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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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2
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Gowans LJJ, Comnick CL, Mossey PA, Eshete MA, Adeyemo WL, Naicker T, Awotoye WA, Petrin A, Adeleke C, Donkor P, Busch TD, James O, Ogunlewe MO, Li M, Olotu J, Hassan M, Adeniyan OA, Obiri-Yeboah S, Arthur FKN, Agbenorku P, Oti AA, Olatosi O, Adamson OO, Fashina AA, Zeng E, Marazita ML, Adeyemo AA, Murray JC, Butali A. Genome-Wide Scan for Parent-of-Origin Effects in a sub-Saharan African Cohort With Nonsyndromic Cleft Lip and/or Cleft Palate (CL/P). Cleft Palate Craniofac J 2022; 59:841-851. [PMID: 34382870 PMCID: PMC9884465 DOI: 10.1177/10556656211036316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip and/or cleft palate (NSCL/P) have multifactorial etiology where genetic factors, gene-environment interactions, stochastic factors, gene-gene interactions, and parent-of-origin effects (POEs) play cardinal roles. POEs arise when the parental origin of alleles differentially impacts the phenotype of the offspring. The aim of this study was to identify POEs that can increase risk for NSCL/P in humans using a genome-wide dataset. METHODS The samples (174 case-parent trios from Ghana, Ethiopia, and Nigeria) included in this study were from the African only genome wide association studies (GWAS) that was published in 2019. Genotyping of individual DNA using over 2 million multiethnic and African ancestry-specific single-nucleotide polymorphisms from the Illumina Multi-Ethnic Genotyping Array v2 15070954 A2 (genome build GRCh37/hg19) was done at the Center for Inherited Diseases Research. After quality control checks, PLINK was employed to carry out POE analysis employing the pooled subphenotypes of NSCL/P. RESULTS We observed possible hints of POEs at a cluster of genes at a 1 mega base pair window at the major histocompatibility complex class 1 locus on chromosome 6, as well as at other loci encompassing candidate genes such as ASB18, ANKEF1, AGAP1, GABRD, HHAT, CCT7, DNMT3A, EPHA7, FOXO3, lncRNAs, microRNA, antisense RNAs, ZNRD1, ZFAT, and ZBTB16. CONCLUSION Findings from our study suggest that some loci may increase the risk for NSCL/P through POEs. Additional studies are required to confirm these suggestive loci in NSCL/P etiology.
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Affiliation(s)
- LJJ Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana,Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - CL Comnick
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - PA Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - MA Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - WL Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - T Naicker
- Department of Pediatrics, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, South Africa
| | - WA Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - A Petrin
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - C Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - P Donkor
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - TD Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - O James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - MO Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - M Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - J Olotu
- Department of Anatomy, University of Port Harcourt, Nigeria
| | - M Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - OA Adeniyan
- NHS Foundation Trust (Queens Hospital, Belvedere Road, Burton-On-Trent), Staffordshire, UK
| | - S Obiri-Yeboah
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - FKN Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - P Agbenorku
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - AA Oti
- School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - O Olatosi
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - OO Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - AA Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - E Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - ML Marazita
- Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AA Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - JC Murray
- Department of Pediatrics, University of Iowa, Iowa, IA, USA
| | - A Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
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Nguyen DM, Suzuki S, Imura H, Niimi T, Furukawa H, Ta TV, Tong SM, Nguyen TT, Pham LNG, Tran DL, Natsume N. Family based and case-control designs reveal an association of TFAP2A in nonsyndromic cleft lip only among Vietnamese population. Mol Genet Genomic Med 2021; 9:e1754. [PMID: 34310873 PMCID: PMC8457689 DOI: 10.1002/mgg3.1754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Aims Dozens of causative genes and their mechanisms of nonsyndromic cleft lip with or without cleft palate (NSCL/P) were revealed through genome‐wide association and linkage studies. Results were, however, not always replicated in different populations or methodologies. This study used case–control and family based approaches to investigate the etiology of NSCL/P and its two subtypes: nonsyndromic cleft lip only (NSCLO) and nonsyndromic cleft lip and palate (NSCLP) among the Vietnamese population. Methods Two hundred and seventeen NSCL/P case‐parent trios (one affected child and two parents), including 105 NSCLO and 112 NSCLP were involved for a family based design; and 273 ethnic and region‐matched healthy controls with no cleft history in their families were recruited for a case–control design. Three SNPs consisting of TFAP2A (rs1675414 and rs303048) and 8q24 (rs987525) were genotyped using the TaqMan SNP genotyping assay. Results TFAP2A rs1675414 was associated with NSCLO, replicated by both case‐control and family based tests. Other SNPs yielded no evidence of susceptibility to NSCL/P or two subtypes. Conclusion The current investigation suggests an intriguing role of TFAP2A in the etiology of NSCLO among the Vietnamese population. This study used case‐control and family‐based approaches to investigate the etiology of NSCL/P and its two subtypes: nonsyndromic cleft lip only (NSCLO), nonsyndromic cleft lip and palate (NSCLP) among Vietnamese population. TFAP2A rs1675414 was associated with NSCLO, replicated by both case‐control and family‐based tests.
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Affiliation(s)
- Duc Minh Nguyen
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Teruyuki Niimi
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Hiroo Furukawa
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
| | - Thanh-Van Ta
- Center for Gene and Protein Research, Hanoi Medical University, Hanoi, Vietnam
| | - Son Minh Tong
- School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam
| | - Tra Thu Nguyen
- School of Odonto-stomatology, Hanoi Medical University, Hanoi, Vietnam.,Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Loc Nguyen Gia Pham
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Odonto - Maxillo Facial Hospital of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Duy Le Tran
- Nguyen Dinh Chieu General Hopsital, Ben Tre, Vietnam
| | - Nagato Natsume
- Division of Research and Treatment for Oral Maxillofacial Congenital Anomalies, Aichi Gakuin University, Nagoya, Japan.,Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, Nagoya, Japan.,Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, Nagoya, Japan
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Patel J, Bircan E, Tang X, Orloff M, Hobbs CA, Browne ML, Botto LD, Finnell RH, Jenkins MM, Olshan A, Romitti PA, Shaw GM, Werler MM, Li J, Nembhard WN. Paternal genetic variants and risk of obstructive heart defects: A parent-of-origin approach. PLoS Genet 2021; 17:e1009413. [PMID: 33684136 PMCID: PMC7971842 DOI: 10.1371/journal.pgen.1009413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/18/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Previous research on risk factors for obstructive heart defects (OHDs) focused on maternal and infant genetic variants, prenatal environmental exposures, and their potential interaction effects. Less is known about the role of paternal genetic variants or environmental exposures and risk of OHDs. We examined parent-of-origin effects in transmission of alleles in the folate, homocysteine, or transsulfuration pathway genes on OHD occurrence in offspring. We used data on 569 families of liveborn infants with OHDs born between October 1997 and August 2008 from the National Birth Defects Prevention Study to conduct a family-based case-only study. Maternal, paternal, and infant DNA were genotyped using an Illumina Golden Gate custom single nucleotide polymorphism (SNP) panel. Relative risks (RR), 95% confidence interval (CI), and likelihood ratio tests from log-linear models were used to estimate the parent-of-origin effect of 877 SNPs in 60 candidate genes in the folate, homocysteine, and transsulfuration pathways on the risk of OHDs. Bonferroni correction was applied for multiple testing. We identified 3 SNPs in the transsulfuration pathway and 1 SNP in the folate pathway that were statistically significant after Bonferroni correction. Among infants who inherited paternally-derived copies of the G allele for rs6812588 in the RFC1 gene, the G allele for rs1762430 in the MGMT gene, and the A allele for rs9296695 and rs4712023 in the GSTA3 gene, RRs for OHD were 0.11 (95% CI: 0.04, 0.29, P = 9.16x10-7), 0.30 (95% CI: 0.17, 0.53, P = 9.80x10-6), 0.34 (95% CI: 0.20, 0.57, P = 2.28x10-5), and 0.34 (95% CI: 0.20, 0.58, P = 3.77x10-5), respectively, compared to infants who inherited maternally-derived copies of the same alleles. We observed statistically significant decreased risk of OHDs among infants who inherited paternal gene variants involved in folate and transsulfuration pathways. Obstructive heart defects are birth defects that cause obstruction to the blood flow of the developing heart. Common OHDs include coarctation of the aorta, aortic stenosis and pulmonary stenosis. While there is a fair amount of literature indicating an association between maternal genetic variants and OHDs, less is known about the role of paternal genetic variants in the etiology of OHDs. We used a genotype clustering algorithm, SNPMClust, that was developed in-house at the Arkansas Center for Birth Defects Research and Prevention to study the role of paternal genetic variants in the folate, homocysteine and transsulfuration pathways. Maternal, paternal, and infant DNA specimens were collected from participants of the National Birth Defects Prevention Study, a large population-based case-control study in the United States, and were genotyped using an Illumina Golden Gate custom single nucleotide polymorphism (SNP) panel. We identified 4 SNPs in the folate and transsulfuration pathways, rs6812588, rs1762430, rs9296695, and rs4712023, that were associated with a statistically significant decreased risk of OHDs for infants who inherited a paternally-derived copy of the variant allele compared to infants who inherited a maternal copy of the variant allele. In conclusion, we observed a significantly decreased risk and less epigenetic influence of paternal genetic variants on OHDs compared to maternally-derived variants.
