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Larsen LA, Hitz MP. Human Genetics of Atrial Septal Defect. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:467-480. [PMID: 38884726 DOI: 10.1007/978-3-031-44087-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Although atrial septal defects (ASD) can be subdivided based on their anatomical location, an essential aspect of human genetics and genetic counseling is distinguishing between isolated and familiar cases without extracardiac features and syndromic cases with the co-occurrence of extracardiac abnormalities, such as developmental delay. Isolated or familial cases tend to show genetic alterations in genes related to important cardiac transcription factors and genes encoding for sarcomeric proteins. By contrast, the spectrum of genes with genetic alterations observed in syndromic cases is diverse. Currently, it points to different pathways and gene networks relevant to the dysregulation of cardiomyogenesis and ASD pathogenesis. Therefore, this chapter reflects the current knowledge and highlights stable associations observed in human genetics studies. It gives an overview of the different types of genetic alterations in these subtypes, including common associations based on genome-wide association studies (GWAS), and it highlights the most frequently observed syndromes associated with ASD pathogenesis.
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Affiliation(s)
- Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Institute of Medical Genetics, University Medicine Oldenburg, Oldenburg, Germany.
- Department for Paediatric Cardiology, University Hospital Kiel, Kiel, Germany.
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Muroke V, Jalanko M, Ruotsalainen S, Perola M, Helle E, Sinisalo J. Phenotype of ASDs Associated With 4p16 Risk Locus and Novel Genome-Wide Associations of ASD Patients in the Finnish Population. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:486-489. [PMID: 37577800 PMCID: PMC10581411 DOI: 10.1161/circgen.123.004070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Affiliation(s)
- Valtteri Muroke
- Department of Cardiology, Helsinki University Hospital (V.M., M.J., J.S.), University of Helsinki, Finland
| | - Mikko Jalanko
- Department of Cardiology, Helsinki University Hospital (V.M., M.J., J.S.), University of Helsinki, Finland
| | - Sanni Ruotsalainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE (S.R.), University of Helsinki, Finland
| | - Markus Perola
- Finnish Institute for Health and Welfare, Helsinki, Finland (M.P.)
| | - Emmi Helle
- Stem Cells and Metabolism Research Program, Faculty of Medicine (E.H.), University of Helsinki, Finland
- New Children’s Hospital, Pediatric Research Center, Helsinki University Hospital and University of Helsinki, Finland (E.H.)
| | - Juha Sinisalo
- Department of Cardiology, Helsinki University Hospital (V.M., M.J., J.S.), University of Helsinki, Finland
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Rashkin SR, Cleves M, Shaw GM, Nembhard WN, Nestoridi E, Jenkins MM, Romitti PA, Lou XY, Browne ML, Mitchell LE, Olshan AF, Lomangino K, Bhattacharyya S, Witte JS, Hobbs CA. A genome-wide association study of obstructive heart defects among participants in the National Birth Defects Prevention Study. Am J Med Genet A 2022; 188:2303-2314. [PMID: 35451555 PMCID: PMC9283270 DOI: 10.1002/ajmg.a.62759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Obstructive heart defects (OHDs) share common structural lesions in arteries and cardiac valves, accounting for ~25% of all congenital heart defects. OHDs are highly heritable, resulting from interplay among maternal exposures, genetic susceptibilities, and epigenetic phenomena. A genome-wide association study was conducted in National Birth Defects Prevention Study participants (Ndiscovery = 3978; Nreplication = 2507), investigating the genetic architecture of OHDs using transmission/disequilibrium tests (TDT) in complete case-parental trios (Ndiscovery_TDT = 440; Nreplication_TDT = 275) and case-control analyses separately in infants (Ndiscovery_CCI = 1635; Nreplication_CCI = 990) and mothers (case status defined by infant; Ndiscovery_CCM = 1703; Nreplication_CCM = 1078). In the TDT analysis, the SLC44A2 single nucleotide polymorphism (SNP) rs2360743 was significantly associated with OHD (pdiscovery = 4.08 × 10-9 ; preplication = 2.44 × 10-4 ). A CAPN11 SNP (rs55877192) was suggestively associated with OHD (pdiscovery = 1.61 × 10-7 ; preplication = 0.0016). Two other SNPs were suggestively associated (p < 1 × 10-6 ) with OHD in only the discovery sample. In the case-control analyses, no SNPs were genome-wide significant, and, even with relaxed thresholds ( × discovery < 1 × 10-5 and preplication < 0.05), only one SNP (rs188255766) in the infant analysis was associated with OHDs (pdiscovery = 1.42 × 10-6 ; preplication = 0.04). Additional SNPs with pdiscovery < 1 × 10-5 were in loci supporting previous findings but did not replicate. Overall, there was modest evidence of an association between rs2360743 and rs55877192 and OHD and some evidence validating previously published findings.
