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Welzenbach J, Hammond NL, Nikolić M, Thieme F, Ishorst N, Leslie EJ, Weinberg SM, Beaty TH, Marazita ML, Mangold E, Knapp M, Cotney J, Rada-Iglesias A, Dixon MJ, Ludwig KU. Integrative approaches generate insights into the architecture of non-syndromic cleft lip with or without cleft palate. HGG ADVANCES 2021; 2:100038. [PMID: 35047836 PMCID: PMC8756534 DOI: 10.1016/j.xhgg.2021.100038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common congenital facial malformation with a multifactorial etiology. Genome-wide association studies (GWASs) have identified multiple genetic risk loci. However, functional interpretation of these loci is hampered by the underrepresentation in public resources of systematic functional maps representative of human embryonic facial development. To generate novel insights into the etiology of nsCL/P, we leveraged published GWAS data on nsCL/P as well as available chromatin modification and expression data on mid-facial development. Our analyses identified five novel risk loci, prioritized candidate target genes within associated regions, and highlighted distinct pathways. Furthermore, the results suggest the presence of distinct regulatory effects of nsCL/P risk variants throughout mid-facial development and shed light on its regulatory architecture. Our integrated data provide a platform to advance hypothesis-driven molecular investigations of nsCL/P and other human facial defects.
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Affiliation(s)
- Julia Welzenbach
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nigel L. Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolić
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
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Denault WRP, Romanowska J, Haaland ØA, Lyle R, Taylor J, Xu Z, Lie RT, Gjessing HK, Jugessur A. Wavelet Screening identifies regions highly enriched for differentially methylated loci for orofacial clefts. NAR Genom Bioinform 2021; 3:lqab035. [PMID: 33987535 PMCID: PMC8092375 DOI: 10.1093/nargab/lqab035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/04/2022] Open
Abstract
DNA methylation is the most widely studied epigenetic mark in humans and plays an essential role in normal biological processes as well as in disease development. More focus has recently been placed on understanding functional aspects of methylation, prompting the development of methods to investigate the relationship between heterogeneity in methylation patterns and disease risk. However, most of these methods are limited in that they use simplified models that may rely on arbitrarily chosen parameters, they can only detect differentially methylated regions (DMRs) one at a time, or they are computationally intensive. To address these shortcomings, we present a wavelet-based method called 'Wavelet Screening' (WS) that can perform an epigenome-wide association study (EWAS) of thousands of individuals on a single CPU in only a matter of hours. By detecting multiple DMRs located near each other, WS identifies more complex patterns that can differentiate between different methylation profiles. We performed an extensive set of simulations to demonstrate the robustness and high power of WS, before applying it to a previously published EWAS dataset of orofacial clefts (OFCs). WS identified 82 associated regions containing several known genes and loci for OFCs, while other findings are novel and warrant replication in other OFCs cohorts.
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Affiliation(s)
- William R P Denault
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, 0450, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch and Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences (NIH/NIEHS), 27709, Durham, North Carolina, USA
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, 0473, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, 5006, Bergen, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, 0473, Oslo, Norway
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3
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Kariyawasam D, Jahanfar S. The Prevalence of Nonsyndromic Oral Clefts in Twins Compared to Singletons: The Association With Birth Weight. Cleft Palate Craniofac J 2020; 58:718-727. [PMID: 34047210 DOI: 10.1177/1055665620974566] [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: 11/15/2022] Open
Abstract
PURPOSE To examine the prevalence of nonsyndromic oral clefts in twins compared to singletons in the United States and to evaluate the association between birth weight and nonsyndromic oral clefts. DESIGN A large population-based cross-sectional study was performed using the data from the US National Center for Health Statistics database in 2017. PARTICIPANTS Our sample consisted of 128 310 twins and 3 723 273 singletons. METHODS The variables collected were sociodemographic variables, environmental predictors, and clinical measures. Descriptive analysis, bivariate, and multivariate logistic regression were performed. MAIN OUTCOME MEASURE The main outcome variable in our study is nonsyndromic oral clefts. RESULTS The prevalence of nonsyndromic oral clefts was 5.22 per 10 000 in twins and 5.12 per 10 000 in singletons. Results show no significant risk of nonsyndromic oral clefts in twins compared to singletons (P = .92). There was a significant relationship between birth weight and infant diagnosed with nonsyndromic oral clefts (P = .01). Unadjusted odds ratio for birth weight was 2.52 (95% CI: 2.25-2.82). Adjusted odds for potential confounders such as mother's age, race, mother's education, gender of the infant, APGAR 5-minute score, gestational age, prenatal smoking, number of prenatal care visits, and mother's body mass index were resulted in similar but with a slightly lower odds of 2.11 (95% CI: 1.78-2.50). CONCLUSION Compared to singletons, twins did not have higher risk of nonsyndromic oral clefts. Infants with low birth weight were more prone to have nonsyndromic oral clefts.
