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Awotoye W, Mossey PA, Hetmanski JB, Gowans LJ, Eshete MA, Adeyemo WL, Alade A, Zeng E, Adamson O, James O, Fashina A, Ogunlewe MO, Naicker T, Adeleke C, Busch T, Li M, Petrin A, Oladayo A, Kayali S, Olotu J, Sule V, Hassan M, Pape J, Aladenika ET, Donkor P, Arthur FK, Obiri-Yeboah S, Sabbah DK, Agbenorku P, Ray D, Plange-Rhule G, Oti AA, Albokhari D, Sobreira N, Dunnwald M, Beaty TH, Taub M, Marazita ML, Adeyemo AA, Murray JC, Butali A. Damaging Mutations in AFDN Contribute to Risk of Nonsyndromic Cleft Lip With or Without Cleft Palate. Cleft Palate Craniofac J 2024; 61:697-705. [PMID: 36384317 PMCID: PMC10185709 DOI: 10.1177/10556656221135926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Novel or rare damaging mutations have been implicated in the developmental pathogenesis of nonsyndromic cleft lip with or without cleft palate (nsCL ± P). Thus, we investigated the human genome for high-impact mutations that could explain the risk of nsCL ± P in our cohorts. We conducted next-generation sequencing (NGS) analysis of 130 nsCL ± P case-parent African trios to identify pathogenic variants that contribute to the risk of clefting. We replicated this analysis using whole-exome sequence data from a Brazilian nsCL ± P cohort. Computational analyses were then used to predict the mechanism by which these variants could result in increased risks for nsCL ± P. We discovered damaging mutations within the AFDN gene, a cell adhesion molecule (CAMs) that was previously shown to contribute to cleft palate in mice. These mutations include p.Met1164Ile, p.Thr453Asn, p.Pro1638Ala, p.Arg669Gln, p.Ala1717Val, and p.Arg1596His. We also discovered a novel splicing p.Leu1588Leu mutation in this protein. Computational analysis suggests that these amino acid changes affect the interactions with other cleft-associated genes including nectins (PVRL1, PVRL2, PVRL3, and PVRL4) CDH1, CTNNA1, and CTNND1. This is the first report on the contribution of AFDN to the risk for nsCL ± P in humans. AFDN encodes AFADIN, an important CAM that forms calcium-independent complexes with nectins 1 and 4 (encoded by the genes PVRL1 and PVRL4). This discovery shows the power of NGS analysis of multiethnic cleft samples in combination with a computational approach in the understanding of the pathogenesis of nsCL ± P.
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Affiliation(s)
- Waheed Awotoye
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter A. Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lord J.J Gowans
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A. Eshete
- Addis Ababa University, School Medicine, Surgical Department, Addis Ababa, Ethiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Modupe O Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos Nigeria
| | - Thirona Naicker
- Department of Pediatrics, University of KwaZulu-Natal, South Africa
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Aline Petrin
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt
| | - Veronica Sule
- Department of Operative Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - John Pape
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Emmanuel T. Aladenika
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Fareed K.N. Arthur
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniel K. Sabbah
- Department of Child Oral Health and Orthodontics, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pius Agbenorku
- Department of Surgery, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Debashree Ray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gyikua Plange-Rhule
- Department of Child Health, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander Acheampong Oti
- Department of Maxillofacial Sciences, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Daniah Albokhari
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University
| | | | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Margaret Taub
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Azeez Butali
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA
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Oladayo A, Gowans LJJ, Awotoye W, Alade A, Busch T, Naicker T, Eshete MA, Adeyemo WL, Hetmanski JB, Zeng E, Adamson O, Adeleke C, Li M, Sule V, Kayali S, Olotu J, Mossey PA, Obiri‐Yeboah S, Buxo CJ, Beaty T, Taub M, Donkor P, Marazita ML, Odukoya O, Adeyemo AA, Murray JC, Prince A, Butali A. Clinically actionable secondary findings in 130 triads from sub-Saharan African families with non-syndromic orofacial clefts. Mol Genet Genomic Med 2023; 11:e2237. [PMID: 37496383 PMCID: PMC10568375 DOI: 10.1002/mgg3.2237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023] Open
Abstract
INTRODUCTION The frequency and implications of secondary findings (SFs) from genomic testing data have been extensively researched. However, little is known about the frequency or reporting of SFs in Africans, who are underrepresented in large-scale population genomic studies. The availability of data from the first whole-genome sequencing for orofacial clefts in an African population motivated this investigation. METHODS In total, 130 case-parent trios were analyzed for SFs within the ACMG SFv.3.0 list genes. Additionally, we filtered for four more genes (HBB, HSD32B, G6PD and ACADM). RESULTS We identified 246 unique variants in 55 genes; five variants in four genes were classified as pathogenic or likely pathogenic (P/LP). The P/LP variants were seen in 2.3% (9/390) of the subjects, a frequency higher than ~1% reported for diverse ethnicities. On the ACMG list, pathogenic variants were observed in PRKAG (p. Glu183Lys). Variants in the PALB2 (p. Glu159Ter), RYR1 (p. Arg2163Leu) and LDLR (p. Asn564Ser) genes were predicted to be LP. CONCLUSION This study provides information on the frequency and pathogenicity of SFs in an African cohort. Early risk detection will help reduce disease burden and contribute to efforts to increase knowledge of the distribution and impact of actionable genomic variants in diverse populations.
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Affiliation(s)
- Abimbola Oladayo
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
| | - Lord Jephthah Joojo Gowans
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
- Department of Biochemistry and BiotechnologyKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Department of Epidemiology, College of Public HealthUniversity of IowaIowa CityIowaUSA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Thirona Naicker
- Department of PediatricsUniversity of KwaZulu‐NatalPinetownSouth Africa
| | - Mekonen A. Eshete
- School Medicine, Surgical DepartmentAddis Ababa UniversityAddis AbabaEthiopia
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Jacqueline B. Hetmanski
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Olawale Adamson
- Department of Oral and Maxillofacial SurgeryUniversity of LagosLagosNigeria
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Veronica Sule
- Department of Operative Dentistry, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Sami Kayali
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Joy Olotu
- Department of AnatomyUniversity of Port HarcourtPort HarcourtNigeria
| | | | - Solomon Obiri‐Yeboah
- Department of Surgery, School of Medicine and DentistryKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Carmen J. Buxo
- Dental and Craniofacial Genomics CoreUniversity of Puerto Rico School of Dental MedicineSan JuanPuerto RicoUSA
| | - Terri Beaty
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Margaret Taub
- Department of EpidemiologySchool of Public Health Johns Hopkins UniversityBaltimoreMarylandUSA
| | - Peter Donkor
- Department of Surgery, School of Medicine and DentistryKwame Nkrumah University of Science and TechnologyKumasiGhana
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine, and Department of Human Genetics, Graduate School of Public HealthUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Oluwakemi Odukoya
- Department of Community Health and Primary Care, College of MedicineUniversity of LagosLagosNigeria
| | | | | | - Anya Prince
- College of LawUniversity of IowaIowa CityIowaUSA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Iowa Institute for Oral Health ResearchUniversity of IowaIowa CityIowaUSA
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Ray D, Venkataraghavan S, Zhang W, Leslie EJ, Hetmanski JB, Weinberg SM, Murray JC, Marazita ML, Ruczinski I, Taub MA, Beaty TH. Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios. PLoS Genet 2021; 17:e1009584. [PMID: 34242216 PMCID: PMC8270211 DOI: 10.1371/journal.pgen.1009584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Based on epidemiologic and embryologic patterns, nonsyndromic orofacial clefts- the most common craniofacial birth defects in humans- are commonly categorized into cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which are traditionally considered to be etiologically distinct. However, some evidence of shared genetic risk in IRF6, GRHL3 and ARHGAP29 regions exists; only FOXE1 has been recognized as significantly associated with both CL/P and CP in genome-wide association studies (GWAS). We used a new statistical approach, PLACO (pleiotropic analysis under composite null), on a combined multi-ethnic GWAS of 2,771 CL/P and 611 CP case-parent trios. At the genome-wide significance threshold of 5 × 10-8, PLACO identified 1 locus in 1q32.2 (IRF6) that appears to increase risk for one OFC subgroup but decrease risk for the other. At a suggestive significance threshold of 10-6, we found 5 more loci with compelling candidate genes having opposite effects on CL/P and CP: 1p36.13 (PAX7), 3q29 (DLG1), 4p13 (LIMCH1), 4q21.1 (SHROOM3) and 17q22 (NOG). Additionally, we replicated the recognized shared locus 9q22.33 (FOXE1), and identified 2 loci in 19p13.12 (RAB8A) and 20q12 (MAFB) that appear to influence risk of both CL/P and CP in the same direction. We found locus-specific effects may vary by racial/ethnic group at these regions of genetic overlap, and failed to find evidence of sex-specific differences. We confirmed shared etiology of the two OFC subtypes comprising CL/P, and additionally found suggestive evidence of differences in their pathogenesis at 2 loci of genetic overlap. Our novel findings include 6 new loci of genetic overlap between CL/P and CP; 3 new loci between pairwise OFC subtypes; and 4 loci not previously implicated in OFCs. Our in-silico validation showed PLACO is robust to subtype-specific effects, and can achieve massive power gains over existing approaches for identifying genetic overlap between disease subtypes. In summary, we found suggestive evidence for new genetic regions and confirmed some recognized OFC genes either exerting shared risk or with opposite effects on risk to OFC subtypes.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
| | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wanying Zhang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Seth M. Weinberg
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
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Zhang W, Venkataraghavan S, Hetmanski JB, Leslie EJ, Marazita ML, Feingold E, Weinberg SM, Ruczinski I, Taub MA, Scott AF, Ray D, Beaty TH. Detecting Gene-Environment Interaction for Maternal Exposures Using Case-Parent Trios Ascertained Through a Case With Non-Syndromic Orofacial Cleft. Front Cell Dev Biol 2021; 9:621018. [PMID: 33937227 PMCID: PMC8085423 DOI: 10.3389/fcell.2021.621018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Two large studies of case-parent trios ascertained through a proband with a non-syndromic orofacial cleft (OFC, which includes cleft lip and palate, cleft lip alone, or cleft palate alone) were used to test for possible gene-environment (G × E) interaction between genome-wide markers (both observed and imputed) and self-reported maternal exposure to smoking, alcohol consumption, and multivitamin supplementation during pregnancy. The parent studies were as follows: GENEVA, which included 1,939 case-parent trios recruited largely through treatment centers in Europe, the United States, and Asia, and 1,443 case-parent trios from the Pittsburgh Orofacial Cleft Study (POFC) also ascertained through a proband with an OFC including three major racial/ethnic groups (European, Asian, and Latin American). Exposure rates to these environmental risk factors (maternal smoking, alcohol consumption, and multivitamin supplementation) varied across studies and among racial/ethnic groups, creating substantial differences in power to detect G × E interaction, but the trio design should minimize spurious results due to population stratification. The GENEVA and POFC studies were analyzed separately, and a meta-analysis was conducted across both studies to test for G × E interaction using the 2 df test of gene and G × E interaction and the 1 df test for G × E interaction alone. The 2 df test confirmed effects for several recognized risk genes, suggesting modest G × E effects. This analysis did reveal suggestive evidence for G × Vitamin interaction for CASP9 on 1p36 located about 3 Mb from PAX7, a recognized risk gene. Several regions gave suggestive evidence of G × E interaction in the 1 df test. For example, for G × Smoking interaction, the 1 df test suggested markers in MUSK on 9q31.3 from meta-analysis. Markers near SLCO3A1 also showed suggestive evidence in the 1 df test for G × Alcohol interaction, and rs41117 near RETREG1 (a.k.a. FAM134B) also gave suggestive significance in the meta-analysis of the 1 df test for G × Vitamin interaction. While it remains quite difficult to obtain definitive evidence for G × E interaction in genome-wide studies, perhaps due to small effect sizes of individual genes combined with low exposure rates, this analysis of two large case-parent trio studies argues for considering possible G × E interaction in any comprehensive study of complex and heterogeneous disorders such as OFC.
