1
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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2
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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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3
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
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4
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Slavec L, Karas Kuželički N, Locatelli I, Geršak K. Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis. Sci Rep 2022; 12:1214. [PMID: 35075162 PMCID: PMC8786890 DOI: 10.1038/s41598-021-02159-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
To date, the involvement of various genetic markers in the aetiopathogenesis of non-syndromic orofacial cleft (nsOFC) has been extensively studied. In the present study, we focused on studies performed on populations of European ancestry to systematically review the available literature to define relevant genetic risk factors for nsOFC. Eligible studies were obtained by searching Ovid Medline and Ovid Embase. We gathered the genetic markers from population-based case–control studies on nsOFC, and conducted meta-analysis on the repeatedly reported markers. Whenever possible, we performed stratified analysis based on different nsOFC phenotypes, using allelic, dominant, recessive and overdominant genetic models. Effect sizes were expressed as pooled odds ratios (ORs) with 95% confidence intervals (CIs), and p ≤ 0.05 were considered statistically significant. A total of 84 studies were eligible for this systematic review, with > 700 markers included. Of these, 43 studies were included in the meta-analysis. We analysed 47 genetic variants in 30 genes/loci, which resulted in 226 forest plots. There were statistically significant associations between at least one of the nsOFC phenotypes and 19 genetic variants in 13 genes/loci. These data suggest that IRF6, GRHL3, 8q24, VAX1, TGFA, FOXE1, ABCA4, NOG, GREM1, AXIN2, DVL2, WNT3A and WNT5A have high potential as biomarkers of nsOFC in populations of European descent. Although other meta-analyses that included European samples have been performed on a limited number of genetic variants, this study represents the first meta-analysis of all genetic markers that have been studied in connection with nsOFC in populations of European ancestry.
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Affiliation(s)
- Lara Slavec
- University Medical Centre Ljubljana, Division of Gynaecology and Obstetrics, Research Unit, Ljubljana, Slovenia.,University of Ljubljana, Faculty of Pharmacy, Department of Clinical Biochemistry, Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- University of Ljubljana, Faculty of Pharmacy, Department of Clinical Biochemistry, Ljubljana, Slovenia
| | - Igor Locatelli
- University of Ljubljana, Faculty of Pharmacy, Department of Social Pharmacy, Ljubljana, Slovenia
| | - Ksenija Geršak
- University Medical Centre Ljubljana, Division of Gynaecology and Obstetrics, Research Unit, Ljubljana, Slovenia. .,University of Ljubljana, Faculty of Medicine, Department of Gynaecology and Obstetrics, Ljubljana, Slovenia.
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5
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Curtis SW, Chang D, Lee MK, Shaffer JR, Indencleef K, Epstein MP, Cutler DJ, Murray JC, Feingold E, Beaty TH, Claes P, Weinberg SM, Marazita ML, Carlson JC, Leslie EJ. The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. HGG ADVANCES 2021; 2:100025. [PMID: 33817668 PMCID: PMC8018676 DOI: 10.1016/j.xhgg.2021.100025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Nonsyndromic orofacial clefts (OFCs) are a common birth defect and are phenotypically heterogenous in the structure affected by the cleft - cleft lip (CL) and cleft lip and palate (CLP) - as well as other features, such as the severity of the cleft. Here, we focus on bilateral and unilateral clefts as one dimension of OFC severity, because the genetic architecture of these subtypes is not well understood. We tested for subtype-specific genetic associations in 44 bilateral CL (BCL) cases, 434 unilateral CL (UCL) cases, 530 bilateral CLP cases (BCLP), 1123 unilateral CLP (UCLP) cases, and unrelated controls (N = 1626), using a mixed-model approach. While no novel loci were found, the genetic architecture of UCL was distinct compared to BCL, with 44.03% of suggestive loci having different effects between the two subtypes. To further understand the subtype-specific genetic risk factors, we performed a genome-wide scan for modifiers and found a significant modifier locus on 20p11 (p=7.53×10-9), 300kb downstream of PAX1, that associated with higher odds of BCL vs. UCL, and replicated in an independent cohort (p=0.0018) with no effect in BCLP (p>0.05). We further found that this locus was associated with normal human nasal shape. Taken together, these results suggest bilateral and unilateral clefts may have different genetic architectures. Moreover, our results suggest BCL, the rarest form of OFC, may be genetically distinct from the other OFC subtypes. This expands our understanding of modifiers for OFC subtypes and further elucidates the genetic mechanisms behind the phenotypic heterogeneity in OFCs.