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Affiliation(s)
- Jenil Patel
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston (UTHealth) School of Public Health, Dallas, TX, United States of America
| | - Emine Bircan
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Xinyu Tang
- Biostatistics Program, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR, United States of America
| | - Mohammed Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Charlotte A. Hobbs
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, United States of America
| | - Marilyn L. Browne
- Birth Defects Research Section, New York State Department of Health, Albany, NY, United States of America
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY, United States of America
| | - Lorenzo D. Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, UT, United States of America
| | - Richard H. Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States of America
| | - Mary M. Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Andrew Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA, United States of America
| | - Gary M. Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States of America
| | - Martha M. Werler
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, United States of America
| | - Jingyun Li
- Biostatistics Program, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Research Institute, Little Rock, AR, United States of America
| | - Wendy N. Nembhard
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Arkansas Center for Birth Defects Research and Prevention, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- * E-mail:
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5
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Bezamat M, Souza JF, Silva FMF, Corrêa EG, Fatturi AL, Brancher JA, Carvalho FM, Cavallari T, Bertolazo L, Machado-Souza C, Koruyucu M, Bayram M, Racic A, Harrison BM, Sweat YY, Letra A, Studen-Pavlovich D, Seymen F, Amendt B, Werneck RI, Costa MC, Modesto A, Vieira AR. Gene-environment interaction in molar-incisor hypomineralization. PLoS One 2021; 16:e0241898. [PMID: 33406080 PMCID: PMC7787379 DOI: 10.1371/journal.pone.0241898] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/22/2020] [Indexed: 01/12/2023] Open
Abstract
Molar incisor hypomineralization (MIH) is an enamel condition characterized by lesions ranging in color from white to brown which present rapid caries progression, and mainly affects permanent first molars and incisors. These enamel defects usually occur when there are disturbances during the mineralization or maturation stage of amelogenesis. Both genetic and environmental factors have been suggested to play roles in MIH’s development, but no conclusive risk factors have shown the source of the disease. During head and neck development, the interferon regulatory factor 6 (IRF6) gene is involved in the structure formation of the oral and maxillofacial regions, and the transforming growth factor alpha (TGFA) is an essential cell regulator, acting during proliferation, differentiation, migration and apoptosis. In this present study, it was hypothesized that these genes interact and contribute to predisposition of MIH. Environmental factors affecting children that were 3 years of age or older were also hypothesized to play a role in the disease etiology. Those factors included respiratory issues, malnutrition, food intolerance, infection of any sort and medication intake. A total of 1,065 salivary samples from four different cohorts were obtained, and DNA was extracted from each sample and genotyped for nine different single nucleotide polymorphisms. Association tests and logistic regression implemented in PLINK were used for analyses. A potential interaction between TGFA rs930655 with all markers tested in the cohort from Turkey was identified. These interactions were not identified in the remaining cohorts. Associations (p<0.05) between the use of medication after three years of age and MIH were also found, suggesting that conditions acquired at the age children start to socialize might contribute to the development of MIH.
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Affiliation(s)
- Mariana Bezamat
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Juliana F. Souza
- Department of Stomatology, Federal University of Paraná, Curitiba, State of Paraná, Brazil
| | - Fernanda M. F. Silva
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emilly G. Corrêa
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Aluhe L. Fatturi
- Department of Stomatology, Federal University of Paraná, Curitiba, State of Paraná, Brazil
| | - João A. Brancher
- Graduate Program of Dentistry, Positivo University, Curitiba, State of Pará, Brazil
| | - Flávia M. Carvalho
- Department of Genetics, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tayla Cavallari
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Laís Bertolazo
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Cleber Machado-Souza
- Graduate Program of Applied Biotechnology to Child and Adolescent Health, Pequeno Príncipe College, Curitiba, State of Pará, Brazil
| | - Mine Koruyucu
- Department of Pedodontics, Istanbul University, Istanbul, Turkey
| | - Merve Bayram
- Department of Pedodontics, Medipol Istanbul University, Istanbul, Turkey
| | - Andrea Racic
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin M. Harrison
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yan Y. Sweat
- Craniofacial Anomalies Research Center and Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, Iowa, United States of America
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, and Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston, Texas, United States of America
| | - Deborah Studen-Pavlovich
- Department of Pediatric Dentistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Figen Seymen
- Department of Pedodontics, Istanbul University, Istanbul, Turkey
| | - Brad Amendt
- Craniofacial Anomalies Research Center and Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, Iowa, United States of America
| | - Renata I. Werneck
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Marcelo C. Costa
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana Modesto
- Department of Pediatric Dentistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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6
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Garland MA, Reynolds K, Zhou CJ. Environmental mechanisms of orofacial clefts. Birth Defects Res 2020; 112:1660-1698. [PMID: 33125192 PMCID: PMC7902093 DOI: 10.1002/bdr2.1830] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022]
Abstract
Orofacial clefts (OFCs) are among the most common birth defects and impart a significant burden on afflicted individuals and their families. It is increasingly understood that many nonsyndromic OFCs are a consequence of extrinsic factors, genetic susceptibilities, and interactions of the two. Therefore, understanding the environmental mechanisms of OFCs is important in the prevention of future cases. This review examines the molecular mechanisms associated with environmental factors that either protect against or increase the risk of OFCs. We focus on essential metabolic pathways, environmental signaling mechanisms, detoxification pathways, behavioral risk factors, and biological hazards that may disrupt orofacial development.
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Affiliation(s)
- Michael A. Garland
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
| | - Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, CA 95616
| | - Chengji J. Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, CA 95616
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[Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52. [PMID: 33047712 PMCID: PMC7653437 DOI: 10.19723/j.issn.1671-167x.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios. METHODS We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction. RESULTS A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10-4). CONCLUSION Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.