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Affiliation(s)
- Wanying Zhang
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Sowmya Venkataraghavan
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, United States
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, School of Dental Medicine and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ingo Ruczinski
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Margaret A. Taub
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Alan F. Scott
- Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Debashree Ray
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Terri H. Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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5
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Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muñeton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ. Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am J Hum Genet 2020; 107:124-136. [PMID: 32574564 PMCID: PMC7332647 DOI: 10.1016/j.ajhg.2020.05.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.
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Affiliation(s)
- Madison R. Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly K. Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miranda Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nandita Mukhopadhyay
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | | | - Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Yah Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Philip K. Chen
- Craniofacial Centre, Taipei Medical University Hospital and Taipei Medical University, Taipei, Taiwan
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael P. Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA,Corresponding author
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Mukhopadhyay N, Bishop M, Mortillo M, Chopra P, Hetmanski JB, Taub MA, Moreno LM, Valencia-Ramirez LC, Restrepo C, Wehby GL, Hecht JT, Deleyiannis F, Butali A, Weinberg SM, Beaty TH, Murray JC, Leslie EJ, Feingold E, Marazita ML. Whole genome sequencing of orofacial cleft trios from the Gabriella Miller Kids First Pediatric Research Consortium identifies a new locus on chromosome 21. Hum Genet 2020; 139:215-226. [PMID: 31848685 PMCID: PMC6981325 DOI: 10.1007/s00439-019-02099-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/07/2019] [Indexed: 12/30/2022]
Abstract
Orofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic, and the genetic etiology of non-syndromic OFCs is only partially determined. Here, we analyze whole genome sequence (WGS) data for association with risk of OFCs in European and Colombian families selected from a multicenter family-based OFC study. This is the first large-scale WGS study of OFC in parent-offspring trios, and a part of the Gabriella Miller Kids First Pediatric Research Program created for the study of childhood cancers and structural birth defects. WGS provides deeper and more specific genetic data than using imputation on present-day single nucleotide polymorphic (SNP) marker panels. Genotypes of case-parent trios at single nucleotide variants (SNV) and short insertions and deletions (indels) spanning the entire genome were called from their sequences using human GRCh38 genome assembly, and analyzed for association using the transmission disequilibrium test. Among genome-wide significant associations, we identified a new locus on chromosome 21 in Colombian families, not previously observed in other larger OFC samples of Latin American ancestry. This locus is situated within a region known to be expressed during craniofacial development. Based on deeper investigation of this locus, we concluded that it contributed risk for OFCs exclusively in the Colombians. This study reinforces the ancestry differences seen in the genetic etiology of OFCs, and underscores the need for larger samples when studying for OFCs and other birth defects in populations with diverse ancestry.
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Affiliation(s)
- Nandita Mukhopadhyay
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
| | - Madison Bishop
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Michael Mortillo
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Lina M Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | | | - Claudia Restrepo
- Fundación Clínica Noel (http://www.clinicanoel.org.co/), Medellín, Colombia
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX, 77030, USA
| | | | - Azeez Butali
- Iowa Institute of Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Eleanor Feingold
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA
- Department of Biostatistics Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Bridgeside Point Suite 500, 100 Technology Dr., Pittsburgh, PA, 15219, USA.
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
- Department of Psychiatry, School of Medicine and Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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7
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Holzinger ER, Li Q, Parker MM, Hetmanski JB, Marazita ML, Mangold E, Ludwig KU, Taub MA, Begum F, Murray JC, Albacha‐Hejazi H, Alqosayer K, Al‐Souki G, Albasha Hejazi A, Scott AF, Beaty TH, Bailey‐Wilson JE. Analysis of sequence data to identify potential risk variants for oral clefts in multiplex families. Mol Genet Genomic Med 2017; 5:570-579. [PMID: 28944239 PMCID: PMC5606860 DOI: 10.1002/mgg3.320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Nonsyndromic oral clefts are craniofacial malformations, which include cleft lip with or without cleft palate. The etiology for oral clefts is complex with both genetic and environmental factors contributing to risk. Previous genome-wide association (GWAS) studies have identified multiple loci with small effects; however, many causal variants remain elusive. METHODS In this study, we address this by specifically looking for rare, potentially damaging variants in family-based data. We analyzed both whole exome sequence (WES) data and whole genome sequence (WGS) data in multiplex cleft families to identify variants shared by affected individuals. RESULTS Here we present the results from these analyses. Our most interesting finding was from a single Syrian family, which showed enrichment of nonsynonymous and potentially damaging rare variants in two genes: CASP9 and FAT4. CONCLUSION Neither of these candidate genes has previously been associated with oral clefts and, if confirmed as contributing to disease risk, may indicate novel biological pathways in the genetic etiology for oral clefts.
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Affiliation(s)
- Emily R. Holzinger
- Computational and Statistical Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland
- National Institute of General Medical SciencesNational Institutes of HealthBethesdaMaryland
| | - Qing Li
- Computational and Statistical Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland
| | - Margaret M. Parker
- Channing Division of Network MedicineBrigham and Women's HospitalBostonMassachusetts
- Harvard Medical SchoolCambridgeMassachusetts
| | | | - Mary L. Marazita
- Department of Oral BiologyCenter for Craniofacial and Dental GeneticsSchool of Maryland Dental MedicineUniversity of PittsburghPittsburghPennsylvania
| | | | - Kerstin U. Ludwig
- Institute of Human GeneticsUniversity of BonnBonnGermany
- Department of GenomicsLife & Brain CenterUniversity of BonnBonnGermany
| | - Margaret A. Taub
- Department of BiostatisticsJohns Hopkins Bloomberg School of Public HealthBaltimoreMaryland
| | - Ferdouse Begum
- Department of EpidemiologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMaryland
| | | | | | | | | | | | - Alan F. Scott
- Center for Inherited Disease ResearchJohns Hopkins School of MedicineBaltimoreMaryland
- Institute of Genetic MedicineJohns Hopkins School of MedicineBaltimoreMaryland
| | - Terri H. Beaty
- Department of EpidemiologyJohns Hopkins Bloomberg School of Public HealthBaltimoreMaryland
| | - Joan E. Bailey‐Wilson
- Computational and Statistical Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBaltimoreMaryland
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8
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Xiao Y, Taub MA, Ruczinski I, Begum F, Hetmanski JB, Schwender H, Leslie EJ, Koboldt DC, Murray JC, Marazita ML, Beaty TH. Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios. Genet Epidemiol 2016; 41:244-250. [PMID: 28019042 DOI: 10.1002/gepi.22023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/21/2016] [Accepted: 09/27/2016] [Indexed: 11/07/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans, affecting 1 in 700 live births. This malformation has a complex etiology where multiple genes and several environmental factors influence risk. At least a dozen different genes have been confirmed to be associated with risk of NSCL/P in previous studies. However, all the known genetic risk factors cannot fully explain the observed heritability of NSCL/P, and several authors have suggested gene-gene (G × G) interaction may be important in the etiology of this complex and heterogeneous malformation. We tested for G × G interactions using common single nucleotide polymorphic (SNP) markers from targeted sequencing in 13 regions identified by previous studies spanning 6.3 Mb of the genome in a study of 1,498 NSCL/P case-parent trios. We used the R-package trio to assess interactions between polymorphic markers in different genes, using a 1 degree of freedom (1df) test for screening, and a 4 degree of freedom (4df) test to assess statistical significance of epistatic interactions. To adjust for multiple comparisons, we performed permutation tests. The most significant interaction was observed between rs6029315 in MAFB and rs6681355 in IRF6 (4df P = 3.8 × 10-8 ) in case-parent trios of European ancestry, which remained significant after correcting for multiple comparisons. However, no significant interaction was detected in trios of Asian ancestry.
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Affiliation(s)
- Yanzi Xiao
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ferdouse Begum
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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9
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Begum F, Ruczinski I, Hokanson JE, Lutz SM, Parker MM, Cho MH, Hetmanski JB, Scharpf RB, Crapo JD, Silverman EK, Beaty TH. Hemizygous Deletion on Chromosome 3p26.1 Is Associated with Heavy Smoking among African American Subjects in the COPDGene Study. PLoS One 2016; 11:e0164134. [PMID: 27711239 PMCID: PMC5053531 DOI: 10.1371/journal.pone.0164134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/20/2016] [Indexed: 02/04/2023] Open
Abstract
Many well-powered genome-wide association studies have identified genetic determinants of self-reported smoking behaviors and measures of nicotine dependence, but most have not considered the role of structural variants, such as copy number variation (CNVs), influencing these phenotypes. Here, we included 2,889 African American and 6,187 non-Hispanic White subjects from the COPDGene cohort (http://www.copdgene.org) to carefully investigate the role of polymorphic CNVs across the genome on various measures of smoking behavior. We identified a CNV component (a hemizygous deletion) on chromosome 3p26.1 associated with two quantitative phenotypes related to smoking behavior among African Americans. This polymorphic hemizygous deletion is significantly associated with pack-years and cigarettes smoked per day among African American subjects in the COPDGene study. We sought evidence of replication in African Americans from the population based Atherosclerosis Risk in Communities (ARIC) study. While we observed similar CNV counts, the extent of exposure to cigarette smoking among ARIC subjects was quite different and the smaller sample size of heavy smokers in ARIC severely limited statistical power, so we were unable to replicate our findings from the COPDGene cohort. But meta-analyses of COPDGene and ARIC study subjects strengthened our association signal. However, a few linkage studies have reported suggestive linkage to the 3p26.1 region, and a few genome-wide association studies (GWAS) have reported markers in the gene (GRM7) nearest to this 3p26.1 area of polymorphic deletions are associated with measures of nicotine dependence among subjects of European ancestry.