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Abstract
Orofacial clefts (OFCs) are the most common congenital birth defects in humans and immediately recognized at birth. The etiology remains complex and poorly understood and seems to result from multiple genetic and environmental factors along with gene-environment interactions. It can be classified into syndromic (30%) and nonsyndromic (70%) clefts. Nonsyndromic OFCs include clefts without any additional physical or cognitive deficits. Recently, various genetic approaches, such as genome-wide association studies (GWAS), candidate gene association studies, and linkage analysis, have identified multiple genes involved in the etiology of OFCs. This article provides an insight into the multiple genes involved in the etiology of OFCs. Identification of specific genetic causes of clefts helps in a better understanding of the molecular pathogenesis of OFC. In the near future, it helps to provide a more accurate diagnosis, genetic counseling, personalized medicine for better clinical care, and prevention of OFCs.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth CS
- Department of Orthodontics & Dentofacial Orthopedics, DAPM R.V. Dental College, Bangalore, Karnataka, India
| | - Narasimha Murthy Srinath
- Department of Oral & Maxillofacial Surgery, Krishnadevaraya College of Dental Sciences, Bangalore, Karnataka, India
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The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate. Eur J Hum Genet 2019; 28:453-460. [PMID: 31780810 PMCID: PMC7080719 DOI: 10.1038/s41431-019-0549-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Previous genome-wide association study of nonsyndromic cleft lip with or without cleft palate (NSCL/P) identified a susceptible variant (rs4791774). We hypothesized that the functional single nucleotide polymorphism (SNP) may be in linkage disequilibrium with this lead SNP. The potential functional SNP (rs4791331) was identified by bioinformatic analysis. A case–control study with 891 orofacial cleft cases and 830 controls was designed to investigate its association with orofacial cleft. The allele-specific DNA-protein binding preference was predicted by JASPAR database. Cell proliferation, cycle and apoptosis, luciferase activity and netrin-1 (NTN1) expression were examined after transfection with the rs4791331 C/T vector in HEK-293 and HEPM cell lines. Forty-six lip tissues of NSCL/P patients were collected to detect NTN1 expression. ntn1a knockout zebrafish models were generated by CRISPR/Cas9 and observed with micro-CT. In the case–control study, the rs4791331-T allele was associated with an increased risk of nonsyndromic orofacial cleft (OR = 1.41, 95% CI = 1.19–1.68), as well as the subgroups cleft lip only (OR = 1.46, 95% CI = 1.14–1.87) and cleft lip and palate (OR = 1.58, 95% CI = 1.27–1.96). The T allele of rs4791331 exhibited anti-apoptotic effects and promoted cell cycle progression at the G1/S transition. Decreased enhancer activity and reduced NTN1 expression following transfection of the T allele were observed. Carriers of the CT/TT genotypes showed significantly lower expression of NTN1 than CC carriers. The ntn1a−/− zebrafish showed relatively wider intermaxillary fissures. These results indicate that rs4791331 (C > T) disrupted motif binding and led to abnormal expression of NTN1, which may be involved in the development of NSCL/P.
