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Yin B, Shi JY, Shi B, Zheng Q, Jia ZL. Association Between SNPs in 1q32.2 and NSCL ± P in Han Chinese Population. Cleft Palate Craniofac J 2021; 59:1520-1526. [PMID: 34730443 DOI: 10.1177/10556656211052837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Non-syndromic cleft lip with or without cleft palate (NSCL ± P) is one of the most common birth malformations. Currently, numerous susceptibility SNPs have been reported by GWA studies, however, the replications of them among NSCL ± P from Han Chinese were very limited. DESIGN In this study, we selected 16 SNPs around 1q32.2 based on the published GWA studies and replicated them among 302 trios with NSCL ± P from Han Chinese Population. The genotypic data was analyzed with FBAT, PLINK and R package. SETTING The study was conducted in a tertiary medical center. PATIENTS, PARTICIPANTS 302 patients with CL ± P and their parents. MAIN OUTCOME MEASURES To ascertain the genetic variants in 1q32.2 in patients with CL ± P in Han Chinese Population. INTERVENTIONS Blood samples were collected. RESULTS We found T allele (Z = 4.26, p = 0.00002) and T/T homozygotes (Z = 4.4, p = 0.000011) at rs12063989 was significantly over-transmitted among non-syndromic cleft lip with or without cleft palate (NSCL ± P). CONCLUSIONS We found rs12063989 exhibited significant association with the occurrence of NSCL ± P, which would provide new evidence for the future study in the etiology of NSCL ± P.
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Affiliation(s)
- Bin Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, USA
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Qian Zheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of cleft lip and palate, West China Hospital of Stomatology, 12530Sichuan University, Chengdu, China
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2
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Maili L, Letra A, Silva R, Buchanan EP, Mulliken JB, Greives MR, Teichgraeber JF, Blackwell SJ, Ummer R, Weber R, Chiquet B, Blanton SH, Hecht JT. PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate. Birth Defects Res 2019; 112:234-244. [PMID: 31825181 DOI: 10.1002/bdr2.1630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023]
Abstract
Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.
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Affiliation(s)
- Lorena Maili
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Renato Silva
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Endodontics, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Edward P Buchanan
- Department of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | | | - Matthew R Greives
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - John F Teichgraeber
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | | | - Rohit Ummer
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Ryan Weber
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Brett Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Pediatric Dentistry, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Susan H Blanton
- Dr. John T. MacDonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
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Wu-Chou YH, Lu YC, Chen KTP, Chang HF, Lin YT, Lo LJ. Association Studies Between Regulatory Regions of IRF6/ TP63 Genes and Nonsyndromic Oral Clefts. Cleft Palate Craniofac J 2018; 56:778-785. [PMID: 30419764 DOI: 10.1177/1055665618809244] [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] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE To evaluate genetic variants within the regulatory regions of interferon regulatory factor 6 (IRF6) and TP63 for the etiology of nonsyndromic oral clefts risk factors. DESIGN We performed allelic transmission disequilibrium test analysis on 5 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/palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. RESULTS We found all 3 selected SNPs of the IRF6 gene show significant association with nonsyndromic oral clefts (rs2235371, P = 5.10E-07; rs642961, P = .00194; and rs77542756, P = 9.08E-07). Haplotype analyses identified 3 possible SNP combination haplotypes in the IRF6 gene and found that C-G-G showed significant undertransmission (P = .058), whereas 2 other haplotypes, T-G-A and C-A-G (P = 2.71E-06 and P = 5.00E-04, respectively), were significantly overtransmitted to the NSCL/P children but not to the NSCPO children. For the TP63 gene, we failed to detect evidence of nonsyndromic oral cleft association in the 2 SNPs within the TP63 large intron 1 region. CONCLUSIONS We used a family-based analysis in 334 Taiwanese case-parent trios to evaluate selected SNPs of IRF6 genes and TP63 genes for a risk of orofacial clefting. This study provides additional evidence for an association between IRF6 and NSCL/P, including the genetic variants within the 5'-noncoding region of the gene. We also confirmed that NSCL/P and NSCPO individuals belong to different groups. For the TP63, our data did not favor the direct involvement of TAp63 isoforms during orofacial development.