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Affiliation(s)
- Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Sharon M. Lutz
- Department of Biostatisitics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Margaret M. Parker
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert B. Scharpf
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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10
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Begum F, Ruczinski I, Li S, Silverman EK, Cho MH, Lynch DA, Curran-Everett D, Crapo J, Scharpf RB, Parker MM, Hetmanski JB, Beaty TH. Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort. Genet Epidemiol 2015; 40:81-8. [PMID: 26643968 DOI: 10.1002/gepi.21943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 09/21/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive disease with both environmental and genetic risk factors. Genome-wide association studies (GWAS) have identified multiple genomic regions influencing risk of COPD. To thoroughly investigate the genetic etiology of COPD, however, it is also important to explore the role of copy number variants (CNVs) because the presence of structural variants can alter gene expression and can be causal for some diseases. Here, we investigated effects of polymorphic CNVs on quantitative measures of pulmonary function and chest computed tomography (CT) phenotypes among subjects enrolled in COPDGene, a multisite study. COPDGene subjects consist of roughly one-third African American (AA) and two-thirds non-Hispanic white adult smokers (with or without COPD). We estimated CNVs using PennCNV on 9,076 COPDGene subjects using Illumina's Omni-Express genome-wide marker array. We tested for association between polymorphic CNV components (defined as disjoint intervals of copy number regions) for several quantitative phenotypes associated with COPD within each racial group. Among the AAs, we identified a polymorphic CNV on chromosome 5q35.2 located between two genes (FAM153B and SIMK1, but also harboring several pseudo-genes) giving genome-wide significance in tests of association with total lung capacity (TLCCT ) as measured by chest CT scans. This is the first study of genome-wide association tests of polymorphic CNVs and TLCCT . Although the ARIC cohort did not have the phenotype of TLCCT , we found similar counts of CNV deletions and amplifications among AA and European subjects in this second cohort.
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Affiliation(s)
- Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Shengchao Li
- Cancer Genomics Research Laboratory (CGR), Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David A Lynch
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Douglas Curran-Everett
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, United States of America
| | - James Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Margaret M Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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11
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Bu L, Chen Q, Wang H, Zhang T, Hetmanski JB, Schwender H, Parker M, Chou YHW, Yeow V, Chong SS, Zhang B, Jabs EW, Scott AF, Beaty TH. Novel evidence of association with nonsyndromic cleft lip with or without cleft palate was shown for single nucleotide polymorphisms in FOXF2 gene in an Asian population. ACTA ACUST UNITED AC 2015; 103:857-62. [PMID: 26278207 DOI: 10.1002/bdra.23413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/15/2015] [Accepted: 06/28/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND The forkhead box F2 gene (FOXF2) located in chromosome 6p25.3 has been shown to play a crucial role in palatal development in mouse and rat models. To date, no evidence of linkage or association has been reported for this gene in humans with oral clefts. METHODS Allelic transmission disequilibrium tests were used to robustly assess evidence of linkage and association with nonsyndromic cleft lip with or without cleft palate for nine single nucleotide polymorphisms (SNPs) in and around FOXF2 in both Asian and European trios using PLINK. RESULTS Statistically significant evidence of linkage and association was shown for two SNPs (rs1711968 and rs732835) in 216 Asian trios where the empiric P values with permutation tests were 0.0016 and 0.005, respectively. The corresponding estimated odds ratios for carrying the minor allele at these SNPs were 2.05 (95% confidence interval = 1.41, 2.98) and 1.77 (95% confidence interval = 1.26, 2.49), respectively. CONCLUSION Our results provided statistical evidence of linkage and association between FOXF2 and nonsyndromic cleft lip with or without cleft palate.
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Affiliation(s)
- Lingxue Bu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qianqian Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,National Center for Public Health Surveillance and Information Services, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,Ministry of Health KeyLaboratory of Reproductive Health, Beijing, China
| | - Tianxiao Zhang
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Margaret Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Yah-Huei Wu Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Vincent Yeow
- Department of Plastic Surgery, K K Women's and Children's Hospital, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore
| | - Bo Zhang
- Department of Biomedical Engineering, Xi'an JiaoTong University, Xi'an, China
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA. Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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12
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Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FWB, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet 2015; 96:397-411. [PMID: 25704602 PMCID: PMC4375420 DOI: 10.1016/j.ajhg.2015.01.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/09/2015] [Indexed: 11/21/2022] Open
Abstract
Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.
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Affiliation(s)
- Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Huan Liu
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA; State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 430072 Wuhan, China
| | - Karyn Meltz Steinberg
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Qunyuan Zhang
- Department of Statistical Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jenna C Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hang Wang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Youssef A Kousa
- Department of Biochemistry and Molecular Biology, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ali Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ferdouse Begum
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tamara Busch
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Rigdon
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alan F Scott
- Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, 5230 Odense, Denmark
| | - Andrew E Czeizel
- Foundation for the Community Control of Hereditary Diseases, Budapest 1148, Hungary
| | - Frederic W-B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO 80045, USA
| | - Brian C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew C Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - George M Weinstock
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06117, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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13
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Li Q, Kim Y, Suktitipat B, Hetmanski JB, Marazita ML, Duggal P, Beaty TH, Bailey-Wilson JE. Gene-Gene Interaction Among WNT Genes for Oral Cleft in Trios. Genet Epidemiol 2015; 39:385-94. [PMID: 25663376 DOI: 10.1002/gepi.21888] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/15/2014] [Accepted: 12/18/2014] [Indexed: 10/24/2022]
Abstract
Genome-wide association studies (GWAS) for nonsyndromic cleft lip with or without cleft palate (CL/P) have identified multiple genes as important in the etiology of this common birth defect. We performed a candidate gene/pathway analysis explicitly considering gene-gene (G × G) interaction to further explore the etiology of CL/P. Animal models have shown the WNT signaling pathway plays an important role in mid-facial development, and various genes in this pathway have been associated with nonsyndromic CL/P in previous studies. We propose a combined approach to search for possible G × G interactions using machine learning and regression-based methods to test for interactions between genes in the WNT family, and between these genes and other genes identified by GWAS in case-parent trios. Using this combined approach of regression-based and machine learning methods in CL/P case-parent trios, we found robust evidence of G × G interaction between markers in WNT5B and MAFB (empiric P-values = 0.0076 among Asian trios and P-values = 0.018 among European trios). Additional evidence for epistatic interaction between markers in WNT5A, IRF6, and C1orf107 was seen among Asian trios, and markers in the 8q24 region and WNT5B among European trios.
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Affiliation(s)
- Qing Li
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Yoonhee Kim
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Bhoom Suktitipat
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America.,Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Mary L Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
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14
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Parker MM, Foreman MG, Abel HJ, Mathias RA, Hetmanski JB, Crapo JD, Silverman EK, Beaty TH. Admixture mapping identifies a quantitative trait locus associated with FEV1/FVC in the COPDGene Study. Genet Epidemiol 2014; 38:652-9. [PMID: 25112515 DOI: 10.1002/gepi.21847] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 06/30/2014] [Accepted: 07/03/2014] [Indexed: 12/31/2022]
Abstract
African Americans are admixed with genetic contributions from European and African ancestral populations. Admixture mapping leverages this information to map genes influencing differential disease risk across populations. We performed admixture and association mapping in 3,300 African American current or former smokers from the COPDGene Study. We analyzed estimated local ancestry and SNP genotype information to identify regions associated with FEV1 /FVC, the ratio of forced expiratory volume in one second to forced vital capacity, measured by spirometry performed after bronchodilator administration. Global African ancestry inversely associated with FEV1 /FVC (P = 0.035). Genome-wide admixture analysis, controlling for age, gender, body mass index, current smoking status, pack-years smoked, and four principal components summarizing the genetic background of African Americans in the COPDGene Study, identified a region on chromosome 12q14.1 associated with FEV1 /FVC (P = 2.1 × 10(-6) ) when regressed on local ancestry. Allelic association in this region of chromosome 12 identified an intronic variant in FAM19A2 (rs348644) as associated with FEV1 /FVC (P = 1.76 × 10(-6) ). By combining admixture and association mapping, a marker on chromosome 12q14.1 was identified as being associated with reduced FEV1 /FVC ratio among African Americans in the COPDGene Study.
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Affiliation(s)
- Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland, United States of America
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15
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Cho MH, McDonald MLN, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, Lange C, Litonjua AA, Sparrow D, Casaburi R, Barr RG, Regan EA, Make BJ, Hokanson JE, Lutz S, Dudenkov TM, Farzadegan H, Hetmanski JB, Tal-Singer R, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. Lancet Respir Med 2014; 2:214-25. [PMID: 24621683 DOI: 10.1016/s2213-2600(14)70002-5] [Citation(s) in RCA: 233] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The genetic risk factors for susceptibility to chronic obstructive pulmonary disease (COPD) are still largely unknown. Additional genetic variants are likely to be identified by genome-wide association studies in larger cohorts or specific subgroups. We sought to identify risk loci for moderate to severe and severe COPD with data from several cohort studies. METHODS We combined genome-wide association analysis data from participants in the COPDGene study (non-Hispanic white and African-American ethnic origin) and the ECLIPSE, NETT/NAS, and Norway GenKOLS studies (self-described white ethnic origin). We did analyses comparing control individuals with individuals with moderate to severe COPD and with a subset of individuals with severe COPD. Single nucleotide polymorphisms yielding a p value of less than 5 × 10(-7) in the meta-analysis at loci not previously described were genotyped in individuals from the family-based ICGN study. We combined results in a joint meta-analysis (threshold for significance p<5 × 10(-8)). FINDINGS Analysis of 6633 individuals with moderate to severe COPD and 5704 control individuals confirmed association at three known loci: CHRNA3 (p=6·38 × 10(-14)), FAM13A (p=1·12 × 10(-14)), and HHIP (p=1·57 × 10(-12)). We also showed significant evidence of association at a novel locus near RIN3 (p=5·25 × 10(-9)). In the overall meta-analysis (ie, including data from 2859 ICGN participants), the association with RIN3 remained significant (p=5·4 × 10(-9)). 3497 individuals were included in our analysis of severe COPD. The effect estimates for the loci near HHIP and CHRNA3 were significantly stronger in severe disease than in moderate to severe disease (p<0·01). We also identified associations at two additional loci: MMP12 (overall joint meta-analysis p=2·6 × 10(-9)) and TGFB2 (overall joint meta-analysis p=8·3 × 10(-9)). INTERPRETATION We have confirmed associations with COPD at three known loci and identified three new genome-wide significant associations. Genetic variants other than in α-1 antitrypsin increase the risk of COPD. FUNDING US National Heart, Lung, and Blood Institute; the Alpha-1 Foundation; the COPD Foundation through contributions from AstraZeneca, Boehringer Ingelheim, Novartis, and Sepracor; GlaxoSmithKline; Centers for Medicare and Medicaid Services; Agency for Healthcare Research and Quality; and US Department of Veterans Affairs.