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Affiliation(s)
- Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | | | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Peter Claes
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Jenna C. Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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6
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Mukhopadhyay N, Bishop M, Mortillo M, Chopra P, Hetmanski JB, Taub MA, Moreno LM, Valencia-Ramirez LC, Restrepo C, Wehby GL, Hecht JT, Deleyiannis F, Butali A, Weinberg SM, Beaty TH, Murray JC, Leslie EJ, Feingold E, Marazita ML. Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. Hum Genet 2020; 139:215-226. [PMID: 31848685 PMCID: PMC6981325 DOI: 10.1007/s00439-019-02099-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/07/2019] [Indexed: 12/30/2022]
Abstract
Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic, and the genetic etiology of non-syndromic OFCs is only partially determined. Here, we analyze whole genome sequence (WGS) data for association with risk of OFCs in European and Colombian families selected from a multicenter family-based OFC study. This is the first large-scale WGS study of OFC in parent-offspring trios, and a part of the Gabriella Miller Kids First Pediatric Research Program created for the study of childhood cancers and structural birth defects. WGS provides deeper and more specific genetic data than using imputation on present-day single nucleotide polymorphic (SNP) marker panels. Genotypes of case-parent trios at single nucleotide variants (SNV) and short insertions and deletions (indels) spanning the entire genome were called from their sequences using human GRCh38 genome assembly, and analyzed for association using the transmission disequilibrium test. Among genome-wide significant associations, we identified a new locus on chromosome 21 in Colombian families, not previously observed in other larger OFC samples of Latin American ancestry. This locus is situated within a region known to be expressed during craniofacial development. Based on deeper investigation of this locus, we concluded that it contributed risk for OFCs exclusively in the Colombians. This study reinforces the ancestry differences seen in the genetic etiology of OFCs, and underscores the need for larger samples when studying for OFCs and other birth defects in populations with diverse ancestry.
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Affiliation(s)
- Nandita Mukhopadhyay
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
| | - Madison Bishop
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Michael Mortillo
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lina M Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Claudia Restrepo
- Fundación Clínica Noel (http://www.clinicanoel.org.co/), Medellín, Colombia
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX, 77030, USA
| | | | - Azeez Butali
- Iowa Institute of Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Eleanor Feingold
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Biostatistics Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Psychiatry, School of Medicine and Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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7
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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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8
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Azevedo CDMS, Machado RA, Martelli-Júnior H, Reis SRDA, Persuhn DC, Coletta RD, Rangel ALCA. Exploring GRHL3 polymorphisms and SNP-SNP interactions in the risk of non-syndromic oral clefts in the Brazilian population. Oral Dis 2019; 26:145-151. [PMID: 31564061 DOI: 10.1111/odi.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/27/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To investigate the association of single-nucleotide polymorphisms (SNP) in grainyhead-like 3 (GRHL3) and to verify its possible interactions with others genes responsible for craniofacial development in the risk of non-syndromic oral cleft (NSOC). METHODS Applying TaqMan allelic discrimination assays, we evaluated GRHL3 SNPs (rs10903078, rs41268753, and rs4648975) in an ancestry-structured case-control sample composed of 1,127 Brazilian participants [272 non-syndromic cleft palate only (NSCPO), 242 non-syndromic cleft lip only (NSCLO), 319 non-syndromic cleft lip and palate (NSCLP), and 294 healthy controls]. Additionally, SNP-SNP interactions of GRHL3 and previously reported variants in FAM49A, FOXE1, NTN1, and VAX1 were verified in non-syndromic cleft lip with or without cleft palate (NSCL ± P). To eliminate false-positive associations, Bonferroni correction or 1,000 permutation method was applied. RESULTS The multiple logistic regression analysis showed that the CC genotype of rs10903078 (p = .03) and the haplotype C-C formed by the SNPs rs10903078 and rs41268753 (p = .04) were associated with NSCLO, but the p-values did not withstand Bonferroni correction. However, SNP-SNP test revealed significant interactions between GRHL3 SNPs and FAM49A (rs7552), FOXE1 (rs3758249), VAX1 (rs7078160 and rs751231), and NTN1 (rs9891446). CONCLUSIONS Our results confirm the importance of GRHL3 and its interactions with previously NSOC-associated genes, including FAM49A, FOXE1, NTN1, and VAX1, in the pathogenesis of NSOC in the Brazilian population.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
| | - Hercílio Martelli-Júnior
- Dental School, Stomatology Clinic, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano, Alfenas, Brazil
| | | | | | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
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9
