbearing age of 25-29 years (ORfather=0.633; ORmother=0.469), higher parental education level (high school or greater) and folic acid supplementation (OR=0.360) were protective factors against NSCLP. However, positive family history of NSCLP (OR=54.132), positive maternal abortion history (OR=3.698), high or low parental age at time of childbirth, poor maternal education level (primary school) (OR=2.258), maternal common cold during pregnancy (OR=1.464), and drug use during pregnancy (OR=3.364) were significant risk factors for NSCLP. CONCLUSION The findings are beneficial for researchers to understand the etiology of NSCLP and to lay a solid foundation for the prevention of NSCLP in eastern Guangdong through educational programs to teach parents about the benefits of folic acid supplementation, adequate parental age at childbirth (25-29 years), higher parental education level (high school or higher), and the dangers of common cold and drug use during the first trimester of pregnancy, positive family history and maternal abortion history.
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Affiliation(s)
- Yu Lin
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital, Shantou University Medical College, North Dongxia Road, Shantou 515041, Guangdong, People's Republic of China
| | - Shenyou Shu
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital, Shantou University Medical College, North Dongxia Road, Shantou 515041, Guangdong, People's Republic of China
| | - Shijie Tang
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital, Shantou University Medical College, North Dongxia Road, Shantou 515041, Guangdong, People's Republic of China.
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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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11
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Letra A, Fakhouri W, Fonseca RF, Menezes R, Kempa I, Prasad JL, McHenry TG, Lidral AC, Moreno L, Murray JC, Daack-Hirsch S, Marazita ML, Castilla EE, Lace B, Orioli IM, Granjeiro JM, Schutte BC, Vieira AR. Interaction between IRF6 and TGFA genes contribute to the risk of nonsyndromic cleft lip/palate. PLoS One 2012; 7:e45441. [PMID: 23029012 PMCID: PMC3447924 DOI: 10.1371/journal.pone.0045441] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/22/2012] [Indexed: 01/08/2023] Open
Abstract
Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10−6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10−6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10−6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.
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Affiliation(s)
- Ariadne Letra
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Walid Fakhouri
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Renata F. Fonseca
- Department of Genetics, Institute of Biology, Center of Health Sciences; Federal University of Rio de Janeiro; Rio de Janeiro, RJ, Brazil
| | - Renato Menezes
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Inga Kempa
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia
| | - Joanne L. Prasad
- Department of Diagnostic Sciences, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Toby G. McHenry
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Andrew C. Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sandra Daack-Hirsch
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eduardo E. Castilla
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at CEMIC (Center of Medical Education and Clinical Research “Norberto Quirno”), Buenos Aires, Argentina
- CONICET (National Research Council of Argentina), Buenos Aires, Argentina
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ieda M. Orioli
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Jose M. Granjeiro
- Department of Cell and Molecular Biology, Fluminense Federal University, Niterói, RJ, Brazil and INMETRO, Duque de Caxias, RJ, Brazil
| | - Brian C. Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Pediatric Dentistry, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
- * E-mail:
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12
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Freitas JADS, das Neves LT, de Almeida ALPF, Garib DG, Trindade-Suedam IK, Yaedú RYF, Lauris RDCMC, Soares S, Oliveira TM, Pinto JHN. Rehabilitative treatment of cleft lip and palate: experience of the Hospital for Rehabilitation of Craniofacial Anomalies/USP (HRAC/USP)--Part 1: overall aspects. J Appl Oral Sci 2012; 20:9-15. [PMID: 22437671 PMCID: PMC3928765 DOI: 10.1590/s1678-77572012000100003] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 10/08/2011] [Indexed: 11/22/2022] Open
Abstract
Cleft lip and palate is the most common among craniofacial malformations and causes
several esthetic and functional implications that require rehabilitation. This paper
aims to generally describe the several aspects related to this complex pathology and
the treatment protocol used by the Hospital for Rehabilitation of Craniofacial
Anomalies, University of São Paulo (HRAC-USP) along 40 years of experience in the
treatment of individuals with cleft lip and palate.