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Affiliation(s)
- Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Merry-Lynn N McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L Demeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jody S Sylvia
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John Ziniti
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nan M Laird
- Harvard School of Public Health, Boston, MA, USA
| | | | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David Sparrow
- School of Public Health and School of Medicine, Boston University, Boston, MA, USA; Veterans Administration Boston Healthcare System, Boston, MA, USA
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Elizabeth A Regan
- National Jewish Health, Denver, CO, USA; Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Sharon Lutz
- Department of Bioinformatics and Statistics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Tanda Murray Dudenkov
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Homayoon Farzadegan
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline B Hetmanski
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, King Of Prussia, PA, USA
| | | | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Terri H Beaty
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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16
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Wu T, Schwender H, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Parker MM, Wang P, Murray T, Taub M, Li S, Redett RJ, Fallin MD, Liang KY, Wu-Chou YH, Chong SS, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Jee SH, Scott AF, Beaty TH. Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate. PLoS One 2014; 9:e88088. [PMID: 24516586 PMCID: PMC3916361 DOI: 10.1371/journal.pone.0088088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10(-6)<P<10(-4)) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10(-7) in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10(-7) and P = 1.98×10(-7) in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP.
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Affiliation(s)
- Tao Wu
- Peking University Health Science Center, Beijing, China
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Ingo Ruczinski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Jeffrey C. Murray
- University of Iowa, Children’s Hospital, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jacqueline B. Hetmanski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret M. Parker
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Ping Wang
- Peking University Health Science Center, Beijing, China
| | - Tanda Murray
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret Taub
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Shuai Li
- Peking University Health Science Center, Beijing, China
| | - Richard J. Redett
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - M. Daniele Fallin
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Kung Yee Liang
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- National Yang-Ming University, Taipei, Taiwan
| | | | | | - Vincent Yeow
- KK Women’s & Children’s Hospital, Singapore, Singapore
| | - Xiaoqian Ye
- Wuhan University, School of Stomatology, Wuhan, China
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Hong Wang
- Peking University Health Science Center, Beijing, China
| | | | - Ethylin W. Jabs
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Allen J. Wilcox
- NIEHS/NIH, Epidemiology Branch, Durham, North Carolina, United States of America
| | - Sun Ha Jee
- Yonsei University, School of Public Health, Seoul, Korea
| | - Alan F. Scott
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
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17
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Patel PJ, Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Wu T, Murray T, Rose M, Redett RJ, Jin SC, Lie RT, Wu-Chou YH, Wang H, Ye X, Yeow V, Chong S, Jee SH, Shi B, Scott AF. X-linked markers in the Duchenne muscular dystrophy gene associated with oral clefts. Eur J Oral Sci 2013; 121:63-8. [PMID: 23489894 DOI: 10.1111/eos.12025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2012] [Indexed: 02/01/2023]
Abstract
As part of an international consortium, case-parent trios were collected for a genome-wide association study of isolated, non-syndromic oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP). Non-syndromic oral clefts have a complex and heterogeneous etiology. Risk is influenced by genes and environmental factors, and differs markedly by gender. Family-based association tests (FBAT) were used on 14,486 single nucleotide polymorphisms (SNPs) spanning the X chromosome, stratified by type of cleft and racial group. Significant results, even after multiple-comparisons correction, were obtained for the Duchenne muscular dystrophy (DMD) gene, the largest single gene in the human genome, among CL/P (i.e., both CL and CLP combined) trios. When stratified into groups of European and Asian ancestry, stronger signals were obtained for Asian subjects. Although conventional sliding-window haplotype analysis showed no increase in significance, selected combinations of the 25 most significant SNPs in the DMD gene identified four SNPs together that attained genome-wide significance among Asian CL/P trios, raising the possibility of interaction between distant SNPs within the DMD gene.
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18
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Beaty TH, Taub MA, Scott AF, Murray JC, Marazita ML, Schwender H, Parker MM, Hetmanski JB, Balakrishnan P, Mansilla MA, Mangold E, Ludwig KU, Noethen MM, Rubini M, Elcioglu N, Ruczinski I. Confirming genes influencing risk to cleft lip with/without cleft palate in a case-parent trio study. Hum Genet 2013; 132:771-81. [PMID: 23512105 DOI: 10.1007/s00439-013-1283-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
A collection of 1,108 case-parent trios ascertained through an isolated, nonsyndromic cleft lip with or without cleft palate (CL/P) was used to replicate the findings from a genome-wide association study (GWAS) conducted by Beaty et al. (Nat Genet 42:525-529, 2010), where four different genes/regions were identified as influencing risk to CL/P. Tagging SNPs for 33 different genes were genotyped (1,269 SNPs). All four of the genes originally identified as showing genome-wide significance (IRF6, ABCA4 and MAF, plus the 8q24 region) were confirmed in this independent sample of trios (who were primarily of European and Southeast Asian ancestry). In addition, eight genes classified as 'second tier' hits in the original study (PAX7, THADA, COL8A1/FILIP1L, DCAF4L2, GADD45G, NTN1, RBFOX3 and FOXE1) showed evidence of linkage and association in this replication sample. Meta-analysis between the original GWAS trios and these replication trios showed PAX7, COL8A1/FILIP1L and NTN1 achieved genome-wide significance. Tests for gene-environment interaction between these 33 genes and maternal smoking found evidence for interaction with two additional genes: GRID2 and ELAVL2 among European mothers (who had a higher rate of smoking than Asian mothers). Formal tests for gene-gene interaction (epistasis) failed to show evidence of statistical interaction in any simple fashion. This study confirms that many different genes influence risk to CL/P.
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Affiliation(s)
- T H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, 615N Wolfe St., Baltimore, MD 21205, USA.
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19
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Murray T, Taub MA, Ruczinski I, Scott AF, Hetmanski JB, Schwender H, Patel P, Zhang TX, Munger RG, Wilcox AJ, Ye X, Wang H, Wu T, Wu-Chou YH, Shi B, Jee SH, Chong S, Yeow V, Murray JC, Marazita ML, Beaty TH. Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and Europeans. Genet Epidemiol 2012; 36:392-9. [PMID: 22508319 DOI: 10.1002/gepi.21633] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 12/31/2022]
Abstract
In a recent genome-wide association study (GWAS) from an international consortium, evidence of linkage and association in chr8q24 was much stronger among nonsyndromic cleft lip/palate (CL/P) case-parent trios of European ancestry than among trios of Asian ancestry. We examined marker information content and haplotype diversity across 13 recruitment sites (from Europe, United States, and Asia) separately, and conducted principal components analysis (PCA) on parents. As expected, PCA revealed large genetic distances between Europeans and Asians, and a north-south cline from Korea to Singapore in Asia, with Filipino parents forming a somewhat distinct Southeast Asian cluster. Hierarchical clustering of SNP heterozygosity revealed two major clades consistent with PCA results. All genotyped SNPs giving P < 10(-6) in the allelic transmission disequilibrium test (TDT) showed higher heterozygosity in Europeans than Asians. On average, European ancestry parents had higher haplotype diversity than Asians. Imputing additional variants across chr8q24 increased the strength of statistical evidence among Europeans and also revealed a significant signal among Asians (although it did not reach genome-wide significance). Tests for SNP-population interaction were negative, indicating the lack of strong signal for 8q24 in families of Asian ancestry was not due to any distinct genetic effect, but could simply reflect low power due to lower allele frequencies in Asians.
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Affiliation(s)
- Tanda Murray
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
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20
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Chen Q, Wang H, Hetmanski JB, Zhang T, Ruczinski I, Schwender H, Liang KY, Fallin MD, Redett RJ, Raymond GV, Wu Chou YH, Chen PKT, Yeow V, Chong SS, Cheah FSH, Jabs EW, Scott AF, Beaty TH. BMP4 was associated with NSCL/P in an Asian population. PLoS One 2012; 7:e35347. [PMID: 22514733 PMCID: PMC3325933 DOI: 10.1371/journal.pone.0035347] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 03/14/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The Bone Morphogenetic Protein 4 gene (BMP4) is located in chromosome 14q22-q23 which has shown evidence of linkage for isolated nonsyndromic cleft lip with or without cleft palate (NSCL/P) in a genome wide linkage analysis of human multiplex families. BMP4 has been shown to play crucial roles in lip and palatal development in animal models. Several candidate gene association analyses also supported its potential risk for NSCL/P, however, results across these association studies have been inconsistent. The aim of the current study was to test for possible association between markers in and around the BMP4 gene and NSCL/P in Asian and Maryland trios. METHODOLOGY/PRINCIPAL FINDINGS Family Based Association Test was used to test for deviation from Mendelian assortment for 12 SNPs in and around BMP4. Nominal significant evidence of linkage and association was seen for three SNPs (rs10130587, rs2738265 and rs2761887) in 221 Asian trios and for one SNP (rs762642) in 76 Maryland trios. Statistical significance still held for rs10130587 after Bonferroni correction (corrected p = 0.019) among the Asian group. Estimated odds ratio for carrying the apparent high risk allele at this SNP was 1.61 (95%CI = 1.20, 2.18). CONCLUSIONS Our results provided further evidence of association between BMP4 and NSCL/P.