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Affiliation(s)
- Yah-Huei Wu-Chou
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Yi-Chieh Lu
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Kuo-Ting Philip Chen
- 2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan.,3 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan
| | - Hsien-Fang Chang
- 4 Center of Genomic Medicine, National Taiwan University, Taipei
| | - Yin-Ting Lin
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Lun-Jou Lo
- 2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan.,3 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan.,5 Graduate Institute of Dental and Craniofacial Science, Chang Gung University, Taoyuan
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4
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Genome-Wide Mapping of SNPs in Non-coding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1094:39-48. [DOI: 10.1007/978-981-13-0719-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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de Souza LT, Kowalski TW, Ferrari J, Monlléo IL, Ribeiro EM, de Souza J, Fett-Conte AC, de Araujo TK, Gil-da-Silva-Lopes VL, Ribeiro-dos-Santos ÂKC, dos Santos SEB, Félix TM. Study ofIRF6and 8q24 region in non-syndromic oral clefts in the Brazilian population. Oral Dis 2016; 22:241-5. [DOI: 10.1111/odi.12432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/24/2015] [Accepted: 12/17/2015] [Indexed: 02/03/2023]
Affiliation(s)
- LT de Souza
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - TW Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - J Ferrari
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
| | - IL Monlléo
- Serviço de Genética Clínica; Faculdade de Medicina; Hospital Universitário Professor Alberto Antunes; Universidade Federal de Alagoas; Maceió Brazil
| | - EM Ribeiro
- Hospital Infantil Albert Sabin; Fortaleza Brazil
| | - J de Souza
- Centro de Atendimento Integral ao Fissurado Lábio-palatal; Curitiba Brazil
| | - AC Fett-Conte
- Serviço de Genética; Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto Brazil
| | - TK de Araujo
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - VL Gil-da-Silva-Lopes
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - ÂKC Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - SEB dos Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - TM Félix
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Serviço de Genética Médica; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
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Jafary F, Nadeali Z, Salehi M, Hosseinzadeh M, Sedghi M, Gholamrezapour T, Nouri N. Significant association between nonsyndromic cleft lip with or without cleft palate and IRF6rs2235371 polymorphism in Iranian familiar population. Mol Biol 2015. [DOI: 10.1134/s0026893315060102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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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8
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Nouri N, Memarzadeh M, Carinci F, Cura F, Scapoli L, Nouri N, Jafary F, Sedghi M, Sadri L, Salehi M. Family-based association analysis between nonsyndromic cleft lip with or without cleft palate and IRF6 polymorphism in an Iranian population. Clin Oral Investig 2014; 19:891-4. [DOI: 10.1007/s00784-014-1305-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 08/15/2014] [Indexed: 11/24/2022]
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9
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Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T, Wang J, Wang L, Li X. SNP@lincTFBS: an integrated database of polymorphisms in human LincRNA transcription factor binding sites. PLoS One 2014; 9:e103851. [PMID: 25075616 PMCID: PMC4116217 DOI: 10.1371/journal.pone.0103851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022] Open
Abstract
Large intergenic non-coding RNAs (lincRNAs) are a new class of functional transcripts, and aberrant expression of lincRNAs was associated with several human diseases. The genetic variants in lincRNA transcription factor binding sites (TFBSs) can change lincRNA expression, thereby affecting the susceptibility to human diseases. To identify and annotate these functional candidates, we have developed a database SNP@lincTFBS, which is devoted to the exploration and annotation of single nucleotide polymorphisms (SNPs) in potential TFBSs of human lincRNAs. We identified 6,665 SNPs in 6,614 conserved TFBSs of 2,423 human lincRNAs. In addition, with ChIPSeq dataset, we identified 139,576 SNPs in 304,517 transcription factor peaks of 4,813 lincRNAs. We also performed comprehensive annotation for these SNPs using 1000 Genomes Project datasets across 11 populations. Moreover, one of the distinctive features of SNP@lincTFBS is the collection of disease-associated SNPs in the lincRNA TFBSs and SNPs in the TFBSs of disease-associated lincRNAs. The web interface enables both flexible data searches and downloads. Quick search can be query of lincRNA name, SNP identifier, or transcription factor name. SNP@lincTFBS provides significant advances in identification of disease-associated lincRNA variants and improved convenience to interpret the discrepant expression of lincRNAs. The SNP@lincTFBS database is available at http://bioinfo.hrbmu.edu.cn/SNP_lincTFBS.
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Affiliation(s)
- Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zuxianglan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jingrun Ye
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ronghong Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tingting Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jianjian Wang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Lihua Wang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, China
- * E-mail: (LW); (XL)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- * E-mail: (LW); (XL)
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Syazana MSN, Wan Sulaiman WA, Halim AS, Sarina S. Skin Tissue Surface Morphology and Quality of RNA and Protein Extracted from Fresh and Stabilized Human Cleft Lip and Palate Tissue. Open Access Maced J Med Sci 2014. [DOI: 10.3889/oamjms.2014.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Cleft lip palate is a human congenital disorder worldwide and the study of this genetic disease requires molecular genetic analysis. This analysis required the use of nucleic acid and protein, thus good quality and quantity of its extraction is important. We are comparing RNA and protein extractions from tissue biopsy of cleft lip palate in both fresh and stabilized condition. Tissue morphology was also captured using Scanning Electron Microscopy (SEM) for any morphology differences. Tissue homogenization may destroy nucleic acid stability but not its morphology. Low RNA concentration from stabilized tissue was found. However, there was no crucial issue of protein extraction, degradation or concentration. Tissue morphology was slight different between normal and CL/P tissue.