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Senaldi L, Smith-Raska M. Evidence for germline non-genetic inheritance of human phenotypes and diseases. Clin Epigenetics 2020; 12:136. [PMID: 32917273 PMCID: PMC7488552 DOI: 10.1186/s13148-020-00929-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
It is becoming increasingly apparent that certain phenotypes are inherited across generations independent of the information contained in the DNA sequence, by factors in germ cells that remain largely uncharacterized. As evidence for germline non-genetic inheritance of phenotypes and diseases continues to grow in model organisms, there are fewer reports of this phenomenon in humans, due to a variety of complications in evaluating this mechanism of inheritance in humans. This review summarizes the evidence for germline-based non-genetic inheritance in humans, as well as the significant challenges and important caveats that must be considered when evaluating this process in human populations. Most reports of this process evaluate the association of a lifetime exposure in ancestors with changes in DNA methylation or small RNA expression in germ cells, as well as the association between ancestral experiences and the inheritance of a phenotype in descendants, down to great-grandchildren in some cases. Collectively, these studies provide evidence that phenotypes can be inherited in a DNA-independent manner; the extent to which this process contributes to disease development, as well as the cellular and molecular regulation of this process, remain largely undefined.
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Affiliation(s)
- Liana Senaldi
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA
| | - Matthew Smith-Raska
- Division of Newborn Medicine, Department of Pediatrics, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, NY, USA. .,Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA.
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9
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Parental transmission effect of PDGF-C gene variants on non-syndromic cleft lip with or without cleft palate. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Shu X, Shu S, Yang L. Association between methylenetetrahydrofolate reductase polymorphisms and non-syndromic cleft lip with or without palate susceptibility: an updated systematic review and meta-analysis. Br J Oral Maxillofac Surg 2019; 57:819-830. [PMID: 31303355 DOI: 10.1016/j.bjoms.2019.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 06/17/2019] [Indexed: 02/05/2023]
Abstract
Methylenetetrahydrofolate reductase (MTHFR) polymorphisms are thought to be involved in the development of cleft lip with or without cleft palate (NSCL/P), but published results are contradictory. We therefore designed an updated meta-analysis to pool eligible studies and to evaluate further the possible relations between MTHFR polymorphisms (c.677C>T and c.1298A>C) and susceptibility to NSCL/P. A comprehensive search based on PubMed, Medline, Web of Science, and Embase databases was made up to February 2018. Twenty-three case-control and 10 case-parent trio studies (including 1149 cases and 1161 controls) were retrieved. Odds ratio (OR) with 95% CI were used to estimate the pooled strength of association under different genetic models. The Q test and I2 test were used to estimate heterogeneity among studies, the quality of which was assessed using the Newcastle-Ottawa scale. In the MTHFR c.677C>T polymorphism group, there were significant overall results for the recessive (OR 1.231, 95%CI 1.092 to 1.387) and homozygote (OR 1.252, 95%CI 1.078 to 1.456) models. Subgroup analysis by subjects and ethnicity identified only associations in European mothers for the recessive model and the homozygote model. For the c.1298A>C group, there were no significant results for either European or Asian patients for all genetic models. The MTHFR c.677C>T polymorphism might increase susceptibility to NSCL/P in European mothers, but was negatively associated in Asian patients, and the MTHFR c.1298A>C polymorphism is not involved in the development of NSCL/P in either European or Asian patients.
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Affiliation(s)
- X Shu
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - S Shu
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - L Yang
- Cleft Lip and Palate Treatment Center, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
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11
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Nembhard WN, Tang X, Li J, MacLeod SL, Levy J, Schaefer GB, Hobbs CA. A parent-of-origin analysis of paternal genetic variants and increased risk of conotruncal heart defects. Am J Med Genet A 2018; 176:609-617. [PMID: 29399948 DOI: 10.1002/ajmg.a.38611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/04/2017] [Accepted: 12/26/2017] [Indexed: 12/12/2022]
Abstract
The association between conotruncal heart defects (CTHDs) and maternal genetic and environmental exposures is well studied. However, little is known about paternal genetic or environmental exposures and risk of CTHDs. We assessed the effect of paternal genetic variants in the folate, homocysteine, and transsulfuration pathways on risk of CTHDs in offspring. We utilized National Birth Defects Prevention Study data to conduct a family-based case only study using 616 live-born infants with CTHDs, born October 1997-August 2008. Maternal, paternal and infant DNA was genotyped using an Illumina® Golden Gate custom single nucleotide polymorphism (SNP) panel. Relative risks (RR) and 95% confidence intervals (CI) from log-linear models determined parent of origin effects for 921 SNPs in 60 candidate genes involved in the folate, homocysteine, and transsulfuration pathways on risk of CTHDs. The risk of CTHD among children who inherited a paternally derived copy of the A allele on GLRX (rs17085159) or the T allele of GLRX (rs12109442) was 0.23 (95%CI: 0.12, 0.42; p = 1.09 × 10-6 ) and 0.27 (95%CI: 0.14, 0.50; p = 2.06 × 10-5 ) times the risk among children who inherited a maternal copy of the same allele. The paternally inherited copy of the GSR (rs7818511) A allele had a 0.31 (95%CI: 0.18, 0.53; p = 9.94 × 10-6 ] risk of CTHD compared to children with the maternal copy of the same allele. The risk of CTHD is less influenced by variants in paternal genes involved in the folate, homocysteine, or transsulfuration pathways than variants in maternal genes in those pathways.
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Affiliation(s)
- Wendy N Nembhard
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas.,Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Xinyu Tang
- Division of Biostatistics, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Jingyun Li
- Division of Biostatistics, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Stewart L MacLeod
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Joseph Levy
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Gerald B Schaefer
- Division of Genetics and Metabolism, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
| | - Charlotte A Hobbs
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children's Research Institute, Little Rock, Arkansas
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12
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Liu D, Schwender H, Wang M, Wang H, Wang P, Zhu H, Zhou Z, Li J, Wu T, Beaty TH. Gene-gene interaction between MSX1 and TP63 in Asian case-parent trios with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res 2018; 110:317-324. [PMID: 29341488 DOI: 10.1002/bdr2.1139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/27/2017] [Accepted: 09/06/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P). METHODS A total of 130 single-nucleotide polymorphisms (SNPs) in or near SUMO1, MSX1, and TP63 was analyzed among 1,038 Asian NSCL/P trios ascertained through an international consortium. Conditional logistic regression models were used to explore gene-gene (G × G) and gene-environment (G × E) interaction involving maternal environmental tobacco smoke and multivitamin supplementation. Bonferroni correction was used for G × E analysis and permutation tests were used for G × G analysis. RESULTS While transmission disequilibrium tests and gene-environment interaction analysis showed no significant results, we did find signals of gene-gene interaction between SNPs near MSX1 and TP63. Three pairwise interactions yielded significant p values in permutation tests (rs884690 and rs9290890 with p = 9.34 × 10-5 and empirical p = 1.00 × 10-4 , rs1022136 and rs4687098 with p = 2.41 × 10-4 and empirical p = 2.95 × 10-4 , rs6819546 and rs9681004 with p = 5.15 × 10-4 and empirical p = 3.02 × 10-4 ). CONCLUSION Gene-gene interaction between MSX1 and TP63 may influence the risk of NSCL/P in Asian populations. Our study provided additional understanding of the genetic etiology of NSCL/P and underlined the importance of considering gene-gene interaction in the etiology of this common craniofacial malformation.