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Affiliation(s)
- Qianqian Chen
- 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
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Tianxiao Zhang
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri, United States of America
| | - Ingo Ruczinski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Holger Schwender
- Department of Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Kung Yee Liang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - M. Daniele Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Richard J. Redett
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gerald V. Raymond
- Kennedy Krieger Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yah-Huei Wu Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taipei, Taiwan
| | | | - Vincent Yeow
- Department of Plastic Surgery, K K Women's and Children's Hospital, Singapore, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Felicia S. H. Cheah
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Ethylin Wang Jabs
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, New York, United States of America
| | - Alan F. Scott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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21
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Wang H, Hetmanski JB, Ruczinski I, Liang KY, Fallin MD, Redett RJ, Raymond GV, Chou YHW, Chen PKT, Yeow V, Chong SS, Cheah FS, Jabs EW, Scott AF, Beaty TH. ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population. Chin Med J (Engl) 2012; 125:476-480. [PMID: 22490406 PMCID: PMC3384720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND The receptor tyrosine kinase-like orphan receptor 2 (ROR2) gene has been recently shown to play important roles in palatal development in animal models and resides in the chromosomal region linked to non syndromic cleft lip with or without cleft palate in humans. The aim of this study was to investigate the possible association between ROR2 gene and non-syndromic oral clefts. METHODS Here we tested 38 eligible single-nucleotide polymorphisms (SNPs) in ROR2 gene in 297 non-syndromic cleft lip with or without cleft palate and in 82 non-syndromic cleft palate case parent trios recruited from Asia and Maryland. Family Based Association Test was used to test for deviation from Mendelian inheritance. Plink software was used to test potential parent of origin effect. Possible maternally mediated in utero effects were assessed using the TRIad Multi-Marker approach under an assumption of mating symmetry in the population. RESULTS Significant evidence of linkage and association was shown for 3 SNPs (rs7858435, rs10820914 and rs3905385) among 57 Asian non-syndromic cleft palate trios in Family Based Association Tests. P values for these 3 SNPs equaled to 0.000068, 0.000115 and 0.000464 respectively which were all less than the significance level (0.05/38 = 0.0013) adjusted by strict Bonferroni correction. Relevant odds ratios for the risk allele were 3.42 (1.80 - 6.50), 3.45 (1.75 - 6.67) and 2.94 (1.56 - 5.56), respectively. Statistical evidence of linkage and association was not shown for study groups other than non-syndromic cleft palate. Neither evidence for parent-of-origin nor maternal genotypic effect was shown for any of the ROR2 markers in our analysis for all study groups. CONCLUSION Our results provided evidence of linkage and association between the ROR2 gene and a gene controlling risk to non-syndromic cleft palate.
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Affiliation(s)
- Hong Wang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China.
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Cho MH, Castaldi PJ, Wan ES, Siedlinski M, Hersh CP, Demeo DL, Himes BE, Sylvia JS, Klanderman BJ, Ziniti JP, Lange C, Litonjua AA, Sparrow D, Regan EA, Make BJ, Hokanson JE, Murray T, Hetmanski JB, Pillai SG, Kong X, Anderson WH, Tal-Singer R, Lomas DA, Coxson HO, Edwards LD, MacNee W, Vestbo J, Yates JC, Agusti A, Calverley PMA, Celli B, Crim C, Rennard S, Wouters E, Bakke P, Gulsvik A, Crapo JD, Beaty TH, Silverman EK. A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. Hum Mol Genet 2011; 21:947-57. [PMID: 22080838 DOI: 10.1093/hmg/ddr524] [Citation(s) in RCA: 180] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The genetic risk factors for chronic obstructive pulmonary disease (COPD) are still largely unknown. To date, genome-wide association studies (GWASs) of limited size have identified several novel risk loci for COPD at CHRNA3/CHRNA5/IREB2, HHIP and FAM13A; additional loci may be identified through larger studies. We performed a GWAS using a total of 3499 cases and 1922 control subjects from four cohorts: the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE); the Normative Aging Study (NAS) and National Emphysema Treatment Trial (NETT); Bergen, Norway (GenKOLS); and the COPDGene study. Genotyping was performed on Illumina platforms with additional markers imputed using 1000 Genomes data; results were summarized using fixed-effect meta-analysis. We identified a new genome-wide significant locus on chromosome 19q13 (rs7937, OR = 0.74, P = 2.9 × 10(-9)). Genotyping this single nucleotide polymorphism (SNP) and another nearby SNP in linkage disequilibrium (rs2604894) in 2859 subjects from the family-based International COPD Genetics Network study (ICGN) demonstrated supportive evidence for association for COPD (P = 0.28 and 0.11 for rs7937 and rs2604894), pre-bronchodilator FEV(1) (P = 0.08 and 0.04) and severe (GOLD 3&4) COPD (P = 0.09 and 0.017). This region includes RAB4B, EGLN2, MIA and CYP2A6, and has previously been identified in association with cigarette smoking behavior.
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Affiliation(s)
- Michael H Cho
- Channing Laboratory, Brigham & Women’s Hospital, Boston, MA 02115, USA.
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25
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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] [What about the content of this article? (0)] [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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26
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Beaty TH, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Murray T, Redett RJ, Fallin MD, Liang KY, Wu T, Patel PJ, Jin SC, Zhang TX, Schwender H, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Lie RT, Jee SH, Christensen K, Doheny KF, Pugh EW, Ling H, Scott AF. Evidence for gene-environment interaction in a genome wide study of nonsyndromic cleft palate. Genet Epidemiol 2011; 35:469-78. [PMID: 21618603 DOI: 10.1002/gepi.20595] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/07/2011] [Accepted: 04/19/2011] [Indexed: 11/09/2022]
Abstract
Nonsyndromic cleft palate (CP) is a common birth defect with a complex and heterogeneous etiology involving both genetic and environmental risk factors. We conducted a genome-wide association study (GWAS) using 550 case-parent trios, ascertained through a CP case collected in an international consortium. Family-based association tests of single nucleotide polymorphisms (SNP) and three common maternal exposures (maternal smoking, alcohol consumption, and multivitamin supplementation) were used in a combined 2 df test for gene (G) and gene-environment (G × E) interaction simultaneously, plus a separate 1 df test for G × E interaction alone. Conditional logistic regression models were used to estimate effects on risk to exposed and unexposed children. While no SNP achieved genome-wide significance when considered alone, markers in several genes attained or approached genome-wide significance when G × E interaction was included. Among these, MLLT3 and SMC2 on chromosome 9 showed multiple SNPs resulting in an increased risk if the mother consumed alcohol during the peri-conceptual period (3 months prior to conception through the first trimester). TBK1 on chr. 12 and ZNF236 on chr. 18 showed multiple SNPs associated with higher risk of CP in the presence of maternal smoking. Additional evidence of reduced risk due to G × E interaction in the presence of multivitamin supplementation was observed for SNPs in BAALC on chr. 8. These results emphasize the need to consider G × E interaction when searching for genes influencing risk to complex and heterogeneous disorders, such as nonsyndromic CP.
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Affiliation(s)
- Terri H Beaty
- School of Public Health, Johns Hopkins University, 615 N. Wolfe St., Baltimore, Maryland, USA.
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27
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Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Park BY, Jee SH, Jabs EW, Redett R, Scott AF, Beaty TH. Maternal transmission effects of the PAX genes among cleft case-parent trios from four populations. Eur J Hum Genet 2009; 17:831-9. [PMID: 19142206 DOI: 10.1038/ejhg.2008.250] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Isolated cleft lip with or without cleft palate (CL/P) is among the most common human birth defects, with a prevalence of 1 in 700 live births. The paired box (PAX) genes have been suggested as candidate genes for CL/P based largely on mouse models; however, few human studies have focused on this gene family. This study tests for association between markers in four PAX genes and CL/P using a case-parent trio design considering parent-of-origin effects. Trios from four populations (76 from Maryland, 146 from Taiwan, 35 from Singapore, and 40 from Korea) were genotyped for 34 single nucleotide polymorphisms (SNPs) in the PAX3, PAX6, PAX7, and PAX9 genes. We performed the transmission disequilibrium test (TDT) on individual SNPs. Parent-of-origin effects were assessed using the transmission asymmetry test (TAT) and the parent-of-origin likelihood ratio test (PO-LRT). TDT analysis showed one SNP (rs766325) in PAX7 yielding evidence of linkage and association when parent-of-origin was not considered, with an OR(transmission)=1.62 (P=0.003), and five SNPs in PAX6 (including two pairs in near perfect linkage disequilibrium). TAT analysis of all trios revealed two SNPs in PAX7 and four SNPs in PAX3 showing significant excess maternal transmission. For these six SNPs, the maternal OR(transmission) ranged between 1.74 and 2.40, and PO-LRT was also significant (P-values=0.035-0.012). When this analysis was limited to trios with male cases, SNPs in PAX7 showed higher maternal OR(transmission) and greater significance. PAX genes may influence the risk of CL/P through maternal effects, possibly imprinting, which seems to be stronger among male cases.
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Affiliation(s)
- Jae Woong Sull
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Korea
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28
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Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park J, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Park BY, Jee SH, Jabs EW, Redett R, Jung E, Ruczinski I, Scott AF, Beaty TH. Differential parental transmission of markers in RUNX2 among cleft case-parent trios from four populations. Genet Epidemiol 2008; 32:505-12. [PMID: 18357615 DOI: 10.1002/gepi.20323] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Isolated cleft lip with or without cleft palate (CL/P) is among the most common human birth defects, with a prevalence around 1 in 700 live births. The Runt-related transcription factor 2 (RUNX2) gene has been suggested as a candidate gene for CL/P based largely on mouse models; however, no human studies have focused on RUNX2 as a risk factor for CL/P. This study examines the association between markers in RUNX2 and isolated, nonsyndromic CL/P using a case-parent trio design, while considering parent-of-origin effects. Case-parent trios from four populations (77 from Maryland, 146 from Taiwan, 35 from Singapore, and 40 from Korea) were genotyped for 24 single nucleotide polymorphisms (SNPs) in the RUNX2 gene. We performed the transmission disequilibrium test on individual SNPs. Parent-of-origin effects were assessed using the transmission asymmetry test and the parent-of-origin likelihood ratio test (PO-LRT). When all trios were combined, the transmission asymmetry test revealed a block of 11 SNPs showing excess maternal transmission significant at the P<0.01 level, plus one SNP (rs1934328) showing excess paternal transmission (P=0.002). For the 11 SNPs showing excess maternal transmission, odds ratios of being transmitted to the case from the mother ranged between 3.00 and 4.00. The parent-of-origin likelihood ratio tests for equality of maternal and paternal transmission were significant for three individual SNPs (rs910586, rs2819861, and rs1934328). Thus, RUNX2 appears to influence risk of CL/P through a parent-of-origin effect with excess maternal transmission.