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. Our new methodology detects if PoO effects are different across environmental strata and is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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7
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and applied them to families with children born with isolated cleft palate only. Here, we used the same genome-wide association study (GWAS) dataset and methodology to screen for PoOxE effects in the larger sample of CL/P triads. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. The methodology applied in the analyses is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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8
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Li B, Ma L, Zhang C, Zhou Z, Yuan H, Jiang H, Pan Y, Tan Q. Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate. Mol Genet Genomic Med 2018; 6:1157-1167. [PMID: 30411541 PMCID: PMC6305670 DOI: 10.1002/mgg3.497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/03/2018] [Accepted: 10/02/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The genetic etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) has not been fully clarified to date. Epidermal growth factor receptor (EGFR) was reportedly involved in its biological establishment and regulation of cell migration during the embryonic stage. METHODS We selected a super pathway of endocytic trafficking of EGFR and investigated the associations of single-nucleotide polymorphisms (SNPs) in the super pathway with the risk of NSCL/P by analyzing our published genome-wide association study (GWAS) data from 504 NSCL/P individuals and 455 controls. After the false discovery rate (FDR) control, we conducted linkage disequilibrium (LD) analyses and conditional regression analyses to obtain independent lead SNPs. We performed LD analyses between the lead SNPs and the reported SNPs to find novel ones from our study. We annotated the lead SNPs and investigated their mapped genes in silico. RESULTS A total of 82 SNPs showed a statistical association with the risk of NSCL/P after FDR control. They contained three reported SNPs which were g.117068049G>A (rs7078160), g.117086783C>G (rs10886040), and g.117101266G>T (rs17095681). Four independent lead SNPs were obtained, including g.116979803 T>C (rs1905539) and g.117037960A>G (rs7902502) at 10q25.3, g.35720163G>C (rs75656820) at 17q12, and g.156864512G>A (rs1800877) at 1q23.1. Three of them were in low LD (r2 < 0.5) with the reported SNPs except g.117037960A>G (rs7902502), so these three were newly identified. Lead SNPs were mapped to three genes: SHTN1, AP2B1, and NTRK1. The three genes were relatively more highly expressed in the human craniofacial region and in the proximal maxillary location during the craniofacial development stage of the embryonic mouse. CONCLUSION Our results suggested that SHTN1, AP2B1, and NTRK1 might be associated with the development of NSCL/P.
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Affiliation(s)
- Bing Li
- Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Chi Zhang
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zhixuan Zhou
- Department of Polyclinic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Hongbing Jiang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Qian Tan
- Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, China.,Department of Burns and Plastic Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
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9
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Genome-wide analysis of parent-of-origin interaction effects with environmental exposure (PoOxE): An application to European and Asian cleft palate trios. PLoS One 2017; 12:e0184358. [PMID: 28898263 PMCID: PMC5595425 DOI: 10.1371/journal.pone.0184358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/22/2017] [Indexed: 11/19/2022] Open
Abstract
Cleft palate only is a common birth defect with high heritability. Only a small fraction of this heritability is explained by the genetic variants identified so far, underscoring the need to investigate other disease mechanisms, such as gene-environment (GxE) interactions and parent-of-origin (PoO) effects. Furthermore, PoO effects may vary across exposure levels (PoOxE effects). Such variation is the focus of this study. We upgraded the R-package Haplin to enable direct tests of PoOxE effects at the genome-wide level. From a previous GWAS, we had genotypes for 550 case-parent trios, of mainly European and Asian ancestry, and data on three maternal exposures (smoking, alcohol, and vitamins). Data were analyzed for Europeans and Asians separately, and also for all ethnicities combined. To account for multiple testing, a false discovery rate method was used, where q-values were generated from the p-values. In the Europeans-only analyses, interactions with maternal smoking yielded the lowest q-values. Two SNPs in the 'Interactor of little elongation complex ELL subunit 1' (ICE1) gene had a q-value of 0.14, and five of the 20 most significant SNPs were in the 'N-acetylated alpha-linked acidic dipeptidase-like 2' (NAALADL2) gene. No evidence of PoOxE effects was found in the other analyses. The connections to ICE1 and NAALADL2 are novel and warrant further investigation. More generally, the new methodology presented here is easily applicable to other traits and exposures in which a family-based study design has been implemented.