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Affiliation(s)
- Sara R Rashkin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Mario Cleves
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Health Informatics Institute, Tampa, Florida, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Wendy N Nembhard
- Department of Epidemiology and Arkansas Center for Birth Defects and Prevention, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Eirini Nestoridi
- Massachusetts Center for Birth Defects Research and Prevention, Massachusetts Department of Public Health, Boston, Massachusetts, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul A Romitti
- Department of Epidemiology, University of Iowa, Iowa City, Iowa, USA
| | - Xiang-Yang Lou
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Marilyn L Browne
- Birth Defects Research Section, New York State Department of Health, Albany, New York, USA
- Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, New York, USA
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, USA
| | - Andrew F Olshan
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sudeepa Bhattacharyya
- Bioinformatics and Data Science at University of Arkansas, Little Rock, Arkansas, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
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Liu Y, Williams SG, Jones HR, Keavney BD, Choy MK. A novel RNA-mediated mechanism causing down-regulation of insulating promoter interactions in human embryonic stem cells. Sci Rep 2021; 11:23233. [PMID: 34853328 PMCID: PMC8636647 DOI: 10.1038/s41598-021-02373-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Abstract
The genome-wide promoter interactome is primarily maintained and regulated by architectural proteins such as CTCF and cohesin. However, some studies suggest a role for non-coding RNAs (ncRNAs) in this process. We aimed to characterise the regulatory role of RNA-mediated promoter interactions in the control of gene expression. We integrated genome-wide datasets of RNA-chromatin and promoter-genome interactions in human embryonic stem cells (hESCs) to identify putative RNA-mediated promoter interactions. We discovered that CTCF sites were enriched in RNA-PIRs (promoter interacting regions co-localising with RNA-chromatin interaction sites) and genes interacting with RNA-PIRs containing CTCF sites showed higher expression levels. One of the long noncoding RNAs (lncRNAs) expressed in hESCs, Syntaxin 18-Antisense 1 (STX18-AS1), appeared to be involved in an insulating promoter interaction with the neighbouring gene, MSX1. By knocking down STX18-AS1, the MSX1 promoter-PIR interaction was intensified and the target gene (MSX1) expression was down-regulated. Conversely, reduced MSX1 promoter-PIR interactions, resulting from CRISPR-Cas9 deletion of the PIR, increased the expression of MSX1. We conclude that STX18-AS1 RNA antagonised local CTCF-mediated insulating promoter interactions to augment gene expression. Such down-regulation of the insulating promoter interactions by this novel mechanism may explain the higher expression of genes interacting with RNA-PIRs linked to CTCF sites.
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Affiliation(s)
- Yingjuan Liu
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Simon G Williams
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Hayden R Jones
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Bernard D Keavney
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK
- Manchester Heart Institute, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Mun-Kit Choy
- Division of Cardiovascular Sciences, The University of Manchester, Manchester, M13 9PT, UK.
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Li M, Lyu C, Huang M, Do C, Tycko B, Lupo PJ, MacLeod SL, Randolph CE, Liu N, Witte JS, Hobbs CA. Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease. BMC Genom Data 2021; 22:20. [PMID: 34112112 PMCID: PMC8194170 DOI: 10.1186/s12863-021-00975-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/02/2021] [Indexed: 12/27/2022] Open
Abstract
Background Most congenital heart defects (CHDs) result from complex interactions among genetic susceptibilities, epigenetic modifications, and maternal environmental exposures. Characterizing the complex relationship between genetic, epigenetic, and transcriptomic variation will enhance our understanding of pathogenesis in this important type of congenital disorder. We investigated cis-acting effects of genetic single nucleotide polymorphisms (SNPs) on local DNA methylation patterns within 83 cardiac tissue samples and prioritized their contributions to CHD risk by leveraging results of CHD genome-wide association studies (GWAS) and their effects on cardiac gene expression. Results We identified 13,901 potential methylation quantitative trait loci (mQTLs) with a false discovery threshold of 5%. Further co-localization analyses and Mendelian randomization indicated that genetic variants near the HLA-DRB6 gene on chromosome 6 may contribute to CHD risk by regulating the methylation status of nearby CpG sites. Additional SNPs in genomic regions on chromosome 10 (TNKS2-AS1 gene) and chromosome 14 (LINC01629 gene) may simultaneously influence epigenetic and transcriptomic variations within cardiac tissues. Conclusions Our results support the hypothesis that genetic variants may influence the risk of CHDs through regulating the changes of DNA methylation and gene expression. Our results can serve as an important source of information that can be integrated with other genetic studies of heart diseases, especially CHDs. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00975-2.