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Affiliation(s)
- Jae Woong Sull
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205, USA
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29
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Sull JW, Liang KY, Hetmanski JB, Fallin MD, Ingersoll RG, Park JW, Wu-Chou YH, Chen PK, Chong SS, Cheah F, Yeow V, Park BY, Jee SH, Jabs EW, Redett R, Scott AF, Beaty TH. Excess maternal transmission of markers in TCOF1 among cleft palate case-parent trios from three populations. Am J Med Genet A 2008; 146A:2327-31. [PMID: 18688869 DOI: 10.1002/ajmg.a.32302] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isolated cleft palate is among the most common human birth defects. The TCOF1 gene has been suggested as a candidate gene for cleft palate based on animal models. This study tests for association between markers in TCOF1 and isolated, nonsyndromic cleft palate using a case-parent trio design considering parent-of-origin effects. Case-parent trios from three populations (comprising a total of 81 case-parent trios) were genotyped for single nucleotide polymorphisms (SNPs) in the TCOF1 gene. We used the transmission disequilibrium test and the transmission asymmetry test on individual SNPs. When all trios were combined, the odds ratio for transmission of the minor allele, OR(transmission), was significant for SNP rs15251 (OR = 2.88, P = 0.007), as well as rs2255796 and rs2569062 (OR = 2.08, P = 0.03; OR = 2.43, P = 0.041; respectively) when parent of origin was not considered. The transmission asymmetry test also revealed one SNP (rs15251) showing excess maternal transmission significant at the P = 0.005 level (OR = 6.50). Parent-of-origin effects were assessed using the parent-of-origin likelihood ratio test on both SNPs and haplotypes. While the parent-of-origin likelihood ratio test was only marginally significant for this SNP (P = 0.136), analysis of haplotypes of rs2255796 and rs15251 suggested excess maternal transmission. Therefore, these data suggest TCOF1 may influence risk of cleft palate through a parent-of-origin effect.
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Affiliation(s)
- Jae Woong Sull
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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Park JW, McIntosh I, Hetmanski JB, Jabs EW, Vander Kolk CA, Wu-Chou YH, Chen PK, Chong SS, Yeow V, Jee SH, Park BY, Fallin MD, Ingersoll R, Scott AF, Beaty TH. Association between IRF6 and nonsyndromic cleft lip with or without cleft palate in four populations. Genet Med 2007; 9:219-27. [PMID: 17438386 PMCID: PMC2846512 DOI: 10.1097/gim.0b013e3180423cca] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
PURPOSE The interferon regulatory factor 6 (IRF6), the gene that causes van der Woude syndrome has been shown to be associated with nonsyndromic cleft lip with or without palate in several populations. This study aimed to confirm the contribution of IRF6 to cleft lip with or without palate risk in additional Asian populations. METHODS A set of 13 single nucleotide polymorphisms was tested for association with cleft lip with or without palate in 77 European American, 146 Taiwanese, 34 Singaporean, and 40 Korean case-parent trios using both the transmission disequilibrium test and conditional logistic regression models. RESULTS Evidence of linkage and association was observed among all four populations; and two specific haplotypes [GC composed of rs2235373-rs2235371 (p.V274I) and AAG of rs599021-rs2235373-rs595918] showed the most significant over- and undertransmission among Taiwanese cases (P=9x10(-6) and P=5x10(-6), respectively). The AGC/CGC diplotype composed of rs599021-rs2235373-rs2013162 showed almost a 7-fold increase in risk among the Taiwanese sample (P<10(-3)). These results confirmed the contribution of this gene to susceptibility of oral clefts across different populations; however, the specific single nucleotide polymorphisms showing statistical significance differed among ethnic groups. CONCLUSION The high-risk genotypes and diplotypes identified here may provide a better understanding of the etiological role of this gene in oral clefts and potential options for genetic counseling.
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Affiliation(s)
- Ji Wan Park
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA, and Department of Medical Research and Craniofacial Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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31
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Beaty TH, Hetmanski JB, Fallin MD, Park JW, Sull JW, McIntosh I, Liang KY, Vanderkolk CA, Redett RJ, Boyadjiev SA, Jabs EW, Chong SS, Cheah FSH, Wu-Chou YH, Chen PK, Chiu YF, Yeow V, Ng ISL, Cheng J, Huang S, Ye X, Wang H, Ingersoll R, Scott AF. Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. Hum Genet 2006; 120:501-18. [PMID: 16953426 DOI: 10.1007/s00439-006-0235-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 07/13/2006] [Accepted: 07/17/2006] [Indexed: 02/07/2023]
Abstract
Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.
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Affiliation(s)
- T H Beaty
- Johns Hopkins University, Baltimore, MD, USA.
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32
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Park JW, Hetmanski JB, Jabs EW, VanderKolk C, Wu-Chou Y, Chen KT, Chong SS, Jee SH, Mcintosh I, Fallin MD, Ingersoll R, Scott AF, Beaty TH. Association Between IRF6 and Nonsyndromic Oral Clefts In 4 Populations. Am J Epidemiol 2006. [DOI: 10.1093/aje/163.suppl_11.s127-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Park JW, Cai J, McIntosh I, Jabs EW, Fallin MD, Ingersoll R, Hetmanski JB, Vekemans M, Attie-Bitach T, Lovett M, Scott AF, Beaty TH. High throughput SNP and expression analyses of candidate genes for non-syndromic oral clefts. J Med Genet 2006; 43:598-608. [PMID: 16415175 PMCID: PMC2564555 DOI: 10.1136/jmg.2005.040162] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Recent work suggests that multiple genes and several environmental risk factors influence risk for non-syndromic oral clefts, one of the most common birth defects in humans. Advances in high-throughput genotyping technology now make it possible to test multiple markers in many candidate genes simultaneously. METHODS We present findings from family based association tests of single nucleotide polymorphism (SNP) markers in 64 candidate genes genotyped using the BeadArray approach in 58 case-parent trios from Maryland (USA) to illustrate how multiple markers in multiple genes can be analysed. To assess whether these genes were expressed in human craniofacial structures relevant to palate and lip development, we also analysed data from the Craniofacial and Oral Gene Expression Network (COGENE) consortium, and searched public databases for expression profiles of these genes. RESULTS Thirteen candidate genes showed significant evidence of linkage in the presence of disequilibrium, and ten of these were found to be expressed in relevant embryonic tissues: SP100, MLPH, HDAC4, LEF1, C6orf105, CD44, ALX4, ZNF202, CRHR1, and MAPT. Three other genes showing statistical evidence (ADH1C, SCN3B, and IMP5) were not expressed in the embryonic tissues examined here. CONCLUSIONS This approach demonstrates how statistical evidence on large numbers of SNP markers typed in case-parent trios can be combined with expression data to identify candidate genes for complex disorders. Many of the genes reported here have not been previously studied as candidates for oral clefts and warrant further investigation.
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Affiliation(s)
- J W Park
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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Beaty TH, Fallin MD, Hetmanski JB, McIntosh I, Chong SS, Ingersoll R, Sheng X, Chakraborty R, Scott AF. Haplotype diversity in 11 candidate genes across four populations. Genetics 2005; 171:259-67. [PMID: 15965248 PMCID: PMC1456517 DOI: 10.1534/genetics.105.043075] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.
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Affiliation(s)
- T H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Marazita ML, Murray JC, Lidral AC, Arcos-Burgos M, Cooper ME, Goldstein T, Maher BS, Daack-Hirsch S, Schultz R, Mansilla MA, Field LL, Liu YE, Prescott N, Malcolm S, Winter R, Ray A, Moreno L, Valencia C, Neiswanger K, Wyszynski DF, Bailey-Wilson JE, Albacha-Hejazi H, Beaty TH, McIntosh I, Hetmanski JB, Tunçbilek G, Edwards M, Harkin L, Scott R, Roddick LG. Meta-analysis of 13 genome scans reveals multiple cleft lip/palate genes with novel loci on 9q21 and 2q32-35. Am J Hum Genet 2004; 75:161-73. [PMID: 15185170 PMCID: PMC1216052 DOI: 10.1086/422475] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2004] [Accepted: 05/07/2004] [Indexed: 11/03/2022] Open
Abstract
Isolated or nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect with a complex etiology. A 10-cM genome scan of 388 extended multiplex families with CL/P from seven diverse populations (2,551 genotyped individuals) revealed CL/P genes in six chromosomal regions, including a novel region at 9q21 (heterogeneity LOD score [HLOD]=6.6). In addition, meta-analyses with the addition of results from 186 more families (six populations; 1,033 genotyped individuals) showed genomewide significance for 10 more regions, including another novel region at 2q32-35 (P=.0004). These are the first genomewide significant linkage results ever reported for CL/P, and they represent an unprecedented demonstration of the power of linkage analysis to detect multiple genes simultaneously for a complex disorder.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, Division of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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Ding J, Nieto FJ, Beauchamp NJ, Harris TB, Robbins JA, Hetmanski JB, Fried LP, Redline S. Sleep-Disordered Breathing and White Matter Disease in the Brainstem in Older Adults. Sleep 2004; 27:474-9. [PMID: 15164901 DOI: 10.1093/sleep/27.3.474] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
STUDY OBJECTIVES To examine whether sleep-disordered breathing is associated with white matter disease in the brainstem. DESIGN A population-based longitudinal study. SETTING Allegheny County, PA; Sacramento County, CA; and Washington County, MD. PATIENTS OR PARTICIPANTS A total of 789 individuals, aged 68 years or older, drawn from the Sleep Heart Health Study. INTERVENTIONS N/A. MEASUREMENTS AND RESULTS The participants underwent home polysomnography in 1995-1998 and cerebral magnetic resonance imaging in both 1992-1993 and 1997-1998. The apnea-hypopnea index was not associated with white matter disease in the brainstem, with or without adjusting for age, sex, race, community, body mass index, smoking status, alcohol use, systolic blood pressure, and the use of antihypertensive medication. In contrast, the arousal index (number of arousals per hour of sleep) was inversely associated with brainstem white matter disease (odds ratio = 0.75 for a SD increase in the arousal index, 95% confidence interval: 0.62, 0.92). CONCLUSIONS The frequency of apneas and hypopneas was not associated with brainstem white matter disease in these older adults. A unique relationship with arousal frequency suggests that ischemic changes in the brainstem may be associated with arousals during sleep.