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Affiliation(s)
- Dongjing Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Department of Statistics and Information, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, Maryland
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Samadi S, Ebadifar A, Khorram Khorshid HR, Kamali K, Badiee M. Interaction Effect of RsaI and BamHI Polymorphisms of TGFα, BMP2 and BMP4 on the Occurrence of Non-Syndromic Cleft Lip and Palate in Iranian Patients. Avicenna J Med Biotechnol 2018; 10:248-252. [PMID: 30555658 PMCID: PMC6252027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
BACKGROUND Orofacial cleft is the most common congenital defect of the maxillofacial region. Its non-syndromic type is multi-factorial, and several genes are involved in its occurrence. This study aimed to assess the interaction effect of Rsal and BamHI polymorphisms of Transforming Growth Factor-alpha (TGFα) gene and Bone Morphogenetic Protein-2 (BMP2) and BMP4 variants on the occurrence of Non-Syndromic Cleft Lip and Palate (NSCLP) in the Iranian population. METHODS This case-control study was conducted on 120 children with NSCLP and 215 healthy children. Genotyping of the TGFA/BamHI (rs11466297), TGFA/RsaI (rs37322-48), BMP4 (rs17563) and BMP2 (rs235768) was performed by Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP) methods. Logistic regression was applied to determine the effective factors and the interaction effect of different variants on the occurrence of NSCLP. RESULTS Gender of patients had no significant association with the occurrence of NSCLP (p=0.335). Multiple logistic regression showed that the interaction effect of the aforementioned polymorphisms on the occurrence of NSCLP was not statistically significant (p=1.000). CONCLUSION Although the individual effect of each of the BMP4, BMP2, RsaI and BamHI variants on the occurrence of NSCLP in the Iranian population has been previously confirmed, their interaction does not play a role in this respect.
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Affiliation(s)
| | - Asghar Ebadifar
- Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Department of Orthodontic, Faculty of Dentistry, Shahid Behehsti University of Medical Sciences, Tehran, Iran,Corresponding author: Asghar Ebadifar, Ph.D., Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran, Tel: +98 9122173808, E-mail:
| | | | - Koorosh Kamali
- Department of Public Health, Faculty of Public Health, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammadreza Badiee
- Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Liu D, Wang H, Schwender H, Marazita ML, Wang Z, Yuan Y, Wang P, Liang KY, Wu-Chou YH, Wang M, Shi B, Zhu H, Wu T, Beaty TH. Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios. Am J Med Genet A 2017; 173:1489-1494. [PMID: 28402597 DOI: 10.1002/ajmg.a.38190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/13/2016] [Accepted: 02/01/2017] [Indexed: 11/07/2022]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G × G, as well as G × E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G × G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P = 7.2 × 10-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G × G interactions for the genetic association analysis of NSCL/P.
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Affiliation(s)
- Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zhuqing Wang
- School of Public Health, Peking University, Beijing, China
| | - Yuan Yuan
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | | | | | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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Du J, Deng J. Associations Between TGFA/TGFB3/MSX1 Gene Polymorphisms and Congenital Non-Syndromic Hearing Impairment in a Chinese Population. Med Sci Monit 2016; 22:2253-2266. [PMID: 27356075 PMCID: PMC4930271 DOI: 10.12659/msm.896527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/17/2015] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND The aim of this study was to investigate whether the TGFA/TGFB3/MSX1 gene polymorphisms and haplotypes lead to individual differences between congenital non-syndromic hearing impairment (NSHI) patients and normal people in a Chinese population and to analyze the risk factors for NSHI. MATERIAL AND METHODS Between December 2010 and September 2014, 343 congenital NSHI patients were recruited as cases, and 272 healthy subjects were recruited as controls. Denaturing high-performance liquid chromatography (DHPLC) was used to identify genotypes, SHEsis software was used to conduct gene linkage disequilibrium and haplotype analyses, and regression analysis was performed to identify risk factors for congenital NSHI. RESULTS The distribution of genotype frequencies and allele frequencies of TGFA rs3771494, TGFB3 rs3917201 and rs2268626, and MSX1 rs3821949 and rs62636562 were significantly different between the case and the control groups (all P<0.05). TGFA/TGFB3/MSX1 gene rs3771494, rs1058213, rs3917201, rs2268626, rs3821949, and rs62636562 haplotype analysis showed that haplotype CCGTAC and TTACGT might be protective factors (both P<0.001), while TTGCGC might be a risk factor for the normal population (P<0.001). The other risk factors include paternal smoking, advanced maternal age, maternal sickness history, maternal contact with pesticides or similar drugs, maternal abortion history, maternal medication history, maternal passive smoking history during pregnancy, rs3771494 CT, rs2268626 CC and TC, and rs3821949 GG and AG genotypes were risk factors (all P<0.05), while maternal vitamin supplements during pregnancy, rs3917201 GA, rs62636562 TT and CT genotypes were protective factors for congenital NSHI (all P<0.05). CONCLUSIONS rs3771494, rs3917201, rs2268626, rs3821949 and rs62636562 might be associated with congenital NSHI.
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Mehrotra D. Genomic expression in non syndromic cleft lip and palate patients: A review. J Oral Biol Craniofac Res 2015; 5:86-91. [PMID: 26258020 DOI: 10.1016/j.jobcr.2015.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.
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Affiliation(s)
- D Mehrotra
- Professor, Department of Oral & Maxillofacial Surgery, King George Medical University, Lucknow, India
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Kim BM, Kim YH, Kim DH, Park JW, Baek SH. Genetic Effect of Transforming Growth Factor Alpha Gene Variants on the Risk of Nonsyndromic Cleft Lip with or without Palate in Korean Populations. Cleft Palate Craniofac J 2015; 52:293-300. [DOI: 10.1597/13-067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective To identify the contribution of TGFA gene variants to the risk of nonsyndromic cleft lip with or without palate (NS-CL±P). Design The samples were from 142 Korean NS-CL±P families and 119 control parents having nonaffected children. Minor allele frequency, heterozygosity, and χ2 test for Hardy-Weinberg equilibrium were calculated for each of 10 selected single-nucleotide polymorphisms (SNPs). Ten SNPs were used to examine the association of case-parent trios with the transmission disequilibrium test (TDT) and conditional logistic regression models (CLRMs). Both allelic and genotypic TDTs for individual SNPs and sliding windows of haplotypes consisting of two to five SNPs were tested using family- and haplotype-based association test programs. Genotypic odd ratios (GORs) were obtained from CLRMs using STATA software. The parent-of-origin effect was evaluated for 10 SNPs, and a comparison between 218 case parents and 119 control parents was performed to investigate paternal and maternal ORs. Results Family-based TDT and haplotype analysis exhibited no statistical significance, but a relatively meaningful association was shown with rs3771497 (all P < .05; two SNPs, rs3771497 and rs3755377; five SNPs, rs3771497, rs3755377, rs3771485, rs11466212, and rs3771475). G/G homozygotes at rs3771497 have a significant decreased risk of NS-CL±P (GOR = 0.30, P < .01). No SNPs showed parent-of-origin effects. However, in the comparison between case parents and control parents, a single-marker analysis of maternal line showed a significant association with NS-CL±P in rs3771497 ( P < .001, recessive model). Conclusion The association of the TGFA gene with NS-CL±P in Korean populations was not clearly found. However, the etiologic effect of the TGFA gene on NS-CL±P patients should be investigated in terms of maternal genotype influence.