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Xing Y, Zhang W, Wan X, Hong Z, Zhao H, Liang W, Shi L, Chen J, Zhong X, Zhou J, Tang S. Association Between an Interferon Regulatory Factor 6 Gene Polymorphism and Nonsyndromic Cleft Palate Risk. Genet Test Mol Biomarkers 2019; 23:652-663. [PMID: 31448957 DOI: 10.1089/gtmb.2018.0315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: Involvement of interferon regulatory factor 6 (IRF6) gene polymorphisms in nonsyndromic cleft palate (NSCP) risk remains controversial. This investigation was performed to evaluate the relationship between IRF6 gene polymorphisms and NSCP risk. Materials and Methods: Two hundred forty-one patients with NSCP (including 103 complete trio families) were recruited, and 242 unaffected individuals were included as controls. Polymorphisms for the IRF6 rs2235371, rs801619, rs642961, rs44844880, and rs8049367 loci were characterized in both groups. Furthermore, eligible studies were identified from the databases through June 1, 2017, and were included in a meta-analysis to enhance the robustness of our conclusions. Results: The IRF6 rs2235371 A allele and AA genotype in the case group were found at higher frequencies than in the control group (A allele: p < 0.0016; AA genotype: p < 0.0049). The IRF6 rs801619 AA genotype and G allele were associated with NSCP risk (G allele: p < 0.0061; AA genotype: p < 0.0195). At the IRF6 rs642961, rs44844880, and rs8049367 loci genotype and allele frequencies were not statistically different between the NSCP group and normal controls. In the meta-analysis, the IRF6 A/G gene polymorphism (rs2235371) and IRF6 A/G gene polymorphism (rs642961) were associated with NSCP risk in the general population, whereas the IRF6 A/C gene polymorphism (rs2013162) was not. Conclusion: The IRF6 A/G gene polymorphisms at rs2235371 and rs642961, but not the IRF6 A/C gene polymorphism rs2013162, were associated with NSCP risk.
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Affiliation(s)
- Yue Xing
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Wancong Zhang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xinhong Wan
- Central Laboratory, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Zhiqian Hong
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hanxing Zhao
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Weijie Liang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Lungang Shi
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiasheng Chen
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaoping Zhong
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Jianda Zhou
- Department of Plastic and Reconstructive Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shijie Tang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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10
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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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11
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Rafighdoost H, Hashemi M, Danesh H, Bizhani F, Bahari G, Taheri M. Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with Non-Syndromic Cleft Lip with or without Cleft Palate in a sample of the southeast Iranian population. J Appl Oral Sci 2018; 25:650-656. [PMID: 29211286 PMCID: PMC5701535 DOI: 10.1590/1678-7757-2017-0191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/30/2017] [Indexed: 01/25/2023] Open
Abstract
Non-syndromic cleft lip with or without palate (NSCL/P) is a common congenital malformation worldwide, with complex etiology. It has been proposed that interaction of genes and environmental factors play a role in the predisposition to this disease.
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Affiliation(s)
- Houshang Rafighdoost
- Zahedan University of Medical Sciences, Cellular and Molecular Research Center, Zahedan, Iran.,Zahedan University of Medical Sciences, School of Medicine, Department of Anatomy, Zahedan, Iran
| | - Mohammad Hashemi
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Hiva Danesh
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Fatemeh Bizhani
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Gholamreza Bahari
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Mohsen Taheri
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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12
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Assis Machado R, de Toledo IP, Martelli-Júnior H, Reis SR, Neves Silva Guerra E, Coletta RD. Potential genetic markers for nonsyndromic oral clefts in the Brazilian population: A systematic review and meta-analysis. Birth Defects Res 2018; 110:827-839. [DOI: 10.1002/bdr2.1208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
| | - Isabela Porto de Toledo
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | | | | | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
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13
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Starink E, Hokken-Koelega ACS, Visser TJ, Baan J, Peeters RP, de Graaff LCG. Genetic analysis of IRF6, a gene involved in craniofacial midline formation, in relation to pituitary and facial morphology of patients with idiopathic growth hormone deficiency. Pituitary 2017; 20:499-508. [PMID: 28593555 PMCID: PMC5606942 DOI: 10.1007/s11102-017-0808-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Growth hormone is secreted by the pituitary gland, which forms part of the craniofacial midline. IRF6 encodes a transcription factor involved in the development of the craniofacial midline and mutations in IRF6 are known to disturb craniofacial development. Craniofacial and pituitary development are closely related. After whole exome sequencing revealed a new mutation in IRF6 in a family with Idiopathic Growth Hormone Deficiency (IGHD), we screened the remainder of our IGHD cohort for mutations in this gene and related their genotypes to pituitary and craniofacial morphology. MATERIALS AND METHODS We sequenced all coding exons and exon-intron boundaries of IRF6 in 81 patients with IGHD. We performed a multiplex ligation-dependent probe amplification (MLPA) in order to exclude copy number variations in IRF6. We analyzed facial measurements taken from standardized digital pictures of 48 patients. RESULTS We found two new variants and eleven polymorphisms. Apart from the new mutation found in the index family (p.Arg233Cys), we found one other new heterozygous missense mutation in IRF6 (Pro456Ser). p.Arg233Cys was reported as extremely rare in exome databases (1 allele out of 120.852 alleles sequenced), strictly conserved among species and was predicted deleterious by all variant predictor programs. Pro456Ser was predicted to be benign. MLPA did not reveal any exon deletions or duplications in any of the patients. CONCLUSION This is the first report of IRF6 analysis in an IGHD cohort. We found one new mutation which, based on in silico analysis, could be of functional relevance. However, we did not find any mutations in the other patients. Therefore, we conclude that IRF6 defects are rare in IGHD patients and further research should focus on new candidate genes.