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Roosenboom J, Indencleef K, Hens G, Peeters H, Christensen K, Marazita ML, Claes P, Leslie EJ, Weinberg SM. Testing the face shape hypothesis in twins discordant for nonsyndromic orofacial clefting. Am J Med Genet A 2017; 173:2886-2892. [PMID: 28884971 DOI: 10.1002/ajmg.a.38471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/28/2017] [Accepted: 08/12/2017] [Indexed: 12/26/2022]
Abstract
Nonsyndromic orofacial clefts (OFCs) are complex traits characterized by multifactorial inheritance and wide phenotypic variability. Numerous studies have shown subtle differences in the faces of unaffected relatives from cleft families compared to controls, the implication being that such outward differences are an incomplete expression reflecting an underlying genetic predisposition. Twins discordant for OFCs provide a unique opportunity to further test this idea, as the unaffected co-twin shares on average 50% (for dizygotic twins) and 100% (for monozygotic twins) of the genetic risk factors as the affected twin. We used 3D surface imaging and spatially-dense morphometry to compare facial shape in a sample of 44 unaffected co-twins and age- and sex-matched unaffected controls (n = 241). Unaffected co-twins showed statistically significant differences in the midface, lateral upper face, and forehead regions, compared to controls. Furthermore, co-twins were characterized by a distinct pattern of midfacial retrusion, broader upper faces, and greater protrusion of the mandible and brow ridges. This same general facial pattern was shown in both unaffected monozygotic and dizygotic co-twin subsets. These results provide additional support that altered facial shape is a phenotypic marker for OFC susceptibility.
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Affiliation(s)
- Jasmien Roosenboom
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium
| | - Greet Hens
- Multidisciplinary Cleft Lip and Palate Team Leuven, University Hospitals Leuven, Leuven, Belgium.,Department of Otorhinolaryngology, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Peeters
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Kaare Christensen
- Department of Epidemiology, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium.,Murdoch Childrens Research Institute, Victoria, Australia
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
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11
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Leslie EJ, Carlson JC, Cooper ME, Christensen K, Weinberg SM, Marazita ML. Exploring Subclinical Phenotypic Features in Twin Pairs Discordant for Cleft Lip and Palate. Cleft Palate Craniofac J 2016; 54:90-93. [PMID: 26882109 DOI: 10.1597/15-190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Monozygotic twins of an individual with an orofacial cleft have a significantly elevated risk for orofacial cleft compared with the general population, but still the concordance rate for orofacial cleft in monozygotic twins is about 40% to 50%. The goal of this study was to determine whether unaffected cotwins have an increased frequency of orbicularis oris muscle defects, a subclinical form of orofacial cleft. The presence of such defects may reduce the overall rate of discordance. METHOD A total of 63 discordant monozygotic and dizygotic twin pairs, 262 unaffected nontwin siblings, and 543 controls with no history of orofacial clefts were assessed for orbicularis oris defects by high-resolution ultrasound. Frequencies were compared by the Fisher exact test. RESULTS Unaffected cotwins from discordant monozygotic pairs had a higher frequency of defects (12.5%) than the other test groups (6.38% to 6.99%), but the difference was not statistically significant (P = .74). CONCLUSIONS In this study, orbicularis oris defects were not statistically significantly more common among the unaffected twins from orofacial cleft discordant twin pairs. The trends in the results warrant future studies with larger sample sizes and additional subclinical phenotypes.
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12
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Goodwin AF, Kim R, Bush JO, Klein OD. From Bench to Bedside and Back: Improving Diagnosis and Treatment of Craniofacial Malformations Utilizing Animal Models. Curr Top Dev Biol 2015; 115:459-92. [PMID: 26589935 DOI: 10.1016/bs.ctdb.2015.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Craniofacial anomalies are among the most common birth defects and are associated with increased mortality and, in many cases, the need for lifelong treatment. Over the past few decades, dramatic advances in the surgical and medical care of these patients have led to marked improvements in patient outcomes. However, none of the treatments currently in clinical use address the underlying molecular causes of these disorders. Fortunately, the field of craniofacial developmental biology provides a strong foundation for improved diagnosis and for therapies that target the genetic causes of birth defects. In this chapter, we discuss recent advances in our understanding of the embryology of craniofacial conditions, and we focus on the use of animal models to guide rational therapies anchored in genetics and biochemistry.
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Affiliation(s)
- Alice F Goodwin
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA; Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
| | - Rebecca Kim
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA; Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA
| | - Jeffrey O Bush
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA; Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, California, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.
| | - Ophir D Klein
- Program in Craniofacial Biology, University of California San Francisco, San Francisco, California, USA; Department of Orofacial Sciences, University of California San Francisco, San Francisco, California, USA; Department of Pediatrics, University of California San Francisco, San Francisco, California, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA.