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Pegelow M, Koillinen H, Magnusson M, Fransson I, Unneberg P, Kere J, Karsten A, Peyrard-Janvid M. Association and Mutation Analyses of the IRF6 Gene in Families with Nonsyndromic and Syndromic Cleft Lip and/or Cleft Palate. Cleft Palate Craniofac J 2014; 51:49-55. [DOI: 10.1597/11-220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Objectives (1) To detect interferon regulatory factor 6 gene ( IRF6) mutations in newly recruited Van der Woude syndrome (VWS) and popliteal pterygium syndrome (PPS) families. (2) To test for association, in nonsyndromic cleft lip and/or cleft palate (NSCL/P) and in VWS/PPS families, the single nucleotide polymorphism (SNP) rs642961, from the IRF6 enhancer AP-2α region, alone or as haplotype with rs2235371, a coding SNP (Val274Ile). Design IRF6 mutation screening was performed by direct sequencing and genotyping of rs642961 and rs2235371 by TaqMan technology. Patients Seventy-one Swedish NSCL/P families, 24 Finnish cleft palate (CP) families, and 24 VWS/PPS families (seven newly recruited) were studied. Results Allelic and genotypic frequencies in each phenotype were compared to those of the controls, and no significant difference could be observed. IRF6 gene mutation was detected in six of the seven new VWS/PPS families. Association analysis of the entire VWS/PPS sample set revealed the A allele from rs642961 to be a risk allele. Significant association was detected in the Swedish CP subset of our NSCL/P collection where the G-C haplotype for rs642961-rs2235371 were at risk ( P= .013). Conclusions Our results do not support the previously reported association between the A allele of rs642961 and the NSCL phenotype. However, in the VWS/PPS families, the A allele was a risk allele and was, in a large majority (>80%), transmitted on the same chromosome as the IRF6 mutation.
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Affiliation(s)
- M. Pegelow
- Department of Dental Medicine, Division of Orthodontics, Unit of Jaw Orthopedics, Karolinska Institutet, Huddinge, Sweden; on the Stockholm Craniofacial Team, Karolinska University Hospital, Solna, Sweden; and at the Department of Orthodontics in Eskilstuna, Folktandvården, Sörmland, Sweden
| | - H. Koillinen
- Neuropediatric Unit, Rehabilitative Services, Department of Health Care and Social Services, City of Turku, Finland
| | - M. Magnusson
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - I. Fransson
- Molecular Genetics Unit, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - P. Unneberg
- Molecular Genetics Unit, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Department of Medical Genetics, Biomedicum, University of Helsinki, Helsinki, Finland; and Science for Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - J. Kere
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - A. Karsten
- Department of Dental Medicine, Division of Orthodontics, Unit of Jaw Orthopedics, Karolinska Institutet, Huddinge, Sweden; and on the Stockholm Craniofacial Team, Karolinska University Hospital, Solna, Sweden
| | - M. Peyrard-Janvid
- Molecular Genetics Unit, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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de Aquino SN, Messetti AC, Bagordakis E, Martelli-Júnior H, Swerts MSO, Graner E, Coletta RD. Polymorphisms in FGF12, VCL, CX43 and VAX1 in Brazilian patients with nonsyndromic cleft lip with or without cleft palate. BMC MEDICAL GENETICS 2013; 14:53. [PMID: 23679094 PMCID: PMC3660181 DOI: 10.1186/1471-2350-14-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/09/2013] [Indexed: 11/21/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common orofacial birth defect with a wide range prevalence among different populations. Previous association studies with populations from Europe and Asia have identified putative susceptibility markers for NSCL/P in fibroblast growth factor 12 (FGF12), vinculin (VCL), connexin 43 (CX43) and in a region close to the ventral anterior homeobox 1 (VAX1) gene. However, there have thus far been no studies of these markers in NSCL/P Brazilian patients, and as the genetic ancestry of the Brazilian population is highly varied, the predisposition to those disease markers can be different. METHODS Herein we conducted a structured association study conditioned on the individual ancestry proportions to determine the role of 16 polymorphic markers within those genes in 300 patients with NSCL/P and 385 unaffected controls. RESULTS None of the alleles and genotypes showed association with NSCL/P, though there was a significant association of the haplotype formed by VAX1 rs10787760, rs6585429 and rs1871345 polymorphisms with NSCL/P that did not persist Bonferroni correction for multiple tests. CONCLUSIONS Our results are consistent with a lack of involvement of FGF12, VCL and CX43 variants with NSCL/P pathogenesis in Brazilian patients. Furthermore, the higher frequency of a haplotype of VAX1 with NSCL/P patients suggests a low penetrant gene for oral cleft, and warrants further studies.