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Affiliation(s)
- Eline Starink
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Anita C S Hokken-Koelega
- Pediatrics, Subdiv. Endocrinology, Erasmus MC, Rotterdam, The Netherlands
- Dutch Growth Research Foundation, Rotterdam, The Netherlands
| | - Theo J Visser
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Janneke Baan
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Robin P Peeters
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Laura C G de Graaff
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands.
- Dutch Growth Research Foundation, Rotterdam, The Netherlands.
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14
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Salagovic J, Klimcakova L, Zabavnikova M, Behunova J, Hudakova T, Fedeles J, Molnarova A, Podracka L. Polymorphisms at 1q32, 8q24, and 17q22 loci are associated with nonsyndromic cleft lip with or without cleft palate risk in the Slovak population. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:152-157. [PMID: 28422192 DOI: 10.5507/bp.2017.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is the most common orofacial birth defect with an aetiology involving both genetic and environmental factors. Genome-wide association studies (GWAS) have identified several genomic susceptibility regions for nsCL/P. In the present study, the three well established single nucleotide polymorphisms (SNPs) identified by GWAS (rs987525 at 8q24, rs7078160 at 10q25, and rs227731 at 17q22 loci) and one SNP identified by candidate gene study (rs642961 in IRF6 gene at 1q32 locus) were analysed for an association with nsCL/P in Slovak population. METHODS Nucleotide variants were genotyped in 165 nsCL/P patients and 326 unaffected controls. All variants of interest were genotyped using high-resolution melting analysis after real-time PCR. RESULTS We found significant differences between patient and control groups with respect to the allele and genotype frequencies for the SNPs at the 1q32, 8q24, and 17q22 loci. SNP at the 10q25 locus showed a trend toward association with nsCL/P risk. CONCLUSIONS The results suggest that SNPs at the 1q32, 8q24 and 17q22 loci may contribute to the nsCL/P risk in Slovak population.
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Affiliation(s)
- Jan Salagovic
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Lucia Klimcakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Marianna Zabavnikova
- Department of Plastic, Reconstructive and Aesthetic Surgery, LP University Hospital, Kosice, Slovak Republic
| | - Jana Behunova
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,Institut fur Medizinische Genetik, Medizinische Universitat Wien, Austria
| | - Terezia Hudakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Jozef Fedeles
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Agata Molnarova
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Ludmila Podracka
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,1st Department of Paediatrics, Faculty of Medicine, Comenius University and Children's University Hospital, Bratislava, Slovak Republic
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15
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Wattanawong K, Rattanasiri S, McEvoy M, Attia J, Thakkinstian A. Association between IRF6 and 8q24 polymorphisms and nonsyndromic cleft lip with or without cleft palate: Systematic review and meta-analysis. ACTA ACUST UNITED AC 2016; 106:773-88. [PMID: 27511269 PMCID: PMC5095821 DOI: 10.1002/bdra.23540] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/07/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND We conducted a systematic review and meta-analysis of interferon regulatory factor 6 and 8q24 polymorphisms with nonsyndromic cleft lip with/without cleft palate (NSCL/P). METHODS Data extraction was independently performed by two reviewers. Genotypic effects of four polymorphisms from 31 studies were pooled separately by ethnicity using a mixed-effect logit model with accounting for heterogeneity. RESULTS For rs2235371, AA and GA carried, respectively, 51% (95% confidence interval [CI], 37%-61%) and 42% (95% CI, 32%-50%) lower risks of NSCL/P than GG genotypes in Asians, but these genotypes were not significant in Caucasians. For rs2013162, only AA was significant, that is, carried 0.65 (95% CI, 0.52-0.82) times lower odds than CC in Caucasians but not for Asians. For rs642961, AA and GA genotypes, respectively, carried 2.47 (95% CI, 1.41-4.35) and 1.40 (95% CI, 1.12-1.75) times higher odds in Asian, and 2.03 (95% CI, 1.52-2.71) and 1.58 (95% CI, 1.37-1.82) times higher odds in Caucasians compare with GG genotypes. For rs987525, AA and CA genotypes carried 2.27 (95% CI, 1.43-3.60) and 1.34 (95% CI, 1.02-1.77) times higher odds in Asian, and 5.25 (95% CI, 3.98-6.91) and 2.13 (95% CI-1.82, 2.49) times higher odds in Caucasians, and 1.42 (95% CI, 1.10-1.82) and 1.28 (95% CI, 1.09-1.50) times higher odds in mixed ethnicities compared with CC genotypes. These variant effects remained significant based on applying Bonferroni corrected-thresholds, except in the mixed ethnicity. CONCLUSION We show robust variant effects in NSCL/P. Considering them with other genes and risk factors might be useful to improve prediction of NSCL/P occurrence. Birth Defects Research (Part A) 106:773-788, 2016. © 2016 The Authors Birth Defects Research Part A: Clinical and Molecular Teratology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kachin Wattanawong
