1
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Pan Y, Liu M, Zhang S, Mei H, Wu J. Whole-exome sequencing revealed novel genetic alterations in patients with tetralogy of Fallot. Transl Pediatr 2023; 12:1835-1841. [PMID: 37969115 PMCID: PMC10644019 DOI: 10.21037/tp-23-449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/06/2023] [Indexed: 11/17/2023] Open
Abstract
Background The most prevalent cyanotic congenital heart disease (CHD) phenotype is tetralogy of Fallot (TOF). Rare genetic variations have been identified as significant risk factors for CHD. Thus, this research sought to identify the pathogenic variations and molecular etiologies of TOF. Methods This study employed whole-exome sequencing (WES) and Sanger sequencing to identify pathogenic variations in DNA samples from patients with TOF. The pathogenicity of the variations was predicted using an in-silico approach. Results We enrolled 17 patients with TOF in this study. Among these patients, 14 had mutations in TOF-related genes, including GJB2, TBX15, CTNS, SPINK1, GATA6, PRIMOL, GDF15, SLC17A9, AIFM1, FOXC2, KLF13, ABCA4, CPA6, FKBP10, ASPA, SBF1, HBA2, IGLL1, GNE, and KLHL10. We also gathered WES data from three participants without TOF, who comprised the control group, but no variations were found in the indicated genes. Further analysis showed that the patients with FKBP10 and GNE variants had more serious clinical symptoms. Sanger sequencing confirmed that the two variants were heterozygous in TOF patients. Conclusions We identified several genetic variants associated with TOF and confirmed that FKBP10 and GNE variants were associated with TOF severity. The findings of this study help researchers and clinicians on genetic counseling with the verification of the potential of WES in detecting TOF and help implement early interventions for patients with TOF.
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Affiliation(s)
- Yu Pan
- Department of Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
| | - Manli Liu
- Department of Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
| | - Songsong Zhang
- Department of Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
| | - Huaxian Mei
- Department of Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
| | - Jing Wu
- Department of Intensive Care Unit, Guizhou Provincial People's Hospital, Guiyang, China
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2
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Li R, Zhou L, Yang C, Xu WD, Huang AF. Relationship between SHP2 gene polymorphisms and systemic lupus erythematosus risk. Int J Rheum Dis 2023; 26:1485-1494. [PMID: 37270672 DOI: 10.1111/1756-185x.14761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/11/2023] [Accepted: 05/21/2023] [Indexed: 06/05/2023]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a complex autoimmune disorder. SHP2, a non-transmembrane member of the protein tyrosine phosphatase (PTP) family, can be involved in multiple signaling pathways in inflammatory response. To date, it remains to be investigated whether polymorphisms in the SHP2 gene are correlated with SLE in the Chinese Han population. METHOD A study comprising 320 SLE patients and 400 healthy individuals was performed. Three single nucleotide polymorphisms (rs4767860, rs7132778, rs7953150) of the SHP2 gene were genotyped using the Kompetitive Allele-Specific Polymerase Chain Reaction method. RESULTS Genotypes of rs4767860 (AA, AG + AA) and rs7132778 (AA, AC + AA), and alleles of rs4767860 (A) and rs7132778 (A) were associated with SLE risk. Genotype AA of rs7132778 and allele A of rs7132778 and rs7953150 were associated with oral ulcers in SLE patients. Allele C of rs7132778 and genotype AA and allele A of rs7953150 were associated with pyuria. Patients who carried AA genotype and allele A of rs7953150 are more likely to develop hypocomplementemia. AA and AG genotype frequencies are more raised in patients with SLE with alopecia than in those without alopecia. Patients who carried AA and AG genotypes of rs4767860 had elevated C-reactive protein levels. CONCLUSION Gene polymorphisms of SHP2 (rs4767860, rs7132778) are relevant to SLE susceptibility.