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13
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Cvjetkovic N, Maili L, Weymouth KS, Hashmi SS, Mulliken JB, Topczewski J, Letra A, Yuan Q, Blanton SH, Swindell EC, Hecht JT. Regulatory variant in FZD6 gene contributes to nonsyndromic cleft lip and palate in an African-American family. Mol Genet Genomic Med 2015; 3:440-51. [PMID: 26436110 PMCID: PMC4585452 DOI: 10.1002/mgg3.155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/06/2015] [Accepted: 04/10/2015] [Indexed: 12/30/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect affecting 135,000 newborns worldwide each year. While a multifactorial etiology has been suggested as the cause, despite decades of research, the genetic underpinnings of NSCLP remain largely unexplained. In our previous genome-wide linkage study of a large NSCLP African-American family, we identified a candidate locus at 8q21.3-24.12 (LOD = 2.98). This region contained four genes, Frizzled-6 (FZD6), Matrilin-2 (MATN2), Odd-skipped related 2 (OSR2) and Solute Carrier Family 25, Member 32 (SLC25A32). FZD6 was located under the maximum linkage peak. In this study, we sequenced the coding and noncoding regions of these genes in two affected family members, and identified a rare variant in intron 1 of FZD6 (rs138557689; c.-153 + 432A>C). The variant C allele segregated with NSCLP in this family, through affected and unaffected individuals, and was found in one other NSCLP African-American family. Functional assays showed that this allele creates an allele-specific protein-binding site and decreases promoter activity. We also observed that loss and gain of fzd6 in zebrafish contributes to craniofacial anomalies. FZD6 regulates the WNT signaling pathway, which is involved in craniofacial development, including midfacial formation and upper labial fusion. We hypothesize, therefore, that alteration in FZD6 expression contributes to NSCLP in this family by perturbing the WNT signaling pathway.
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Affiliation(s)
- Nevena Cvjetkovic
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
- Graduate School of Biomedical Sciences, University of Texas Health Science CenterHouston, Texas
| | - Lorena Maili
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
| | - Katelyn S Weymouth
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
- Graduate School of Biomedical Sciences, University of Texas Health Science CenterHouston, Texas
| | - S Shahrukh Hashmi
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
| | | | - Jacek Topczewski
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children’s Hospital of Chicago Research CenterChicago, Illinois
| | - Ariadne Letra
- Graduate School of Biomedical Sciences, University of Texas Health Science CenterHouston, Texas
- University of Texas School of Dentistry at HoustonHouston, Texas
| | - Qiuping Yuan
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
| | - Susan H Blanton
- Dr. John T. Macdonald Department of Human Genetics, Hussman Institute for Human Genomics, University of Miami Miller School of MedicineMiami, Florida
| | - Eric C Swindell
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Medical School at HoustonHouston, Texas
- Graduate School of Biomedical Sciences, University of Texas Health Science CenterHouston, Texas
- University of Texas School of Dentistry at HoustonHouston, Texas
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14
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Sun Y, Huang Y, Yin A, Pan Y, Wang Y, Wang C, Du Y, Wang M, Lan F, Hu Z, Wang G, Jiang M, Ma J, Zhang X, Ma H, Ma J, Zhang W, Huang Q, Zhou Z, Ma L, Li Y, Jiang H, Xie L, Jiang Y, Shi B, Cheng J, Shen H, Wang L, Yang Y. Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate. Nat Commun 2015; 6:6414. [DOI: 10.1038/ncomms7414] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/27/2015] [Indexed: 01/24/2023] Open
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15
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Wang J, Bai Y, Li H, Greene SB, Klysik E, Yu W, Schwartz RJ, Williams TJ, Martin JF. MicroRNA-17-92, a direct Ap-2α transcriptional target, modulates T-box factor activity in orofacial clefting. PLoS Genet 2013; 9:e1003785. [PMID: 24068957 PMCID: PMC3777996 DOI: 10.1371/journal.pgen.1003785] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/25/2013] [Indexed: 01/23/2023] Open
Abstract
Among the most common human congenital anomalies, cleft lip and palate (CL/P) affects up to 1 in 700 live births. MicroRNA (miR)s are small, non-coding RNAs that repress gene expression post-transcriptionally. The miR-17-92 cluster encodes six miRs that have been implicated in human cancers and heart development. We discovered that miR-17-92 mutant embryos had severe craniofacial phenotypes, including incompletely penetrant CL/P and mandibular hypoplasia. Embryos that were compound mutant for miR-17-92 and the related miR-106b-25 cluster had completely penetrant CL/P. Expression of Tbx1 and Tbx3, the DiGeorge/velo-cardio-facial (DGS) and Ulnar-mammary syndrome (UMS) disease genes, was expanded in miR-17-92 mutant craniofacial structures. Both Tbx1 and Tbx3 had functional miR seed sequences that mediated gene repression. Analysis of miR-17-92 regulatory regions uncovered conserved and functional AP-2α recognition elements that directed miR-17-92 expression. Together, our data indicate that miR-17-92 modulates expression of critical T-box transcriptional regulators during midface development and is itself a target of Bmp-signaling and the craniofacial pioneer factor AP-2α. Our data are the first genetic evidence that an individual miR or miR cluster is functionally important in mammalian CL/P.