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sasivimol Rattanasiri
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Mark McEvoy
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - John Attia
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - Ammarin Thakkinstian
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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16
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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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17
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Mukherjee K, Ishii K, Pillalamarri V, Kammin T, Atkin JF, Hickey SE, Xi QJ, Zepeda CJ, Gusella JF, Talkowski ME, Morton CC, Maas RL, Liao EC. Actin capping protein CAPZB regulates cell morphology, differentiation, and neural crest migration in craniofacial morphogenesis†. Hum Mol Genet 2016; 25:1255-70. [PMID: 26758871 DOI: 10.1093/hmg/ddw006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022] Open
Abstract
CAPZB is an actin-capping protein that caps the growing end of F-actin and modulates the cytoskeleton and tethers actin filaments to the Z-line of the sarcomere in muscles. Whole-genome sequencing was performed on a subject with micrognathia, cleft palate and hypotonia that harbored a de novo, balanced chromosomal translocation that disrupts the CAPZB gene. The function of capzb was analyzed in the zebrafish model. capzb(-/-) mutants exhibit both craniofacial and muscle defects that recapitulate the phenotypes observed in the human subject. Loss of capzb affects cell morphology, differentiation and neural crest migration. Differentiation of both myogenic stem cells and neural crest cells requires capzb. During palate morphogenesis, defective cranial neural crest cell migration in capzb(-/-) mutants results in loss of the median cell population, creating a cleft phenotype. capzb is also required for trunk neural crest migration, as evident from melanophores disorganization in capzb(-/-) mutants. In addition, capzb over-expression results in embryonic lethality. Therefore, proper capzb dosage is important during embryogenesis, and regulates both cell behavior and tissue morphogenesis.
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Affiliation(s)
- Kusumika Mukherjee
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Kana Ishii
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Department of Biochemistry and Molecular Biology, Nippon Medical School, Bunkyo, Tokyo 113-0022, Japan, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Vamsee Pillalamarri
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tammy Kammin
- Department of Obstetrics, Gynecology and Reproductive Biology
| | - Joan F Atkin
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA, Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA, Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Qiongchao J Xi
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | | | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA and Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Cynthia C Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Department of Pathology and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA and Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Richard L Maas
- Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - Eric C Liao
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Harvard Medical School, Harvard University, Boston, MA 02114, USA
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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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Kerameddin S, Namipashaki A, Ebrahimi S, Ansari-Pour N. IRF6 Is a Marker of Severity in Nonsyndromic Cleft Lip/Palate. J Dent Res 2015; 94:226S-32S. [DOI: 10.1177/0022034515581013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nonsyndromic cleft lip with or without palate (CL/P) is thought to be caused by the interplay of genetic and environmental factors, and this has thus hindered the process of identifying genetic causative factors. Numerous studies in the past decade have implicated IRF6 in CL/P, but this has not often been replicated in other populations. In specific, the only etiologic single-nucleotide polymorphism (SNP) identified in the IRF6 locus (rs642961) has recently been shown not to be associated with CL/P in diverse populations. We therefore used a genewide tagging SNP (tagSNP) haplotyping approach (including rs642961 as a tagSNP) to detect all potential risk-conferring haplotypes and combined this with detailed subphenotyping of CL/P cases ( N = 150) according to severity. We observed a significant overrepresentation of a tagSNP haplotype carrying the rs642961 risk allele in the most severe subphenotype of CL/P (complete bilateral CL/P; P = 0.008, odds ratio = 4.97, 95% confidence interval = 1.33 to 18.46). It was recently shown that >80% of IRF6 mutations in syndromic CL/P occur on the same haplotype background. We therefore suggest that IRF6 is a marker of CL/P severity.