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Affiliation(s)
- Ming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA.
| | - Chen Lyu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Manyan Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - Catherine Do
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, 07110, USA
| | | | | | | | - Nianjun Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E. Seventh Street, Bloomington, 47405, IN, USA
| | - John S Witte
- University of California at San Francisco, San Francisco, CA, 94158, USA
| | - Charlotte A Hobbs
- Rady Children's Institute for Genomic Medicine, San Diego, CA, 92123, USA
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Lahm H, Jia M, Dreßen M, Wirth F, Puluca N, Gilsbach R, Keavney BD, Cleuziou J, Beck N, Bondareva O, Dzilic E, Burri M, König KC, Ziegelmüller JA, Abou-Ajram C, Neb I, Zhang Z, Doppler SA, Mastantuono E, Lichtner P, Eckstein G, Hörer J, Ewert P, Priest JR, Hein L, Lange R, Meitinger T, Cordell HJ, Müller-Myhsok B, Krane M. Congenital heart disease risk loci identified by genome-wide association study in European patients. J Clin Invest 2021; 131:141837. [PMID: 33201861 PMCID: PMC7810487 DOI: 10.1172/jci141837] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022] Open
Abstract
Genetic factors undoubtedly affect the development of congenital heart disease (CHD) but still remain ill defined. We sought to identify genetic risk factors associated with CHD and to accomplish a functional analysis of SNP-carrying genes. We performed a genome-wide association study (GWAS) of 4034 White patients with CHD and 8486 healthy controls. One SNP on chromosome 5q22.2 reached genome-wide significance across all CHD phenotypes and was also indicative for septal defects. One region on chromosome 20p12.1 pointing to the MACROD2 locus identified 4 highly significant SNPs in patients with transposition of the great arteries (TGA). Three highly significant risk variants on chromosome 17q21.32 within the GOSR2 locus were detected in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence the expression of WNT3, and the variant rs870142 related to septal defects is proposed to influence the expression of MSX1. We analyzed the expression of all 4 genes during cardiac differentiation of human and murine induced pluripotent stem cells in vitro and by single-cell RNA-Seq analyses of developing murine and human hearts. Our data show that MACROD2, GOSR2, WNT3, and MSX1 play an essential functional role in heart development at the embryonic and newborn stages.
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Affiliation(s)
- Harald Lahm
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Meiwen Jia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Felix Wirth
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Nazan Puluca
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Ralf Gilsbach
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site RheinMain, Frankfurt am Main, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Manchester Heart Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Julie Cleuziou
- Department of Congenital and Paediatric Heart Surgery, German Heart Center Munich, Munich, Germany
| | - Nicole Beck
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Olga Bondareva
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Elda Dzilic
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Melchior Burri
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Karl C. König
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Johannes A. Ziegelmüller
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Claudia Abou-Ajram
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Irina Neb
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Zhong Zhang
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Stefanie A. Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
| | - Elisa Mastantuono
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Peter Lichtner
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Gertrud Eckstein
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Jürgen Hörer
- Department of Congenital and Paediatric Heart Surgery, German Heart Center Munich, Munich, Germany
| | - Peter Ewert
- Department of Pediatric Cardiology and Congenital Heart Disease, German Heart Center Munich, Munich, Germany
| | - James R. Priest
- Department of Pediatrics, Division of Pediatric Cardiology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Lutz Hein
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS, Center for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
| | - Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, United Kingdom
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry Munich, Munich, Germany
- Munich Cluster of Systems Biology, SyNergy, Munich, Germany
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, Institute Insure (Institute for Translational Cardiac Surgery), German Heart Center Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research) — Partner Site Munich Heart Alliance, Munich, Germany
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Hernández-Almaguer MD, Calvo-Anguiano G, Cerda-Flores RM, Salinas-Torres VM, Orozco-Galicia F, Glenn E, García-Guerra J, Sánchez-Cortés G, Lugo-Trampe J, Martínez-Garza LE. Genetic Variants at the rs4720169 Locus of TBX20 and the rs12921862 Locus of AXIN1 May Increase the Risk of Congenital Heart Defects in the Mexican Population: A Pilot Study. Genet Test Mol Biomarkers 2020; 23:664-670. [PMID: 31524541 DOI: 10.1089/gtmb.2019.0029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: Congenital heart defects (CHDs) are the most common type of birth defects and a major cause of infant mortality. Although knowledge of genetic risk variants for CHDs is scarce, most cases of CHDs are considered to be due to multifactorial inheritance. Objective: To analyze the association of 14 single nucleotide polymorphic variants previously associated with a risk of CHDs in a Mexican population with isolated CHDs. Materials and Methods: DNA samples obtained