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Affiliation(s)
- Bo-Mi Kim
- Department of Orthodontics, School of Dentistry, Seoul National University, Seoul, South Korea
| | - Young Ho Kim
- Department of Orthodontics, The Institute of Oral Health Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dong-Hyun Kim
- Department of Social Medicine, College of Medicine, Hallym University, Chuncheon, Gangwon Province, South Korea
| | - Ji Wan Park
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, Gangwon Province, South Korea
| | - Seung-Hak Baek
- Department of Orthodontics, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, South Korea
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Role of angiogenesis-related genes in cleft lip/palate: review of the literature. Int J Pediatr Otorhinolaryngol 2014; 78:1579-85. [PMID: 25176321 DOI: 10.1016/j.ijporl.2014.08.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/30/2014] [Accepted: 08/01/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Cleft lip and cleft palate (CLP) are the most common congenital craniofacial anomalies. They have a multifactorial etiology and result from an incomplete fusion of the facial buds. Two main mechanisms, acting alone or interacting with each other, were evidenced in this fusion defect responsible for CLP: defective tissue development and/or defective apoptosis in normal or defective tissues. The objective of this work was to study the implication and role of angiogenesis-related genes in the etiology of CL/P. METHODS Our methodological approach included a systematic and thorough analysis of the genes involved in CL/P (syndromic and non-syndromic forms) including previously identified genes but also genes that could potentially be angiogenesis-related (OMIM, Pub Med).We studied the interactions of these different genes and their relationships with potential environmental factors. RESULTS TGFβ, FGA, PDGFc, PDGFRa, FGF, FGFR1, FGFR2 growth factors as well as MMP and TIMP2 proteolytic enzymes are involved in the genesis of CLP (P>L). Furthermore, 18 genes involved in CLP also interact with angiogenesis-related genes. DISCUSSION Even if the main angiogenesis-related genes involved in CLP formation are genes participating in several biological activities and their implication might not be always related to angiogenesis defects, they nevertheless remain an undeniably important research pathway. Furthermore, their interactions with environmental factors make them good candidates in the field of CLP prevention.
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Hao Y, Mi N, Jiao X, Zheng X, Song T, Zhuang D, Tian S, Feng D. Association of JARID2 polymorphisms with non-syndromic orofacial clefts in northern Chinese Han population. J Oral Pathol Med 2014; 44:386-91. [PMID: 25155265 DOI: 10.1111/jop.12244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Non-syndromic orofacial clefts (NSOC) are the most common human craniofacial malformation in all worldwide populations. Recently, the jumoji AT-rich interaction domain 2 (JARID2) had been reported to be a novel candidate gene for non-syndromic cleft lip with or without cleft palate (CL/P). The SNPs rs2076056, rs2237138 and rs2299043 in JARID2 were highly significant in Italian families. MATERIAL AND METHODS In the current research, a case-control study was conducted to examine the association between these three SNPs and NSOC in a northern Chinese Han population. Genotyping of the three SNPs were performed using SNaPshot minisequencing technique. RESULTS Distribution of rs2237138 genotypes in CL/P group was different from those in the control group (P = 0.04), but significant results did not persist after Benjamini and Hochberg false discovery rate (FDR) correction for multiple tests. Further logistic regression analysis showed that rs2237138 GG genotypes were associated with decreased CL/P susceptibility (OR = 0.34, 95% CI = 0.13-0.84), compared with the AA wild-type homozygote. For the haplotype CGT, a statistically difference was identified between the CL/P group and controls (P = 0.04). And carriers of GAT haplotype were considered to be less frequent among cleft palate only group as compared to controls (P = 0.02). However, both of the haplotypes association did not remain statistically significant after Benjamini and Hochberg FDR correction. CONCLUSION We got a weak association between these polymorphisms and NSOC in both single-marker and haplotype analyses. Our data further strengthen the conclusion that JARID2 polymorphisms are associated with NSOC susceptibility.
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Affiliation(s)
- Yanru Hao
- Department of Oral Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, China
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Connolly S, Heron EA. Review of statistical methodologies for the detection of parent-of-origin effects in family trio genome-wide association data with binary disease traits. Brief Bioinform 2014; 16:429-48. [PMID: 24903222 DOI: 10.1093/bib/bbu017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/14/2014] [Indexed: 11/13/2022] Open
Abstract
The detection of parent-of-origin effects aims to identify whether the functionality of alleles, and in turn associated phenotypic traits, depends on the parental origin of the alleles. Different parent-of-origin effects have been identified through a variety of mechanisms and a number of statistical methodologies for their detection have been proposed, in particular for genome-wide association studies (GWAS). GWAS have had limited success in explaining the heritability of many complex disorders and traits, but successful identification of parent-of-origin effects using trio (mother, father and offspring) GWAS may help shed light on this missing heritability. However, it is important to choose the most appropriate parent-of-origin test or methodology, given knowledge of the phenotype, amount of available data and the type of parent-of-origin effect(s) being considered. This review brings together the parent-of-origin detection methodologies available, comparing them in terms of power and type I error for a number of different simulated data scenarios, and finally offering guidance as to the most appropriate choice for the different scenarios.
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Jung SH, Lee AY, Park JW, Baek SH, Kim YH. Investigation of Parental Transmission of RUNX2 Single Nucleotide Polymorphism and Its Association with Nonsyndromic Cleft Lip with or Without Palate. Cleft Palate Craniofac J 2014; 51:234-9. [DOI: 10.1597/12-312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective To investigate the association and parental transmission of RUNX2 single nucleotide polymorphisms (SNPs) with risk of nonsyndromic cleft lip with or without cleft palate (NS-CL±P). Design Four RUNX2 SNPs in 142 Korean NS-CL±P families (nine cleft lip, 26 cleft lip and alveolus, and 107 cleft lip and palate; 76 trios and 66 dyads) were genotyped. The minor allele frequency, heterozygosity, and chi-square test for Hardy-Weinberg equilibrium at each SNP were computed between parents. Pairwise linkage disequilibrium was computed as D′ and r2 for all SNPs. Both allelic and genotypic transmission disequilibrium tests (TDTs) were performed for individual SNPs using a family-based association test program. Sliding windows of haplotypes consisting of two to four SNPs were tested using a haplotype-based association test program. Genotypic odds ratios (GORs) were calculated from conditional logistic regression models. Parent-of-origin effects were assessed using transmission asymmetry test and parent-of-origin likelihood ratio test. Results The family-based TDT showed significant evidence of linkage and association at rs1934328 ( P = .001). In the haplotype analysis, two, three, and four haplotypes containing rs1934328 revealed significant associations ( P = .0017, P = .0022, and P = .0020, respectively). The genotypes A/T and T/T at rs1934328 were significantly associated with NS-CL±P compared with the genotype A/A (GOR = 2.75, 95% confidence interval [CI] = 1.39–5.45, P =0.0019 in the dominant model; GOR = 5.38, 95% CI = 1.34–21.68, P = .0046 in the additive model). However, no parent-of origin effect was observed. Conclusion These findings suggest possible involvement of RUNX2-rs 194328 in the etiology of NS-CL±P in Korean cleft-parent trios without excess parental transmission.