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Affiliation(s)
- S. Kerameddin
- Department of Plastic and Reconstructive Surgery, Iran University of Medical Sciences, Tehran, Iran
| | - A. Namipashaki
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - S. Ebrahimi
- Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
| | - N. Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
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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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Khandelwal KD, van Bokhoven H, Roscioli T, Carels CE, Zhou H. Genomic approaches for studying craniofacial disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:218-31. [DOI: 10.1002/ajmg.c.31379] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lu Y, Liu Q, Xu W, Li Z, Jiang M, Li X, Zhao N, Liu W, Sui Y, Ma C, Feng W, Han W, Li J. TGFA and IRF6 contribute to the risk of nonsyndromic cleft lip with or without cleft palate in northeast China. PLoS One 2013; 8:e70754. [PMID: 23940636 PMCID: PMC3735505 DOI: 10.1371/journal.pone.0070754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/23/2013] [Indexed: 11/19/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) are common birth defects with a complex etiology. Multiple interacting loci and possible environmental factors influence the risk of NSCL/P. 12 single nucleotide polymorphisms (SNPs) in 7 candidate genes were tested using an allele-specific primer extension for case-control and case-parent analyses in northeast China in 236 unrelated patients, 185 mothers and 154 fathers, including 128 complete trios, and 400 control individuals. TGFA and IRF6 genes showed a significant association with NSCL/P. In IRF6, statistical evidence of an association between rs2235371 (p = 0.003), rs2013162 (p<0.0001) and NSCL/P was observed in case-control analyses. Family based association tests (FBATs) showed over-transmission of the C allele at the rs2235371 polymorphism (p = 0.007). In TGFA, associations between rs3771494, rs3771523 (G3822A), rs11466285 (T3851C) and NSCL/P were observed in case-control and FBAT analyses. Associations between other genes (BCL3, TGFB3, MTHFR, PVRL1 and SUMO1) and NSCL/P were not detected.
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Affiliation(s)
- Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Qiang Liu
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Wei Xu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Zengjian Li
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Miao Jiang
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Xuefu Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Ning Zhao
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wei Liu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Yu Sui
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Chao Ma
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wenhua Feng
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Weitian Han
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
| | - Jianxin Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
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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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Wang M, Pan Y, Zhang Z, Wang L. Three polymorphisms inIRF6and 8q24 are associated with nonsyndromic cleft lip with or without cleft palate: Evidence from 20 studies. Am J Med Genet A 2012; 158A:3080-6. [DOI: 10.1002/ajmg.a.35634] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 07/25/2012] [Indexed: 11/09/2022]
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Genetics and management of the patient with orofacial cleft. PLASTIC SURGERY INTERNATIONAL 2012; 2012:782821. [PMID: 23213504 PMCID: PMC3503281 DOI: 10.1155/2012/782821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 10/01/2012] [Indexed: 01/24/2023]
Abstract
Cleft lip or palate (CL/P) is a common facial defect present in 1 : 700 live births and results in substantial burden to patients. There are more than 500 CL/P syndromes described, the causes of which may be single-gene mutations, chromosomopathies, and exposure to teratogens. Part of the most prevalent syndromic CL/P has known etiology. Nonsyndromic CL/P, on the other hand, is a complex disorder, whose etiology is still poorly understood. Recent genome-wide association studies have contributed to the elucidation of the genetic causes, by raising reproducible susceptibility genetic variants; their etiopathogenic roles, however, are difficult to predict, as in the case of the chromosomal region 8q24, the most corroborated locus predisposing to nonsyndromic CL/P. Knowing the genetic causes of CL/P will directly impact the genetic counseling, by estimating precise recurrence risks, and the patient management, since the patient, followup may be partially influenced by their genetic background. This paper focuses on the genetic causes of important syndromic CL/P forms (van der Woude syndrome, 22q11 deletion syndrome, and Robin sequence-associated syndromes) and depicts the recent findings in nonsyndromic CL/P research, addressing issues in the conduct of the geneticist.