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Affiliation(s)
- Jingzhong Ding
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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Hsu FC, Hetmanski JB, Li L, Markakis D, Jacobs K, Shugart YY. Comparison of significance level at the true location using two linkage approaches: LODPAL and GENEFINDER. BMC Genet 2003; 4 Suppl 1:S46. [PMID: 14975114 PMCID: PMC1866482 DOI: 10.1186/1471-2156-4-s1-s46] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background We compare two new software packages for linkage analysis, LODPAL and GENEFINDER. Both allow for covariate adjustment. Replicates 1 to 3 of Genetic Analysis Workshop 13 simulated data sets were used for the analyses. We described the results of searching for evidence of loci contributing to a simulated quantitative trait related to systolic blood pressure (SBP). Individuals with SBP greater than 130 mm Hg were defined as affected individuals, and all others as unaffected. Total cholesterol was treated as a covariate. Results Using LODPAL, the power of detecting one of the three major genes related to SBP is 44.4% when a LOD score of 1 is used as the cut-off point. The power of GENEFINDER is lower than that of LODPAL. It is 22.2%. Conclusions Based on the limited comparison, LODPAL provided the more reasonable power to detect linkage compared to GENEFINDER. After adjusting for the total cholesterol covariate, the current version of both programs appeared to give a high number of false positives.
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Affiliation(s)
- Fang-Chi Hsu
- Section on Biostatics, Department of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lan Li
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Diane Markakis
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kevin Jacobs
- Division of Genetic Epidemiology, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
- Division of Statistical Genetics and Bioinformatics, The OPAL Group, Cleveland, Ohio, USA
| | - Yin Yao Shugart
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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Zeiger JS, Hetmanski JB, Beaty TH, VanderKolk CA, Wyszynski DF, Bailey-Wilson JE, de Luna RO, Perandones C, Tolarova MM, Mosby T, Bennun R, Segovia M, Calda P, Pugh EW, Doheny K, McIntosh I. Evidence for linkage of nonsyndromic cleft lip with or without cleft palate to a region on chromosome 2. Eur J Hum Genet 2003; 11:835-9. [PMID: 14571267 DOI: 10.1038/sj.ejhg.5201052] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Results from a genome-wide screen of 10 multiplex families ascertained through probands with nonsyndromic cleft lip with or without cleft palate (CL/P) in Mexico, Argentina, and the United States yielded suggestive evidence of linkage to chromosomes 2, 6, 17 and 18. Fine mapping excluded all regions except chromosome 2. Subsequent analysis was performed on the original 10 families plus an additional 16 families using 31 markers on chromosome 2. This analysis showed intriguing evidence of linkage to 2q (Zlr=2.26, empirical P-value=0.028 in a chromosome-wide analysis). Transmission disequilibrium tests also revealed evidence of linkage and disequilibrium for two markers in this region (D2S168 and D2S1400 with P-values=0.022 and 0.006, respectively). A subset of these 26 families provided additional evidence for a susceptibility gene for CL/P on 2q, suggesting that further studies of genes in this region are warranted.
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Affiliation(s)
- Joanna S Zeiger
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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Ding J, Diez Roux AV, Nieto FJ, McNamara RL, Hetmanski JB, Taylor HA, Tyroler HA. Racial disparity in long-term mortality rate after hospitalization for myocardial infarction: the Atherosclerosis Risk in Communities study. Am Heart J 2003; 146:459-64. [PMID: 12947363 DOI: 10.1016/s0002-8703(03)00228-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND The underlying reasons why African American patients have a significantly higher mortality rate than European American patients after a myocardial infarction (MI) remain unclear. This study examined the racial disparity in mortality rates after MI and possible explanatory factors. METHODS A prospective analysis was conducted within the Atherosclerosis Risk in Communities (ARIC) study, a community-based study of 15,792 middle-aged adults. From 1987 to 1998, 642 patients (471 European American and 171 African American) hospitalized for MI without prior history of MI were identified. Of these 642 patients, 129 (82 European American and 47 African American) died during follow-up. RESULTS Cox proportional hazard models were used to analyze the racial difference in mortality rate after MI. After adjusting for age and sex, the relative hazard (RH) comparing African American patients to European American patients was 1.80 (95% CI, 1.24-2.61). The RH decreased after adjusting for vascular risk factors (1.29; 95% CI, 0.83-2.00), socioeconomic position (1.31; 95% CI, 0.83-2.09), severity of MI (1.60; 95% CI, 1.05-2.45), and treatment (1.36; 95% CI, 0.92-2.00). In the final model, which included all factors aforementioned, the RH for race was 1.00 (95% CI, 0.56-1.77). CONCLUSIONS Our findings suggested that vascular risk factors, socioeconomic position, and treatment play major roles in the racial disparity in mortality rate after MI.
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Affiliation(s)
- Jingzhong Ding
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Md 21205, USA.
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Fallin MD, Hetmanski JB, Park J, Scott AF, Ingersoll R, Fuernkranz HA, McIntosh I, Beaty TH. Family-based analysis of MSX1 haplotypes for association with oral clefts. Genet Epidemiol 2003; 25:168-75. [PMID: 12916025 DOI: 10.1002/gepi.10255] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Oral clefts, one of the most common forms of birth defects, are considered to be of complex etiology, including both genetic and environmental causes. To date, however, no particular genetic cause has been confirmed for isolated, nonsyndromic oral clefts. Previous case-control and family-based association studies reported an association between an intronic CA repeat of the MSX1 gene and risk for oral clefts. In this study, we identify eight single-nucleotide polymorphisms (SNPs) in the MSX1 gene, and present genotype results for these SNPs in a set of 206 oral cleft cases and their parents. We performed single-marker and haplotype-based transmission disequilibrium tests (TDTs), and tested for evidence of interaction between MSX1 haplotypes and exposure to maternal smoking in the first trimester, using a case-only approach. The haplotype TDT analyses further implicate this gene, or region, in controlling the risk for oral clefts, particularly for cleft palate. In addition, case-only haplotype analyses suggest an interaction between variation in the MSX1 gene and exposure to maternal smoking. This study encourages further focus on the MSX1 gene region to ultimately determine specific variants predisposing to oral clefts.
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Affiliation(s)
- M Daniele Fallin
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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41
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Ding J, Nieto FJ, Beauchamp NJ, Longstreth WT, Manolio TA, Hetmanski JB, Fried LP. A prospective analysis of risk factors for white matter disease in the brain stem: the Cardiovascular Health Study. Neuroepidemiology 2003; 22:275-82. [PMID: 12902622 DOI: 10.1159/000071190] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND PURPOSE White matter disease (WMD) in the brain stem may be a predictor of poor clinical outcome, independent of WMD in the periventricular and subcortical areas of the brain. Many cardiovascular risk factors such as older age, hypertension, and smoking have been suggested as risk factors for WMD in the periventricular and subcortical areas of the brain. However, no epidemiologic study has examined the associations between cardiovascular risk factors and WMD in the brain stem. METHODS A total of 789 participants, aged 65 years or older, from the Cardiovascular Health Study constituted the present study population. WMD, defined as hyperintensive lesions on magnetic resonance imaging (MRI), in the brain stem was measured in 1992/1993 and 1997/1998. RESULTS Of the 789 participants, 212 (26.9%) had WMD in the brain stem in 1997/1998. In multivariate logistic regression analysis, the presence of WMD in the brain stem in 1997/1998 was significantly associated with several variables measured in 1992/1993: an increase by 5 years of age (OR = 1.51, 95% CI: 1.25-1.83), a 10-pack-years increase in smoking (OR = 1.12, 95% CI: 1.04-1.21), a 0.1-liter increase in first-second forced expiratory volume (OR = 0.95, 95% CI: 0.92-0.99), a 1 micromol/l increase in fibrinogen level (OR = 1.13, 95% CI: 1.03-1.23), and MRI infarction (OR = 2.58, 95% CI: 1.78-3.74). Excluding those (n = 167) with WMD in the brain stem in 1992/1993, the pattern remained. Hypertension was not associated with WMD in the brain stem. CONCLUSIONS Increased age, smoking, lower forced expiratory volume, increased fibrinogen level, and MRI infarction, but not hypertension, may be independent risk factors for WMD in the brain stem in older adults.
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Affiliation(s)
- Jingzhong Ding
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Room W6009, Baltimore, MD 21205, USA.
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Zeiger JS, Beaty TH, Hetmanski JB, Wang H, Scott AF, Kasch L, Raymond G, Jabs EW, VanderKolk C. Genetic and environmental risk factors for sagittal craniosynostosis. J Craniofac Surg 2002; 13:602-6. [PMID: 12218784 DOI: 10.1097/00001665-200209000-00002] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The authors investigated whether genetic and environmental factors influence risk for sagittal craniosynostosis. Cases were ascertained from craniofacial clinics in the Baltimore-Washington metropolitan region. Controls were recruited from the Johns Hopkins newborn nursery and a large pediatric practice in Baltimore County. Forty-two probands with isolated, nonsyndromic sagittal craniosynostosis born in the mid-Atlantic region were included in this analysis. Controls are infants born in Maryland without any known birth defects (n = 182). Odds ratios (OR) and corresponding 95% confidence intervals (CI) were calculated. Cases were genotyped at several loci implicated in malformation syndromes including craniosynostosis. There were no elevated risks for craniosynostosis related to maternal or paternal smoking or maternal vitamin usage. Case mothers consumed less alcohol (OR = 0.38, 95% CI = 0.17-0.85) and had less education than control mothers ( < 0.001). All cases that were sequenced were negative for mutations at the following genes: exon IIIa 755C->G, (exons IIIa and IIIc,), exon IIIa, and exon 1. These findings suggest that whereas TWIST and the genes are important for syndromic craniosynostosis, they are unlikely to be involved in isolated sagittal craniosynostosis. Parental education and alcohol consumption were associated with sagittal craniosynostosis in this study.
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Affiliation(s)
- Joanna S Zeiger
- Johns Hopkins Bloomberg School of Hygiene and Public Health, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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43
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Zandi PP, Klein AP, Addington AM, Hetmanski JB, Roberts L, Peila R, Shrestha S, Shaw CK, Kiat HC, Langefeld CD, Beaty TH. Multilocus linkage analysis of the German asthma data. Genet Epidemiol 2002; 21 Suppl 1:S210-5. [PMID: 11793671 DOI: 10.1002/gepi.2001.21.s1.s210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We analyzed data from the German Asthma Genetics Group with three methods that utilize pedigree-specific nonparametric linkage scores to facilitate the search for multiple independent and interacting susceptibility loci. The three methods included a conditional analysis, logistic regression, and neural networks. Although there were differences, the three methods identified many of the same susceptibility loci. The most consistent evidence was provided for loci on chromosomes 1, 2, 6, 9, and 15. Both the conditional and the logistic regression analyses suggested an epistatic relationship between loci on chromosomes 2 and 9. The logistic regression analysis further revealed evidence for locus heterogeneity between loci on chromosomes 6 and 15. Finally, the neural network analysis identified a potential locus on chromosome 17 that was not identified in the other analyses.