from healthy subjects and from subjects with isolated atrial, ventricular, or atrioventricular septal defects living in Northeastern Mexico were analyzed by real time-polymerase chain reaction for allelic discrimination of genetic variants of the genes TBX1, TBX20, ASTX-18-AS1, AXIN1, MTHFR, NKX2.5, BMP4, and NFATc1. The odds ratios (ORs) for allele and genotype frequencies and inheritance models were obtained. Results: Forty-two patients and 138 controls were included. Two variants were found to confer a risk of CHDs: variant rs4720169 of TBX20 in which the OR for the heterozygous state was 1.88 (95% confidence interval [CI]: 1.12-3.14, p = 0.010), whereas the OR for the homozygous state was 3.82 (95% CI: 1.18-12.3, p = 0.010); and variant rs12921862 of AXIN1 in which the OR for the heterozygous state was 4.15 (95% CI: 2.42-7.10; p ≤ 0.001), whereas the OR for the homozygous state was 9.2 (95% CI: 1.31-64.7, p = 0.008) for allele A. Conclusion: Genetic variants of the TBX20 and AXIN1 genes confer a significantly increased risk of congenital septal heart defects in a population from Northeastern Mexico.
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Affiliation(s)
| | - Geovana Calvo-Anguiano
- Departamento de Genética, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | - Víctor M Salinas-Torres
- Departamento de Genética, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Francisco Orozco-Galicia
- Departamento de Genética, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Eva Glenn
- Facultad de Medicina Mexicali, Universidad Autónoma de Baja California, Mexicali, Mexico
| | | | - Gerardo Sánchez-Cortés
- Departamento de Pediatría, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - José Lugo-Trampe
- Departamento de Genética, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Laura E Martínez-Garza
- Departamento de Genética, Hospital Universitario "Dr. José E. González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
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8
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Association between the 4p16 genomic locus and different types of congenital heart disease: results from adult survivors in the UK Biobank. Sci Rep 2019; 9:16515. [PMID: 31712678 PMCID: PMC6848143 DOI: 10.1038/s41598-019-52969-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/18/2019] [Indexed: 11/17/2022] Open
Abstract
Congenital heart disease is the most common birth defect in newborns and the leading cause of death in infancy, affecting nearly 1% of live births. A locus in chromosome 4p16, adjacent to MSX1 and STX18, has been associated with atrial septal defects (ASD) in multiple European and Chinese cohorts. Here, genotyping data from the UK Biobank was used to test for associations between this locus and congenital heart disease in adult survivors of left ventricular outflow tract obstruction (n = 164) and ASD (n = 223), with a control sample of 332,788 individuals, and a meta-analysis of the new and existing ASD data was performed. The results show an association between the previously reported markers at 4p16 and risk for either ASD or left ventricular outflow tract obstruction, with effect sizes similar to the published data (OR between 1.27–1.45; all p < 0.05). Differences in allele frequencies remained constant through the studied age range (40–70 years), indicating that the variants themselves do not drive lethal genetic defects. Meta-analysis shows an OR of 1.35 (95% CI: 1.25–1.46; p < 10−4) for the association with ASD. The findings show that the genetic associations with ASD can be generalized to adult survivors of both ASD and left ventricular lesions. Although the 4p16 associations are statistically compelling, the mentioned alleles confer only a small risk for disease and their frequencies in this adult sample are the same as in children, likely limiting their clinical significance. Further epidemiological and functional studies may elicit factors triggering disease in interaction with the risk alleles.
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9
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Lupo PJ, Mitchell LE, Jenkins MM. Genome-wide association studies of structural birth defects: A review and commentary. Birth Defects Res 2019; 111:1329-1342. [PMID: 31654503 DOI: 10.1002/bdr2.1606] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 09/21/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND While there is strong evidence that genetic risk factors play an important role in the etiologies of structural birth defects, compared to other diseases, there have been relatively few genome-wide association studies (GWAS) of these conditions. We reviewed the current landscape of GWAS conducted for birth defects, noting novel insights, and future directions. METHODS This article reviews the literature with regard to GWAS of structural birth defects. Key defects included in this review include oral clefts, congenital heart defects (CHDs), biliary atresia, pyloric stenosis, hypospadias, craniosynostosis, and clubfoot. Additionally, other issues related to GWAS are considered, including the assessment of polygenic risk scores and issues related to genetic ancestry, as well as utilizing genome-wide single nucleotide polymorphism array data to evaluate gene-environment interactions and Mendelian randomization. RESULTS For some birth defects, including oral clefts and CHDs, several novel susceptibility loci have been identified and replicated through GWAS, including 8q24 for oral clefts, DGKK for hypospadias, and 4p16 for CHDs. Relatively common birth defects for which there are currently no published GWAS include neural tube defects, anotia/microtia, anophthalmia/microphthalmia, gastroschisis, and omphalocele. CONCLUSIONS Overall, GWAS have been successful in identifying several novel susceptibility genes and genomic regions for structural birth defects. These findings have provided new insights into the etiologies of these phenotypes. However, GWAS have been underutilized for understanding the genetic etiologies of several birth defects.