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Lace B, Kempa I, Klovins J, Stavusis J, Krumina A, Akota I, Barkane B, Vieira AR, Nagle E, Grinfelde I, Maulina I. BCL3 gene role in facial morphology. ACTA ACUST UNITED AC 2012; 94:918-24. [PMID: 23115114 DOI: 10.1002/bdra.23085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 08/23/2012] [Accepted: 08/28/2012] [Indexed: 11/12/2022]
Abstract
BACKGROUND Cleft lip (CL) with or without palate (CLP) and isolated cleft palate (CP) are etiologically complex diseases with interactions among various environmental and genetic factors. The aim of the current study was to identify association with genetic markers and phenotypic craniofacial data in patients with CL/CLP/CP parents. METHODS Posteroanterior and lateral digital radiographs of the cranium were obtained from 74 parents of patients with CL/CLP/CP. One hundred seventy-three patients with CL/CLP/CP and 190 controls were enrolled in the study for the association test. Five genetic markers of the IRF6 gene and 14 markers of the 19q13 locus were genotyped. Linear regression analysis was performed for the relationship of cephalometric measurements with genotype data adjusted for age, gender, and cleft type. Chi-square and transmission disequilibrium tests were performed to evaluate differences in alleles of the BCL3 gene. Positive findings were replicated in an independent sample (n = 95) of patients with CL/CLP/CP parents. RESULTS Genetic markers of the BCL3 gene at 19q13, rs7257231, and rs1979377 in the familial association test and rs10401176 in the case-control association test, were associated with craniofacial phenotype. Carriers of BCL3 allele rs7257231T had longer posterior cranial bases than noncarriers (p(adjusted) = 0.0028), and in the familial-based association test showed the statistically strongest relationship (p(adjusted) = 0.05) to phenotype. Relation of rs7257231 to facial formation was confirmed in the replication group (p = 0.0024). CONCLUSIONS The results indicate that BCL3, which has functions related to cell adhesion and whose downregulation can cause disruption of ectodermal development, is likely to be important in facial formation. Birth Defects Research (Part A), 2012.
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Affiliation(s)
- Baiba Lace
- Latvian Biomedical Study and Research Centre, Riga, Latvia.
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27
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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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Reiter R, Brosch S, Lüdeke M, Fischbein E, Haase S, Pickhard A, Assum G, Schwandt A, Vogel W, Högel J, Maier C. Genetic and environmental risk factors for submucous cleft palate. Eur J Oral Sci 2012; 120:97-103. [PMID: 22409215 DOI: 10.1111/j.1600-0722.2012.00948.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A multifactorial aetiology with genetic and environmental factors is assumed for orofacial clefts. Submucous cleft palate (SMCP), a subgroup of cleft palates with insufficient median fusion of the muscles of the soft palate hidden under the mucosa, has a prevalence of 1:1,250-1:5,000. We described the prevalence of risk factors among 103 German patients with the subtype SMCP and genotyped 24 single nucleotide polymorphisms (SNPs) from 12 candidate genes for orofacial clefts. Analysis of risk factors yielded a positive history for maternal cigarette smoking during pregnancy in 25.2% of the patients, and this was significantly more frequent than in the normal population. The group of patients differed in allele frequencies at SNP rs3917192 of the gene TGFB3 (nominal P = 0.053) and at SNP rs5752638 of the gene MN1 (nominal P = 0.075) compared with 279 control individuals. Our results indicate a potential role of maternal smoking during pregnancy for the formation of SMCP. The analysis of genetic variants hints at the contribution of TGFB3 and MN1 in the aetiology of SMCPs.
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Affiliation(s)
- Rudolf Reiter
- Section of Phoniatrics and Pedaudiology, Department of Otolaryngology, Head and Neck Surgery, University of Ulm, Ulm, Germany.