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MESH Headings
- Adult
- Asthma/epidemiology
- Asthma/genetics
- Child
- Chromosome Mapping/statistics & numerical data
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 2
- Chromosomes, Human, Pair 6
- Chromosomes, Human, Pair 9
- Epistasis, Genetic
- Female
- Genetic Heterogeneity
- Genetic Predisposition to Disease/genetics
- Genetics, Population
- Germany
- Humans
- Male
- Neural Networks, Computer
- Statistics, Nonparametric
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Affiliation(s)
- P P Zandi
- Department of Mental Hygiene, Johns Hopkins School of Hygiene and Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
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Beaty TH, Hetmanski JB, Zeiger JS, Fan YT, Liang KY, VanderKolk CA, McIntosh I. Testing candidate genes for non-syndromic oral clefts using a case-parent trio design. Genet Epidemiol 2002; 22:1-11. [PMID: 11754469 DOI: 10.1002/gepi.1039] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Markers in five candidate genes were examined on 269 case-parent trios ascertained through a child with an isolated, non-syndromic oral cleft (cleft lip, CL; cleft palate, CP; or cleft lip and palate, CLP). Cases and their parents were ascertained through treatment centers in Maryland. Markers at two of the five candidate genes, transforming growth factor beta3 (TGFbeta3) and MSX1, showed consistent evidence of linkage and disequilibrium due to linkage using several statistical tests (e.g., the global chi-square for TGFbeta3 was 21.1 with 12 df, P = 0.03; that for MSX1 was 8.7 with 3 df, P = 0.03). There was little evidence of heterogeneity in the role of TGFbeta3 between different types of oral clefts, but MSX1 did yield marginal evidence for such heterogeneity. MSX1 also showed evidence for interaction between infant's genotype and maternal smoking, giving a likelihood ratio test for heterogeneity between smoker and non-smoker mothers of 7.16 (2 df, P = 0.03). Using a conditional logistic model to test for gene-gene interaction showed no evidence of interaction between TGFbeta3 and MSX1, with both seeming to contribute independently to risk of isolated, non-syndromic oral clefts.
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Affiliation(s)
- Terri H Beaty
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA.
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Beaty TH, Wang H, Hetmanski JB, Fan YT, Zeiger JS, Liang KY, Chiu YF, Vanderkolk CA, Seifert KC, Wulfsberg EA, Raymond G, Panny SR, McIntosh I. A case-control study of nonsyndromic oral clefts in Maryland. Ann Epidemiol 2001; 11:434-42. [PMID: 11454503 DOI: 10.1016/s1047-2797(01)00222-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PURPOSE Isolated, nonsyndromic oral clefts cases (n = 171) and unaffected controls (n = 182) were used to identify both genetic and environmental risk factors. METHODS Infants born in Maryland between 1992 to 1998 with an isolated, nonsyndromic oral cleft [cleft lip (CL), cleft lip and palate (CLP), or cleft palate (CP)] were recruited and exposure plus family history data were collected. Controls were unaffected infants. DNA was collected from all cases and their parents, plus controls. RESULTS No statistically significant association was found between any of the following: maternal smoking, vitamin use, urinary tract infection, or recreational drug use in either univariate analysis or after adjusting for maternal age and education. More control mothers reported alcohol use during the critical time period of pregnancy (one month before conception through the first trimester) as compared to case mothers. There was a 10-fold increase in risk to siblings of cases as compared to siblings of controls. Markers at four candidate genes were examined: transforming growth factor alpha (TGF alpha), transforming growth factor beta 3 (TGF beta 3), MSX1, and BCL3. Only MSX1 showed significant differences in allele frequencies between CP cases and controls. MSX1 also showed significant evidence of linkage disequilibrium with a susceptibility gene controlling risk for CP. CONCLUSION Most environmental risk factors examined here gave little evidence of association with risk to isolated, nonsyndromic oral clefts, although any alcohol consumption seemed protective. MSX1 showed evidence of linkage disequilibrium in both case-control and case-parent trio analysis.
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Affiliation(s)
- T H Beaty
- The Johns Hopkins University, Baltimore, MD, USA
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46
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Mathias RA, Freidhoff LR, Blumenthal MN, Meyers DA, Lester L, King R, Xu JF, Solway J, Barnes KC, Pierce J, Stine OC, Togias A, Oetting W, Marshik PL, Hetmanski JB, Huang SK, Ehrlich E, Dunston GM, Malveaux F, Banks-Schlegel S, Cox NJ, Bleecker E, Ober C, Beaty TH, Rich SS. Genome-wide linkage analyses of total serum IgE using variance components analysis in asthmatic families. Genet Epidemiol 2001; 20:340-55. [PMID: 11255243 DOI: 10.1002/gepi.5] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Variance components models were used to analyze total IgE levels in families ascertained though the Collaborative Study of the Genetics of Asthma (CSGA) using a genome-wide array of polymorphic markers. While IgE levels are known to be associated with clinical asthma and recognized to be under strong genetic control (here the heritability was estimated at 44-60% in the three racial groups), specific genes influencing this trait are still largely unknown. Multipoint analysis of 323 markers yielded little indication of specific regions containing a trait locus controlling total serum IgE levels (adjusted for age and gender). Although a number of regions showed LOD statistics above 1.5 in Caucasian families (chromosome 4) and in African-American families (chromosomes 2 and 4), none yielded consistent evidence in all three racial groups. Analysis of total IgE adjusted for gender, age and Allergy Index (a quantitative score of skin test sensitivity to 14 common aeroallergens) was conducted on these data. In this analysis, a much stronger signal for a trait locus controlling adjusted log[total IgE] was seen on the telomeric end of chromosome 18, but only in Caucasian families. This region accounted for most of the genetic variation in log[total IgE], and may represent a quantitative trait locus for IgE levels independent of atopic response. Oligogenic analysis accounting simultaneously for the contribution of this locus on chromosome 18 and other chromosomal regions showing some evidence of linkage in these Caucasian families (on chromosomes 2, 4 and 20) failed to yield significant evidence for interaction.
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Affiliation(s)
- R A Mathias
- Department of Epidemiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
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Mathias RA, Bickel CA, Beaty TH, Petersen GM, Hetmanski JB, Liang KY, Barnes KC. A study of contemporary levels and temporal trends in inbreeding in the Tangier Island, Virginia, population using pedigree data and isonymy. Am J Phys Anthropol 2000; 112:29-38. [PMID: 10766941 DOI: 10.1002/(sici)1096-8644(200005)112:1<29::aid-ajpa4>3.0.co;2-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this study we describe inbreeding in a large pedigree from Tangier Island, Virginia, in which we compare two commonly used methods to estimate inbreeding in humans: pedigree and isonymy (identical surnames of spouses). Genealogical data on 3,512 individuals dating back to 1722 were used. Using the pedigree method, we determined an average inbreeding coefficient (F) of 0.00873 for the community as a whole, and 0.018 for inbred individuals. Analysis of temporal trends showed that inbreeding began around 1800 and peaked at 0.0109 in 1824-1849 and 1875-1899. Thereafter, inbreeding steadily declined to 0.00565 in 1975-1997. Analysis of pedigree structure complexity over time showed that close consanguinity contributes to inbreeding in the earlier cohorts, and remote consanguinity accounts for much of the inbreeding in the later cohorts. The number of common ancestors increases over time, as does the number of paths connecting inbred individuals to these common ancestors. Inbreeding estimates based on the isonymy approach yielded a 2.2-fold higher value of F (0.01945) compared to the pedigree method. Total isonymy estimates over 25-year cohorts overestimated inbreeding values from pedigree data between 1. 5-8-fold. We speculate that the overestimation is probably due to the inability of our data to satisfy the method's assumption of monophyletic origin of each surname. In conclusion, inbreeding in the Tangier Island population is consistent with the isolated nature of its population, and temporal trends reflect patterns in emigration and a breakdown in isolation over time.
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Affiliation(s)
- R A Mathias
- Department of Epidemiology, The Johns Hopkins School of Hygiene and Public Health, Baltimore, Maryland 21205, USA
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Beaty TH, Maestri NE, Hetmanski JB, Wyszynski DF, Vanderkolk CA, Simpson JC, McIntosh I, Smith EA, Zeiger JS, Raymond GV, Panny SR, Tifft CJ, Lewanda AF, Cristion CA, Wulfsberg EA. Testing for Interaction between Maternal Smoking and TGFA Genotype among Oral Cleft Cases Born in Maryland 1992–1996. Cleft Palate Craniofac J 1997. [DOI: 10.1597/1545-1569(1997)034<0447:tfibms>2.3.co;2] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Beaty TH, Maestri NE, Hetmanski JB, Wyszynski DF, Vanderkolk CA, Simpson JC, McIntosh I, Smith EA, Zeiger JS, Raymond GV, Panny SR, Tifft CJ, Lewanda AF, Cristion CA, Wulfsberg EA. Testing for interaction between maternal smoking and TGFA genotype among oral cleft cases born in Maryland 1992-1996. Cleft Palate Craniofac J 1997; 34:447-54. [PMID: 9345615 DOI: 10.1597/1545-1569_1997_034_0447_tfibms_2.3.co_2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Infants born in Maryland between June 1992 and June 1996 were used in a case-control study of nonsyndromic oral clefts to test for effects of maternal smoking and a polymorphic genetic marker at the transforming growth factor alpha (TGFA) locus, both of which have been reported to be risk factors for these common birth defects. DESIGN AND SETTING Cases were infants with an oral cleft ascertained through three comprehensive treatment centers, with additional ascertainment through a registry of birth defects maintained by the Maryland Health Department. Controls were healthy infants. Medical history information on infants and mothers were collected, along with DNA samples. PATIENTS, PARTICIPANTS Among 286 cases contacted (72% ascertainment), there were 192 nonsyndromic isolated oral clefts (106 M; 86 F) available for this case-control study. MAIN OUTCOME MEASURES The largest group of 149 Caucasian nonsyndromic cases and 86 controls was used to test for association with maternal smoking and genotype at the Taq1 polymorphism in TGFA. RESULTS While this modest sample had limited statistical power to detect gene-environment interaction, there was a significant marginal increase in risk of having an oral cleft if the mother smoked (odds ratio = 1.75, 95% CI = 1.01 to 3.02). We could not demonstrate statistical interaction between maternal smoking and TGFA genotype in this study, however, and the observed increase in the C2 allele among cases was not statistically significant. CONCLUSIONS We could not confirm either the reported association between oral clefts and TGFA genotype or its interaction with maternal smoking. However, these data do show an increased risk if the mother smoked during pregnancy, and this effect was greatest among infants with a bilateral cleft and no close family history of clefts.
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Affiliation(s)
- T H Beaty
- Department of Epidemiology, School of Hygiene & Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA.
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