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Affiliation(s)
- Seung Hee Jung
- Department of Orthodontics, The Institute of Oral Health Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | - Ji Wan Park
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, Gangwon Province, South Korea
| | - Seung-Hak Baek
- Department of Orthodontics, School of Dentistry, Dental Research Institute, Seoul National University, Seoul, South Korea
| | - Young Ho Kim
- Department of Orthodontics, The Institute of Oral Health Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Wu J, Tong S, Zhan Z, Zhang J, Chen C, Hu S, Wang R. TGF-α gene variations and increased susceptibility of gastric cancer in an Eastern Chinese Han population. Biomarkers 2013; 19:9-15. [PMID: 24237184 DOI: 10.3109/1354750x.2013.859736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Transforming growth factor-alpha (TGF-α) correlates with deep invasion, advanced stage and poor prognosis in gastric cancer. Genetic variants in the 3' untranslated region (UTR) of TGF-α gene may influence the stability and post-transcriptional regulation of mRNA and contribute to gastric cancer predisposition. To test this hypothesis, we genotyped five polymorphisms in 3'UTR (rs3771527, rs503314, rs473698, rs3732253 and rs538118) and one in 3' near region (rs11466306) of the TGF-α gene by polymerase chain reaction-ligation detection reaction methods (PCR-LDR). We found that GA/AA genotype of rs11466306 in the 3' near gene could increase the risk of overall gastric cancer (adjusted OR = 1.499, 95%CI: 1.101-2.041), compared to the wild homozygous GG genotype. Meanwhile, the risk effect was more obvious in the intestinal gastric cancer and gastric noncardia cancer (adjusted OR = 1.682, 95%CI: 1.188-2.380; adjusted OR = 1.495, 95%CI: 1.072-2.086, respectively), but not for the diffuse type and gastric cardia cancer (p > 0.05). CT/TT genotype for rs3732253 in the 3' UTR was associated with increased risk of intestinal gastric cancer (adjusted OR = 1.464, 95%CI: 1.036-2.069), compared to their wild homozygous genotypes. These findings indicate that potentially functional TGF-α gene variant may contribute to the risk of intestinal gastric cancer and/or gastric noncardia cancer and could be used as molecular markers for detecting intestinal gastric cancer and/or gastric noncardia cancer in Chinese Han population.
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Affiliation(s)
- Juan Wu
- Discipline of Chinese and Western Integrative Medicine, Nanjing University of Chinese Medicine , Nanjing , China
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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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Zeng N, Wu J, Zhu WC, Ma L, Jia ZL, Shi B. Associations between EYA1 single-nucleotide polymorphisms and non-syndromic orofacial clefts in Western Han Chinese. J Oral Pathol Med 2013; 42:711-5. [PMID: 23601008 DOI: 10.1111/jop.12063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Ni Zeng
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
| | - Jun Wu
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
| | - Wen-Chao Zhu
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
| | - Li Ma
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
| | - Zhong-Lin Jia
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
| | - Bing Shi
- State Key Laboratory of Oral Diseases; West China Hospital of Stomatology; Sichuan University; Chengdu China
- Department of Cleft Lip and Palate Surgery; West China Hospital of Stomatology, Sichuan University; Chengdu China
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Wu D, Wang M, Wang X, Yin N, Song T, Li H, Zhang F, Zhang Y, Ye Z, Yu J, Wang DM, Zhao Z. Maternal transmission effect of a PDGF-C SNP on nonsyndromic cleft lip with or without palate from a Chinese population. PLoS One 2012; 7:e46477. [PMID: 23029525 PMCID: PMC3460900 DOI: 10.1371/journal.pone.0046477] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 08/31/2012] [Indexed: 11/30/2022] Open
Abstract
Cleft lip with or without palate (CL/P) is a common congenital anomaly with a high birth prevalence in China. Based on a previous linkage signal of nonsyndromic CL/P (NSCL/P) on the chromosomal region 4q31–q32 from the Chinese populations, we screened the 4q31–q32 region for susceptibility genes in 214 trios of Han Chinese. PDGF-C, an important developmental factor, resides in the region and has been implicated in NSCL/P. However, in our family-based association test (transmission disequilibrium test; TDT), we could not conclude an association between PDGF-C and NSCL/P as previously suggested. Instead, we found strong evidence for parent-of-origin effect at a PDGF-C SNP, rs17035464, by a likelihood ratio test (unadjusted p-value = 0.0018; Im = 2.46). The location of rs17035464 is 13 kb downstream of a previously reported, NSCL/P-associated SNP, rs28999109. Furthermore, a patient from our sample trios was observed with a maternal segmental uniparental isodisomy (UPD) in a region containing rs17035464. Our findings support the involvement of PDGF-C in the development of oral clefts; moreover, the UPD case report contributes to the collective knowledge of rare variants in the human genome.
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Affiliation(s)
- Di Wu
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Mei Wang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xingang Wang
- Department of Stomatology, Beijing Children Hospital Affiliated to Capital University of Medical Sciences, Beijing, People's Republic of China
| | - Ningbei Yin
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Tao Song
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Haidong Li
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Feng Zhang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yongbiao Zhang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenqing Ye
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jun Yu
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Duen-Mei Wang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (DMW); (ZZ)
| | - Zhenmin Zhao
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
- People's Hospital of Jincheng City, Jincheng, Shanxi, People's Republic of China
- * E-mail: (DMW); (ZZ)
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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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Garg P, Borel C, Sharp AJ. Detection of parent-of-origin specific expression quantitative trait loci by cis-association analysis of gene expression in trios. PLoS One 2012; 7:e41695. [PMID: 22912676 PMCID: PMC3422236 DOI: 10.1371/journal.pone.0041695] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/25/2012] [Indexed: 12/02/2022] Open
Abstract
Parent-of-origin (PofO) effects, such as imprinting are a phenomenon in which homologous chromosomes exhibit differential gene expression and epigenetic modifications according to their parental origin. Such non-Mendelian inheritance patterns are generally ignored by conventional association studies, as these tests consider the maternal and paternal alleles as equivalent. To identify regulatory regions that show PofO effects on gene expression (imprinted expression Quantitative Trait Loci, ieQTLs), here we have developed a novel method in which we associate SNP genotypes of defined parental origin with gene expression levels. We applied this method to study 59 HapMap phase II parent-offspring trios. By analyzing mother/father/child trios, rules of Mendelian inheritance allowed the parental origin to be defined for ∼95% of SNPs in each child. We used 680,475 informative SNPs and corresponding expression data for 92,167 probe sets from Affymetrix GeneChip Human Exon 1.0 ST arrays and performed four independent cis-association analyses with the expression level of RefSeq genes within 1 Mb using PLINK. Independent analyses of maternal and paternal genotypes identified two significant cis-ieQTLs (p<10−7) at which expression of genes SFT2D2 and SRRT associated exclusively with maternally inherited SNPs rs3753292 and rs6945374, respectively. 28 additional suggestive cis-associations with only maternal or paternal SNPs were found at a lower stringency threshold of p<10−6, including associations with two known imprinted genes PEG10 and TRAPPC9, demonstrating the efficacy of our method. Furthermore, comparison of our method that utilizes independent analyses of maternal and paternal genotypes with the Likelihood Ratio Test (LRT) showed it to be more effective for detecting imprinting effects than the LRT. Our method represents a novel approach that can identify imprinted regulatory elements that control gene expression, suggesting novel PofO effects in the human genome.
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Affiliation(s)
- Paras Garg
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Christelle Borel
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail:
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Souza LTD, Kowalski TW, Vanz AP, Giugliani R, Félix TM. TGFA/Taq I polymorphism and environmental factors in non-syndromic oral clefts in Southern Brazil. Braz Oral Res 2012; 26:431-5. [DOI: 10.1590/s1806-83242012005000016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/06/2012] [Indexed: 11/22/2022] Open
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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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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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Shi M, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Wu T, Murray T, Redett RJ, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Yeow V, Chong SS, Shi B, Christensen K, Scott AF, Patel P, Cheah F, Beaty TH. Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts. Am J Med Genet A 2012; 158A:784-94. [PMID: 22419666 DOI: 10.1002/ajmg.a.35257] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/19/2011] [Indexed: 12/15/2022]
Abstract
We performed a genome wide association analysis of maternally-mediated genetic effects and parent-of-origin (POO) effects on risk of orofacial clefting (OC) using over 2,000 case-parent triads collected through an international cleft consortium. We used log-linear regression models to test individual SNPs. For SNPs with a P-value <10(-5) for maternal genotypic effects, we also applied a haplotype-based method, TRIMM, to extract potential information from clusters of correlated SNPs. None of the SNPs were significant at the genome wide level. Our results suggest neither maternal genome nor POO effects play major roles in the etiology of OC in our sample. This finding is consistent with previous genetic studies and recent population-based cohort studies in Norway and Denmark, which showed no apparent difference between mother-to-offspring and father-to-offspring recurrence of clefting. We, however, cannot completely rule out maternal genome or POO effects as risk factors because very small effects might not be detectable with our sample size, they may influence risk through interactions with environmental exposures or may act through a more complex network of interacting genes. Thus, the most promising SNPs identified by this study may still be worth further investigation.