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Affiliation(s)
- Sibele Nascimento de Aquino
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Ana Camila Messetti
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Elizabete Bagordakis
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Hercílio Martelli-Júnior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
- Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosário Vellano, Minas Gerais, Brazil
| | - Mario Sergio Oliveira Swerts
- Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosário Vellano, Minas Gerais, Brazil
| | - Edgard Graner
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
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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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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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IRF6 is a risk factor for nonsyndromic cleft lip in the Brazilian population. Am J Med Genet A 2012; 158A:2170-5. [DOI: 10.1002/ajmg.a.35526] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 05/20/2012] [Indexed: 11/07/2022]
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Abstract
Orofacial clefts (OFCs)--primarily cleft lip and cleft palate--are among the most common birth defects in all populations worldwide, and have notable population, ethnicity, and gender differences in birth prevalence. Interest in these birth defects goes back centuries, as does formal scientific interest; scientists often used OFCs as examples or evidence during paradigm shifts in human genetics, and have also used virtually every new method of human genetic analysis to deepen our understanding of OFC. This review traces the evolution of human genetic investigations of OFC, highlights the specific insights gained about OFC through the years, and culminates in a review of recent key OFC genetic findings resulting from the powerful tools of the genomics era. Notably, OFC represents a major success for genome-wide approaches, and the field is poised for further breakthroughs in the near future.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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Brito LA, Paranaiba LMR, Bassi CFS, Masotti C, Malcher C, Schlesinger D, Rocha KM, Cruz LA, Bárbara LK, Alonso N, Franco D, Bagordakis E, Martelli H, Meyer D, Coletta RD, Passos-Bueno MR. Region 8q24 is a susceptibility locus for nonsyndromic oral clefting in Brazil. ACTA ACUST UNITED AC 2012; 94:464-8. [PMID: 22511506 DOI: 10.1002/bdra.23011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2012] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 12/30/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate is a relatively common craniofacial defect with multifactorial inheritance. The association of the rs987525 single nucleotide variant, located in a gene desert at 8q24.21 region, has been consistently replicated in European populations. We performed a structured association approach combined with transcriptional analysis of the MYC gene to dissect the role of rs987525 in oral clefting susceptibility in the ethnically admixed Brazilian population. METHODS We performed the association study conditioned on the individual ancestry proportions in a sample of 563 patients and 336 controls, and in an independent sample of 221 patients and 261 controls. The correlation between rs987525 genotypes and MYC transcriptional levels in orbicularis oris muscle mesenchymal stem cells was also investigated in 42 patients and 4 controls. RESULTS We found a significant association in the larger sample (p = 0.0016; OR = 1.80 [95% confidence interval {CI}, 1.21-2.69], for heterozygous genotype, and 2.71 [95% CI, 1.47-4.96] for homozygous genotype). We did not find a significant correlation between rs987525 genotypes and MYC transcriptional levels (p = 0.14; r = -0.22, Spearman Correlation). CONCLUSIONS We present a positive association of rs987525 in the Brazilian population for the first time, and it is likely that the European contribution to our population is driving this association. We also cannot discard a role of rs987515 in MYC regulation, because this locus behaves as an expression quantitative locus of MYC in another tissue.
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Affiliation(s)
- Luciano Abreu Brito
- Human Genome Research Center, Institute of Biosciences, University of São Paulo, Brazil
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Larrabee YC, Birkeland AC, Kent DT, Flores C, Su GH, Lee JH, Haddad J. Association of common variants, not rare mutations, in IRF6
With nonsyndromic clefts in a honduran population. Laryngoscope 2011; 121:1756-9. [DOI: 10.1002/lary.21870] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Dixon MJ, Marazita ML, Beaty TH, Murray JC. Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet 2011; 12:167-78. [PMID: 21331089 DOI: 10.1038/nrg2933] [Citation(s) in RCA: 1189] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Clefts of the lip and/or palate (CLP) are common birth defects of complex aetiology. CLP can occur in isolation or as part of a broad range of chromosomal, Mendelian or teratogenic syndromes. Although there has been marked progress in identifying genetic and environmental triggers for syndromic CLP, the aetiology of the more common non-syndromic (isolated) forms remains poorly characterized. Recently, using a combination of epidemiology, careful phenotyping, genome-wide association studies and analysis of animal models, several distinct genetic and environmental risk factors have been identified and confirmed for non-syndromic CLP. These findings have advanced our understanding of developmental biology and created new opportunities for clinical translational research.
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Affiliation(s)
- Michael J Dixon
- Faculty of Medical and Human Sciences, Manchester Academic Health Sciences Centre, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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