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Affiliation(s)
- Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, Georgia
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Simpson JL, Rechitsky S. Preimplantation diagnosis and other modern methods for prenatal diagnosis. J Steroid Biochem Mol Biol 2017; 165:124-130. [PMID: 27108943 DOI: 10.1016/j.jsbmb.2016.03.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/16/2016] [Indexed: 12/15/2022]
Abstract
Prenatal treatment of congenital adrenal hyperplasia (CAH) has long involved prenatal treatment with dexamethasone, administered to the pregnant woman to prevent genital masculinization of an affected female fetus. Although it is unnecessary to treat unaffected or affected males because their genital development would not be disturbed, there has only been incremental progress in determining fetal gender sufficiently each to avoid treating males and unaffected females. Invasive procedures were initially necessary, with first-trimester amniocentesis at 15-20 weeks and then chorionic villus sampling (CVS) at 10-12 weeks gestation. Two approaches now allow personalized treatment of affected female fetuses prior to female genital differentiation. Only preimplantation genetic diagnosis (PGD) is available prior to clinical pregnancy. Recent technological advances have further allowed both single gene diagnosis (e.g., CAH) and aneuploidy detection concomitantly, resulting in far better pregnancy rates than heretofore possible in assisted reproduction technology.
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Affiliation(s)
- Joe Leigh Simpson
- March of Dimes Foundation, 1275 Mamaroneck Avenue, White Plains, NY 10605, USA; Florida International University, Herbert Wertheim College of Medicine, 11200 SW 8th Street, AHC2 667, USA; Reproductive Genetics Innovation, 2910 MacArthur Blvd., Northbrook, IL 60062, USA.
| | - Svetlana Rechitsky
- Florida International University, Herbert Wertheim College of Medicine, 11200 SW 8th Street, AHC2 667, USA; Reproductive Genetics Innovation, 2910 MacArthur Blvd., Northbrook, IL 60062, USA
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11
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Pei K, Huang Q, Zhang G, Lu C, Yu B, Yang L. Association Between the 4p16 Susceptibility Locus and the Risk of Atrial Septal Defect in Population from Southeast China. Pediatr Cardiol 2016; 37:120-4. [PMID: 26283177 DOI: 10.1007/s00246-015-1248-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/04/2015] [Indexed: 01/28/2023]
Abstract
Three single nucleotide polymorphisms (SNPs), rs16835979, rs870142 and rs6824295, located in chromosome 4p16 were associated with the risk of ostium secundum atrial septal defect (ASD) in the European population. The 4p16 susceptibility locus in congenital heart disease was replicated in Chinese populations. Here, we analyzed the associations between these three SNPs and ASD in Chinese population from Fujian Province in southeast China. We conducted a case-control study by genotyping three SNPs in 354 non-syndromic ASD patients and 557 non-CHD control subjects. Logistic regression analyses showed that the genotype and allele frequencies of these three SNPs were significantly different between the cases and controls in Fujian Chinese population. The allele A of rs870142, the allele A of rs16835979 and the allele A of rs6824295 were significantly associated with an increased risk of ASD. According to the analysis of the three SNPs, the haplotype of AAA was associated with a significantly increased risk of ASD. Our study further supports that these three SNPs confer the predisposition to ASD phenotype in Chinese population.
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Affiliation(s)
- Kaiyan Pei
- Graduate School of Peking Union Medical College, Beijing, China. .,Department of Genetics, National Research Institute for Family Planning, Beijing, China.
| | - Qiuyu Huang
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Guican Zhang
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Cailing Lu
- Graduate School of Peking Union Medical College, Beijing, China. .,Department of Genetics, National Research Institute for Family Planning, Beijing, China.
| | - Benzhang Yu
- Shengli Oilfield Central Hospital, Dongying, Shandong, China.
| | - Liping Yang
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, China.
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