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Affiliation(s)
- José Alberto de Souza Freitas
- Hospital for Rehabilitation of Craniofacial Anomalies, Department of Stomatology, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
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13
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Jia ZL, Shi B, Chen CH, Shi JY, Wu J, Xu X. Maternal malnutrition, environmental exposure during pregnancy and the risk of non-syndromic orofacial clefts. Oral Dis 2011; 17:584-9. [DOI: 10.1111/j.1601-0825.2011.01810.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Jia ZL, Shi B, Xu X, Kong XL. Interactions Between Small Ubiquitin-Like Modifier 1 and Nonsyndromic Orofacial Clefts. DNA Cell Biol 2011; 30:235-40. [PMID: 21189065 DOI: 10.1089/dna.2010.1110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease, Sichuan University, Chengdu, The People's Republic of China
- Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, The People's Republic of China
| | - Bing Shi
- State Key Laboratory of Oral Disease, Sichuan University, Chengdu, The People's Republic of China
- Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, The People's Republic of China
| | - Xue Xu
- State Key Laboratory of Oral Disease, Sichuan University, Chengdu, The People's Republic of China
- Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, The People's Republic of China
| | - Xiang-Li Kong
- State Key Laboratory of Oral Disease, Sichuan University, Chengdu, The People's Republic of China
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15
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Blanton SH, Henry RR, Yuan Q, Mulliken JB, Stal S, Finnell RH, Hecht JT. Folate pathway and nonsyndromic cleft lip and palate. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2011; 91:50-60. [PMID: 21254359 PMCID: PMC4098909 DOI: 10.1002/bdra.20740] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/19/2010] [Accepted: 08/12/2010] [Indexed: 11/08/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common complex birth defect. Periconceptional supplementation with folic acid, a key component in DNA synthesis and cell division, has reduced the birth prevalence of neural tube defects and may similarly reduce the birth prevalence of other complex birth defects including NSCLP. Past studies investigating the role of two common methylenetetrahydrofolate reductase (MTHFR) single-nucleotide polymorphisms (SNPs), C677T (rs1801133) and A1298C (rs1801131), in NSCLP have produced conflicting results. Most studies of folate pathway genes have been limited in scope, as few genes/SNPs have been interrogated. Here, we asked whether variations in a more comprehensive group of folate pathway genes were associated with NSCLP, and were there detectable interactions between these genes and environmental exposures? METHODS Fourteen folate metabolism-related genes were interrogated using 89 SNPs in multiplex and simplex non-Hispanic white and Hispanic NSCLP families. RESULTS Evidence for a risk association between NSCLP and SNPs in NOS3 and TYMS was detected in the non-Hispanic white group, whereas associations with MTR, BHMT2, MTHFS, and SLC19A1 were detected in the Hispanic group. Evidence for over-transmission of haplotypes and gene interactions in the methionine arm was detected. CONCLUSIONS These results suggest that perturbations of the genes in the folate pathway may contribute to NSCLP. There was evidence for an interaction between several SNPs and maternal smoking, and for one SNP with gender of the offspring. These results provide support for other studies that suggest that high maternal homocysteine levels may contribute to NSCLP and should be further investigated.
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16
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Jia ZL, Li Y, Meng T, Shi B. Association Between Polymorphisms at Small Ubiquitin-Like Modifier 1 and Nonsyndromic Orofacial Clefts in Western China. DNA Cell Biol 2010; 29:675-80. [PMID: 20738159 DOI: 10.1089/dna.2010.1034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Yang Li
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Tian Meng
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, P.R. China
| | - Bing Shi
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, P.R. China
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17
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Letra A, Menezes R, Govil M, Fonseca RF, McHenry T, Granjeiro JM, Castilla EE, Orioli IM, Marazita ML, Vieira AR. Follow-up association studies of chromosome region 9q and nonsyndromic cleft lip/palate. Am J Med Genet A 2010; 152A:1701-10. [PMID: 20583170 DOI: 10.1002/ajmg.a.33482] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cleft lip/palate comprises a large fraction of all human birth defects, and is notable for its significant lifelong morbidity and complex etiology. Several studies have shown that genetic factors appear to play a significant role in the etiology of cleft lip/palate. Human chromosomal region 9q21 has been suggested in previous reports to contain putative cleft loci. Moreover, a specific region (9q22.3-34.1) was suggested to present a approximately 45% probability of harboring a cleft susceptibility gene. Fine mapping of 50 SNPs across the 9q22.3-34.11 region was performed to test for association with cleft lip/palate in families from United States, Spain, Turkey, Guatemala, and China. We performed family-based analyses and found evidence of association of cleft lip/palate with STOM (rs306796) in Guatemalan families (P = 0.004) and in all multiplex families pooled together (P = 0.002). This same SNP also showed borderline association in the US families (P = 0.04). Under a nominal value of 0.05, other SNPs also showed association with cleft lip/palate and cleft subgroups. SNPs in STOM and PTCH genes and nearby FOXE1 were further associated with cleft phenotypes in Guatemalan and Chinese families. Gene prioritization analysis revealed PTCH and STOM ranking among the top fourteen candidates for cleft lip/palate among 339 genes present in the region. Our results support the hypothesis that the 9q22.32-34.1 region harbors cleft susceptibility genes. Additional studies with other populations should focus on these loci to further investigate the participation of these genes in human clefting.