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Affiliation(s)
- Min Shi
- Biostatistics Branch, NIEHS/NIH, Durham, North Carolina, USA.
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32
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Male and female differential reproductive rate could explain parental transmission asymmetry of mutation origin in Hirschsprung disease. Eur J Hum Genet 2012; 20:917-20. [PMID: 22395866 DOI: 10.1038/ejhg.2012.35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Hirschsprung disease (HSCR, aganglionic megacolon) is a complex and heterogeneous disease with an incidence of 1 in 5000 live births. Despite the multifactorial determination of HSCR in the vast majority of cases, there is a monogenic subgroup for which private rare RET coding sequence mutations with high penetrance are found (45% of HSCR familial cases). An asymmetrical parental origin is observed for RET coding sequence mutations with a higher maternal inheritance. A parent-of-origin effect is usually assumed. Here we show that a differential reproductive rate for males and females also leads to an asymmetrical parental origin, which was never considered as a possible explanation till now. In the case of HSCR, we show a positive association between penetrance of the mutation and parental transmission asymmetry: no parental transmission asymmetry is observed in sporadic RET CDS mutation carrier cases for which penetrance of the mutation is low, whereas a parental transmission asymmetry is observed in affected sib-pairs for which penetrance of the mutation is higher. This allows us to conclude that the explanation for this parental asymmetry is that more severe mutations have resulted in a differential reproductive rate between male and female carriers.
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Wu T, Fallin MD, Shi M, Ruczinski I, Liang KY, Hetmanski JB, Wang H, Ingersoll RG, Huang S, Ye X, Wu-Chou YH, Chen PK, Jabs EW, Shi B, Redett R, Scott AF, Murray JC, Marazita ML, Munger RG, Beaty TH. Evidence of gene-environment interaction for the RUNX2 gene and environmental tobacco smoke in controlling the risk of cleft lip with/without cleft palate. ACTA ACUST UNITED AC 2012; 94:76-83. [PMID: 22241686 DOI: 10.1002/bdra.22885] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/09/2011] [Accepted: 11/15/2011] [Indexed: 12/20/2022]
Abstract
This study examined the association between 49 markers in the Runt-related transcription factor 2 (RUNX2) gene and nonsyndromic cleft lip with/without cleft palate (CL/P) among 326 Chinese case-parent trios, while considering gene-environment (GxE) interaction and parent-of-origin effects. Five single-nucleotide polymorphisms (SNPs) showed significant evidence of linkage and association with CL/P and these results were replicated in an independent European sample of 825 case-parent trios. We also report compelling evidence for interaction between markers in RUNX2 and environmental tobacco smoke (ETS). Although most marginal SNP effects (i.e., ignoring maternal exposures) were not statistically significant, eight SNPs were significant when considering possible interaction with ETS when testing for gene (G) and GxE interaction simultaneously or when considering GxE alone. Independent samples from European populations showed consistent evidence of significant GxETS interaction at two SNPs (rs6904353 and rs7748231). Our results suggest genetic variation in RUNX2 may influence susceptibility to CL/P through interacting with ETS.
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Affiliation(s)
- Tao Wu
- Peking University School of Public Health, Beijing, China
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Wang H, Zhang T, Wu T, Hetmanski JB, Ruczinski I, Schwender H, Liang KY, Murray T, Fallin MD, Redett RJ, Raymond GV, Jin SC, Chou YHW, Chen PKT, Yeow V, Chong SS, Cheah FSH, Jee SH, Jabs EW, Scott AF, Beaty TH. The FGF and FGFR Gene Family and Risk of Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2011; 50:96-103. [PMID: 22074045 DOI: 10.1597/11-132] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background : Isolated, nonsyndromic cleft lip with or without cleft palate is a common human congenital malformation with a complex and heterogeneous etiology. Genes coding for fibroblast growth factors and their receptors (FGF/FGFR genes) are excellent candidate genes. Methods : We tested single-nucleotide polymorphic markers in 10 FGF/FGFR genes (including FGFBP1, FGF2, FGF10, FGF18, FGFR1, FGFR2, FGF19, FGF4, FGF3, and FGF9) for genotypic effects, interactions with one another, and with common maternal environmental exposures in 221 Asian and 76 Maryland case-parent trios ascertained through a child with isolated, nonsyndromic cleft lip with or without cleft palate. Results : Both FGFR1 and FGF19 yielded evidence of linkage and association in the transmission disequilibrium test, confirming previous evidence. Haplotypes of three single-nucleotide polymorphisms in FGFR1 were nominally significant among Asian trios. Estimated odds ratios for individual single-nucleotide polymorphic markers and haplotypes of multiple markers in FGF19 ranged from 1.31 to 1.87. We also found suggestive evidence of maternal genotypic effects for markers in FGF2 and FGF10 among Asian trios. Tests for gene-environment (G × E) interaction between markers in FGFR2 and maternal smoking or multivitamin supplementation yielded significant evidence of G × E interaction separately. Tests of gene-gene (G × G) interaction using Cordell's method yielded significant evidence between single-nucleotide polymorphisms in FGF9 and FGF18, which was confirmed in an independent sample of trios from an international consortium. Conclusion : Our results suggest several genes in the FGF/FGFR family may influence risk for isolated, nonsyndromic cleft lip with or without cleft palate through distinct biological mechanisms.
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Munsie JW, Lin S, Browne ML, Campbell KA, Caton AR, Bell EM, Rasmussen SA, Romitti PA, Druschel CM. Maternal bronchodilator use and the risk of orofacial clefts. Hum Reprod 2011; 26:3147-54. [PMID: 21926056 PMCID: PMC6034617 DOI: 10.1093/humrep/der315] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Few epidemiological studies have explored the relationship between orofacial clefts and bronchodilators. We assessed whether mothers who used bronchodilators during early pregnancy were at an increased risk of delivering infants with orofacial clefts. METHODS We used National Birth Defects Prevention Study case-control data from mothers of 2711 infants with orofacial clefts and 6482 mothers of live born infants without birth defects, delivered during 1997 through 2005. Information on medication use from 3 months before pregnancy through delivery was collected using a standardized interview. Logistic regression was used to estimate adjusted odds ratios (aOR) and 95% confidence intervals (CIs) for maternal bronchodilator use during the periconceptional period (1 month before pregnancy through the third month of pregnancy) while controlling for other covariates. RESULTS We observed an association between maternal bronchodilator use during the periconceptional period and cleft lip only (CLO) (aOR = 1.77, 95% CI: 1.08-2.88). The risk of cleft palate only (CPO) (aOR = 1.53, 95% CI: 0.99-2.37) was elevated but was not statistically significant. No association was observed for maternal bronchodilator use and the risk of cleft lip with cleft palate (aOR = 0.78, 95% CI: 0.46-1.31). The most commonly used bronchodilator was albuterol (88.7%). Maternal albuterol use was associated with CLO (aOR = 1.79, 95% CI: 1.07-2.99) and CPO (aOR = 1.65, 95% CI: 1.06-2.58). CONCLUSIONS We observed a statistically significant association between maternal bronchodilator use during the periconceptional period and the risk of CLO after controlling for other risk factors. It is unclear whether the increased odds ratios observed in this study are due to the bronchodilators, the severity of asthma, or both, or to chance alone. Further studies to disentangle the role of asthma or asthma medications would help clarify these findings.