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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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31
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Mangold E, Ludwig KU, Nöthen MM. Breakthroughs in the genetics of orofacial clefting. Trends Mol Med 2011; 17:725-33. [PMID: 21885341 DOI: 10.1016/j.molmed.2011.07.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 01/03/2023]
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Fakhouri WD, Rhea L, Du T, Sweezer E, Morrison H, Fitzpatrick D, Yang B, Dunnwald M, Schutte BC. MCS9.7 enhancer activity is highly, but not completely, associated with expression of Irf6 and p63. Dev Dyn 2011; 241:340-9. [PMID: 22113860 DOI: 10.1002/dvdy.22786] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2011] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND DNA variation in Interferon Regulatory Factor 6 (IRF6) contributes risk for orofacial clefting, including a common DNA variant rs642961. This DNA variant is located in a multi-species conserved sequence that is 9.7 kb upstream from the IRF6 transcriptional start site (MCS9.7). The MCS9.7 element was shown to possess enhancer activity that mimicked the expression of endogenous Irf6 at embryonic day 11.5 in transient transgenic embryos, and also contains a p63 binding site that transactivates IRF6 expression. To analyze whether the MCS9.7 enhancer is sufficient to drive IRF6 expression, we generated stable transgenic murine lines that carry a MCS9.7-lacZ transgene. We hypothesized that MCS9.7 was sufficient to recapitulate the endogenous expression of Irf6 at other time-points during embryonic development. RESULTS We observed that MCS9.7 activity recapitulated endogenous Irf6 expression in most tissues, but not in the medial edge epithelium (MEE) at E14.5, when Irf6 expression was high during secondary palatal fusion. Also, while MCS9.7 activity and Irf6 expression were associated with p63 expression, we observed MCS9.7 activity and Irf6 expression in periderm, although p63 was absent. CONCLUSION These data suggest that MCS9.7 enhancer activity is not sufficient to recapitulate IRF6 expression, and that p63 expression is not always necessary nor sufficient for transactivation of IRF6.
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Affiliation(s)
- Walid D Fakhouri
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48823, USA
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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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Brito LA, Cruz LA, Rocha KM, Barbara LK, Silva CB, Bueno DF, Aguena M, Bertola DR, Franco D, Costa AM, Alonso N, Otto PA, Passos-Bueno MR. Genetic contribution for non-syndromic cleft lip with or without cleft palate (NS CL/P) in different regions of Brazil and implications for association studies. Am J Med Genet A 2011; 155A:1581-7. [DOI: 10.1002/ajmg.a.34036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 03/16/2011] [Indexed: 11/08/2022]
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Nikopensius T, Kempa I, Ambrozaitytė L, Jagomägi T, Saag M, Matulevičienė A, Utkus A, Krjutškov K, Tammekivi V, Piekuse L, Akota I, Barkane B, Krumina A, Klovins J, Lace B, Kučinskas V, Metspalu A. Variation in FGF1, FOXE1, and TIMP2 genes is associated with nonsyndromic cleft lip with or without cleft palate. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2011; 91:218-25. [PMID: 21462296 DOI: 10.1002/bdra.20791] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/19/2011] [Accepted: 01/23/2011] [Indexed: 12/28/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common complex birth defect caused by the interaction between multiple genes and environmental factors. METHODS Five hundred and eighty-seven single nucleotide polymorphisms in 40 candidate genes related to orofacial clefting were tested for association with CL/P in a clefting sample composed of 300 patients and 606 controls from Estonian, Latvian, and Lithuanian populations. RESULTS In case-control comparisons, the minor alleles of FGF1 rs34010 (p = 4.56 × 10(-4) ), WNT9B rs4968282 (p = 0.0013), and FOXE1 rs7860144 (p = 0.0021) were associated with a decreased risk of CL/P. Multiple haplotypes in FGF1, FOXE1, and TIMP2 and haplotypes in WNT9B, PVRL2, and LHX8 were associated with CL/P. The strongest association was found for protective haplotype rs250092/rs34010 GT in the FGF1 gene (p = 5.01 × 10(-4) ). The strongest epistatic interaction was observed between the COL2A1 and WNT3 genes. CONCLUSIONS Our results provide for the first time evidence implicating FGF1 in the occurrence of CL/P, and support TIMP2 and WNT9B as novel loci predisposing to CL/P. We have also replicated recently reported significant associations between variants in or near FOXE1 and CL/P. It is likely that variation in FOXE1, TIMP2, and the FGF and Wnt signaling pathway genes confers susceptibility to nonsyndromic CL/P in Northeastern European populations.
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Affiliation(s)
- Tiit Nikopensius
- Institute of Molecular and Cell Biology, University of Tartu, Estonia.
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Mostowska A, Hozyasz KK, Wojcicki P, Biedziak B, Paradowska P, Jagodzinski PP. Association between genetic variants of reported candidate genes or regions and risk of cleft lip with or without cleft palate in the polish population. ACTA ACUST UNITED AC 2010; 88:538-45. [DOI: 10.1002/bdra.20687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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