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Affiliation(s)
- Ariadne Letra
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, PA 15261, USA
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18
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Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate. Hum Genet 2010; 128:401-10. [PMID: 20652317 DOI: 10.1007/s00439-010-0863-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
Abstract
Although multiple genes have been identified as genetic risk factors for isolated, non-syndromic cleft lip with/without cleft palate (CL/P), a complex and heterogeneous birth defect, interferon regulatory factor 6 gene (IRF6) is one of the best documented genetic risk factors. In this study, we tested for association between markers in IRF6 and CL/P in 326 Chinese case-parent trios, considering gene-environment interaction for two common maternal exposures, and parent-of-origin effects. CL/P case-parent trios from three sites in mainland China and Taiwan were genotyped for 22 single nucleotide polymorphisms (SNPs) in IRF6. The transmission disequilibrium test was used to test for marginal effects of individual SNPs. We used PBAT to screen the SNPs and haplotypes for gene-environment (G×E) interaction and conditional logistic regression models to quantify effect sizes for SNP-environment interaction. After Bonferroni correction, 14 SNPs showed statistically significant association with CL/P. Evidence of G×E interaction was found for both maternal exposures, multivitamin supplementation and environmental tobacco smoke (ETS). Two SNPs showed evidence of interaction with multivitamin supplementation in conditional logistic regression models (rs2076153 nominal P=0.019, rs17015218 nominal P=0.012). In addition, rs1044516 yielded evidence for interaction with maternal ETS (nominal P=0.041). Haplotype analysis using PBAT also suggested interaction between SNPs in IRF6 and both multivitamin supplementation and ETS. However, no evidence for maternal genotypic effects or significant parent-of-origin effects was seen in these data. These results suggest IRF6 gene may influence risk of CL/P through interaction with multivitamin supplementation and ETS in the Chinese population.
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19
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Wu C. Overview of developmental and reproductive toxicity research in China: history, funding mechanisms, and frontiers of the research. BIRTH DEFECTS RESEARCH. PART B, DEVELOPMENTAL AND REPRODUCTIVE TOXICOLOGY 2010; 89:9-17. [PMID: 20135688 DOI: 10.1002/bdrb.20231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Reproductive and developmental toxicology (DART) is the discipline that deals with adverse effects on male and female resulting from exposures to harmful chemical and physical agents. DART research in China boasted a long history, but presently has fallen behind the western world in education and research. The funding mechanisms for DART research in China were similar to that for other toxicological disciplines, and the funding has come from research grants and fellowships provided by national, ministerial, and provincial institutions. Finally, the frontiers of DART research in China could be summarized as follows: (1) use of model animals such as the zebrafish and roundworm, and use of cutting-edge techniques such as stem cell culture, as well as transgenic, metabonomic, and virtual screening to study the mechanisms of developmental toxicity for some important toxicants in China; (2) use of model animals and other lower-level sentinel organisms to evaluate and monitor the developmental toxicogical risk of environmental chemicals or pollutants; (3) epidemiological studies of some important reproductive hazards; (4) in-depth studying of the reproductive and developmental toxicity of some important environmental chemicals; and (5) evaluation and study of the reproductive and developmental toxicity of traditional Chinese medicines.
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Affiliation(s)
- Chunqi Wu
- National Beijing Center for Drug Safety Evaluation and Research, Beijing Institute of Toxicology and Pharmacology, PR China.
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20
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Jia ZL, Li Y, Chen CH, Li S, Wang Y, Zheng Q, Shi B. Association Among Polymorphisms at MYH9, Environmental Factors, and Nonsyndromic Orofacial Clefts in Western China. DNA Cell Biol 2010; 29:25-32. [PMID: 19891592 DOI: 10.1089/dna.2009.0935] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Yang Li
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Chun-Hui Chen
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Sheng Li
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Yan Wang
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Qian Zheng
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Bing Shi
- State Key Laboratory of Oral Disease and Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, People's Republic of China
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