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Affiliation(s)
- JeanPierre W Munsie
- Bureau of Environmental and Occupational Epidemiology, Center for Environmental Health, New York State Department of Health, 547 River Street, Room 200, Troy, NY 12180, USA.
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Rahimov F, Jugessur A, Murray JC. Genetics of nonsyndromic orofacial clefts. Cleft Palate Craniofac J 2011; 49:73-91. [PMID: 21545302 DOI: 10.1597/10-178] [Citation(s) in RCA: 171] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
With an average worldwide prevalence of approximately 1.2/1000 live births, orofacial clefts are the most common craniofacial birth defects in humans. Like other complex disorders, these birth defects are thought to result from the complex interplay of multiple genes and environmental factors. Significant progress in the identification of underlying genes and pathways has benefited from large populations available for study, increased international collaboration, rapid advances in genotyping technology, and major improvements in analytic approaches. Here we review recent advances in genetic epidemiological approaches to complex traits and their applications to studies of nonsyndromic orofacial clefts. Our main aim is to bring together a discussion of new and previously identified candidate genes to create a more cohesive picture of interacting pathways that shape the human craniofacial region. In future directions, we highlight the need to search for copy number variants that affect gene dosage and rare variants that are possibly associated with a higher disease penetrance. In addition, sequencing of protein-coding regions in candidate genes and screening for genetic variation in noncoding regulatory elements will help advance this important area of research.
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Affiliation(s)
- Fedik Rahimov
- Interdisciplinary Ph.D. Program in Genetics, Department of Pediatrics, University of Iowa, Iowa City, Iowa, USA
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Pan Y, Ma J, Zhang W, Du Y, Niu Y, Wang M, Zhang Z, Wang L. IRF6 polymorphisms are associated with nonsyndromic orofacial clefts in a Chinese Han population. Am J Med Genet A 2010; 152A:2505-11. [PMID: 20799332 DOI: 10.1002/ajmg.a.33624] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IRF6 plays an important role in orofacial development. In the present study, we genotyped two polymorphisms (rs642961 and rs2235371) within the IRF6 locus and estimated their associations with risk of nonsyndromic orofacial clefts (NSOC), including the subgroups, in a hospital-based case-control study in a Chinese Han population. In the single locus analyses, we found rs642961 AG and AG/AA genotypes were associated with increased risk of NSOC, especially cleft lip with or without cleft palate (CL/P) and cleft lip with cleft palate (CLP), while significantly decreased risks were associated with rs2235371 CT and CT/TT genotypes. When examining the combined effects of these two polymorphisms and using the rs642961 A and rs2235371 C alleles as the risk alleles, we found genotypes containing 2-4 risk alleles conferred high risk to NSOC, CL/P, and CLP. Furthermore, to test whether rs642961 could modulate IRF6 expression in vivo, we surgically collected lip skin tissues within the adjacent region of lip cleft site and found rs642961 genotypes were associated with differential levels of IRF6 mRNA and protein expression in an allele-dosage manner, providing the first evidence that rs642961 affected IRF6 expression in vivo. Taken together, these findings confirm the contribution of IRF6 genetic variants in the etiology of NSOC in a Chinese Han population.
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Affiliation(s)
- Yongchu Pan
- Institute of Stomatology, Department of Epidemiology, Nanjing Medical University, Nanjing, China
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Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate. Hum Genet 2010; 128:401-10. [PMID: 20652317 DOI: 10.1007/s00439-010-0863-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
Abstract
Although multiple genes have been identified as genetic risk factors for isolated, non-syndromic cleft lip with/without cleft palate (CL/P), a complex and heterogeneous birth defect, interferon regulatory factor 6 gene (IRF6) is one of the best documented genetic risk factors. In this study, we tested for association between markers in IRF6 and CL/P in 326 Chinese case-parent trios, considering gene-environment interaction for two common maternal exposures, and parent-of-origin effects. CL/P case-parent trios from three sites in mainland China and Taiwan were genotyped for 22 single nucleotide polymorphisms (SNPs) in IRF6. The transmission disequilibrium test was used to test for marginal effects of individual SNPs. We used PBAT to screen the SNPs and haplotypes for gene-environment (G×E) interaction and conditional logistic regression models to quantify effect sizes for SNP-environment interaction. After Bonferroni correction, 14 SNPs showed statistically significant association with CL/P. Evidence of G×E interaction was found for both maternal exposures, multivitamin supplementation and environmental tobacco smoke (ETS). Two SNPs showed evidence of interaction with multivitamin supplementation in conditional logistic regression models (rs2076153 nominal P=0.019, rs17015218 nominal P=0.012). In addition, rs1044516 yielded evidence for interaction with maternal ETS (nominal P=0.041). Haplotype analysis using PBAT also suggested interaction between SNPs in IRF6 and both multivitamin supplementation and ETS. However, no evidence for maternal genotypic effects or significant parent-of-origin effects was seen in these data. These results suggest IRF6 gene may influence risk of CL/P through interaction with multivitamin supplementation and ETS in the Chinese population.
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Suazo J, Santos JL, Jara L, Blanco R. Parent-of-origin effects for MSX1 in a Chilean population with nonsyndromic cleft lip/palate. Am J Med Genet A 2010; 152A:2011-6. [DOI: 10.1002/ajmg.a.33528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Moreno LM, Mansilla MA, Bullard SA, Cooper ME, Busch TD, Machida J, Johnson MK, Brauer D, Krahn K, Daack-Hirsch S, L'heureux J, Valencia-Ramirez C, Rivera D, López AM, Moreno MA, Hing A, Lammer EJ, Jones M, Christensen K, Lie RT, Jugessur A, Wilcox AJ, Chines P, Pugh E, Doheny K, Arcos-Burgos M, Marazita ML, Murray JC, Lidral AC. FOXE1 association with both isolated cleft lip with or without cleft palate, and isolated cleft palate. Hum Mol Genet 2009; 18:4879-96. [PMID: 19779022 DOI: 10.1093/hmg/ddp444] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nonsyndromic orofacial clefts are a common complex birth defect caused by genetic and environmental factors and/or their interactions. A previous genome-wide linkage scan discovered a novel locus for cleft lip with or without cleft palate (CL/P) at 9q22-q33. To identify the etiologic gene, we undertook an iterative and complementary fine mapping strategy using family-based CL/P samples from Colombia, USA and the Philippines. Candidate genes within 9q22-q33 were sequenced, revealing 32 new variants. Concurrently, 397 SNPs spanning the 9q22-q33 2-LOD-unit interval were tested for association. Significant SNP and haplotype association signals (P = 1.45E - 08) narrowed the interval to a 200 kb region containing: FOXE1, C9ORF156 and HEMGN. Association results were replicated in CL/P families of European descent and when all populations were combined the two most associated SNPs, rs3758249 (P = 5.01E - 13) and rs4460498 (P = 6.51E - 12), were located inside a 70 kb high linkage disequilibrium block containing FOXE1. Association signals for Caucasians and Asians clustered 5' and 3' of FOXE1, respectively. Isolated cleft palate (CP) was also associated, indicating that FOXE1 plays a role in two phenotypes thought to be genetically distinct. Foxe1 expression was found in the epithelium undergoing fusion between the medial nasal and maxillary processes. Mutation screens of FOXE1 identified two family-specific missense mutations at highly conserved amino acids. These data indicate that FOXE1 is a major gene for CL/P and provides new insights for improved counseling and genetic interaction studies.
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Affiliation(s)
- Lina M Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
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