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Affiliation(s)
- Jun Wang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yan Bai
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, United States of America
| | - Hong Li
- Department of Craniofacial Biology, UC Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Stephanie B. Greene
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Elzbieta Klysik
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wei Yu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Robert J. Schwartz
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Texas Heart Institute, Houston, Texas, United States of America
| | - Trevor J. Williams
- Department of Craniofacial Biology, UC Denver, Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - James F. Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, United States of America
- Texas Heart Institute, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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16
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Abstract
Oral Diseases (2012) Underlying molecular genetic mechanisms of diseases can be deciphered with unbiased strategies using recently developed technologies enabling genome-wide scale investigations. These technologies have been applied in scanning for genetic variations, gene expression profiles, and epigenetic changes for oral and craniofacial diseases. However, these approaches as applied to oral and craniofacial conditions are in the initial stages, and challenges remain to be overcome, including analysis of high throughput data and their interpretation. Here, we review methodology and studies using genome-wide approaches in oral and craniofacial diseases and suggest future directions.
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Affiliation(s)
- H Kim
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD School of Dentistry, University of Maryland, Baltimore, MD, USA
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17
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Budner M, Surowiec Z, Fudalej P, Hozyasz KK. Whole-blood 3-hydroxyisovalerylcarnitine as a risk factor for orofacial clefts. Arch Oral Biol 2013; 58:459-61. [PMID: 23395542 DOI: 10.1016/j.archoralbio.2012.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 10/11/2012] [Accepted: 10/21/2012] [Indexed: 11/26/2022]
Abstract
BACKGROUND/PURPOSE In mice, biotin deficiency is one of the most potent clefting factors. Increased 3-hydroxyisovalerylcarnitine (C5OH) is regarded as a biomarker of biotin deficiency. This retrospective study was undertaken to determine whether increased C5OH in newborns is associated with orofacial clefts. MATERIALS AND METHODS Seventy newborns with non-syndromic cleft lip with or without cleft palate and 140 control newborns without congenital anomalies were investigated. Whole-blood C5OH concentrations were measured using tandem mass spectrometry. RESULTS The median (interquartile range, IQR) concentrations of C5OH in patients with clefts and controls were 0.16 (0.13-0.22)μmoll(-1) and 0.17 (0.13-0.20)μmoll(-1), respectively (p=0.90). The receiver operating characteristic analysis did not find out cut-off values for C5OH discriminating between cases and controls. CONCLUSION There appears to be no association between biotin deficiency, as indexed by an increase of C5OH, and orofacial clefts in the investigated group of patients.
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Affiliation(s)
- Margareta Budner
- Department of Paediatric Surgery, Institute of Mother and Child, Warsaw, Poland
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18
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Ingstrup K, Liang H, Olsen J, Nohr E, Bech B, Wu C, Christensen K, Li J. Maternal bereavement in the antenatal period and oral cleft in the offspring. Hum Reprod 2013; 28:1092-9. [DOI: 10.1093/humrep/des434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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20
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Mangold E, Ludwig KU, Nöthen MM. Breakthroughs in the genetics of orofacial clefting. Trends Mol Med 2011; 17:725-33. [PMID: 21885341 DOI: 10.1016/j.molmed.2011.07.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 07/21/2011] [Accepted: 07/21/2011] [Indexed: 01/03/2023]
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21
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Pan Y, Zhang W, Du Y, Tong N, Han Y, Zhang H, Wang M, Ma J, Wan L, Wang L. Different roles of two novel susceptibility loci for nonsyndromic orofacial clefts in a Chinese Han population. Am J Med Genet A 2011; 155A:2180-5. [DOI: 10.1002/ajmg.a.34170] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Accepted: 05/22/2011] [Indexed: 11/09/2022]
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