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Affiliation(s)
- Rong Li
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Ling Zhou
- Department of Preventive Medicine, School of Public Health, Southwest Medical University, Luzhou, Sichuan, China
| | - Chan Yang
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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3
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Yin XY, Chen HX, Chen Z, Yang Q, Han J, He GW. Genetic Variants of ISL1 Gene Promoter Identified from Congenital Tetralogy of Fallot Patients Alter Cellular Function Forming Disease Basis. Biomolecules 2023; 13:biom13020358. [PMID: 36830727 PMCID: PMC9953631 DOI: 10.3390/biom13020358] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023] Open
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease in newborns. ISL1 is a master transcription factor in second heart field development, whereas the roles of ISL1 gene promoter variants in TOF patients have not been genetically investigated. Total DNA extraction from 601 human subjects, including 308 TOF patients and 293 healthy controls, and Sanger sequencing were performed. Four variants (including one novel heterozygous variant) within the ISL1 gene promoter were only found in TOF patients. Functional analysis of DNA sequence variants was performed by using the dual-luciferase reporter assay and demonstrated that three of the four variants significantly decreased the transcriptional activity of ISL1 gene promoter in HL-1 cells (p < 0.05). Further, the online JASPAR database and electrophoretic mobility shift assay showed that the three variants affected the binding of transcription factors and altered ISL1 expression levels. In conclusion, the current study for the first time demonstrated that the variants identified from the ISL1 gene promoter region are likely involved in the development of TOF by affecting the transcriptional activity and altering the ISL1 expression level. Therefore, these findings may provide new insights into the molecular etiology and potential therapeutic strategy of TOF.
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Affiliation(s)
- Xiu-Yun Yin
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Zhuo Chen
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Jun Han
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
- Correspondence: or ; Tel.: +86-22-6520-9089
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4
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Tabib A, Talebi T, Ghasemi S, Pourirahim M, Naderi N, Maleki M, Kalayinia S. A novel stop-gain pathogenic variant in FLT4 and a nonsynonymous pathogenic variant in PTPN11 associated with congenital heart defects. Eur J Med Res 2022; 27:286. [PMID: 36496429 PMCID: PMC9737984 DOI: 10.1186/s40001-022-00920-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Congenital heart defects (CHDs) are the most common congenital malformations, including structural malformations in the heart and great vessels. CHD complications such as low birth weight, prematurity, pregnancy termination, mortality, and morbidity depend on the type of defect. METHODS In the present research, genetic analyses via whole-exome sequencing (WES) was performed on 3 unrelated pedigrees with CHDs. The candidate variants were confirmed, segregated by PCR-based Sanger sequencing, and evaluated by bioinformatics analysis. RESULTS A novel stop-gain c.C244T:p.R82X variant in the FLT4 gene, as well as a nonsynonymous c.C1403T:p.T468M variant in the PTPN11 gene, was reported by WES. FLT4 encodes a receptor tyrosine kinase involved in lymphatic development and is known as vascular endothelial growth factor 3. CONCLUSIONS We are the first to report a novel c.C244T variant in the FLT4 gene associated with CHDs. Using WES, we also identified a nonsynonymous variant affecting protein-tyrosine phosphatase, the non-receptor type 11 (PTPN11) gene. The clinical implementation of WES can determine gene variants in diseases with high genetic and phenotypic heterogeneity like CHDs.
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Affiliation(s)
- Avisa Tabib
- grid.411746.10000 0004 4911 7066Heart Valve Diseases Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Taravat Talebi
- grid.411746.10000 0004 4911 7066Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Serwa Ghasemi
- grid.411463.50000 0001 0706 2472Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Pourirahim
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Naderi
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Maleki
- grid.411746.10000 0004 4911 7066Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Kalayinia
- grid.411746.10000 0004 4911 7066Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
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5
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Chen Z, Chen HX, Hou HT, Yin XY, Yang Q, He GW. Pathophysiological Role of Variants of the Promoter Region of CITED2 Gene in Sporadic Tetralogy of Fallot Patients with Cellular Function Verification. Biomolecules 2022; 12:1644. [PMID: 36358994 PMCID: PMC9687598 DOI: 10.3390/biom12111644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/26/2023] Open
Abstract
Tetralogy of Fallot (TOF) is a common congenital heart malformation. Genetic variants in the CITED2 coding region are known to be significantly associated with cardiac malformation, but the role of variants in the CITED2 promoter region in the development of TOF remains unclear. In this study, we investigated CITED2 promoter variants in the DNA of 605 subjects, including 312 TOF patients and 293 unrelated healthy controls, by Sanger sequencing. We identified nine CITED2 gene promoter variants (including one novel heterozygous variant). Six were found only in patients with TOF and none in the control group. The transcriptional activity of the CITED2 gene promoter in mouse cardiomyocyte (HL-1) cells was significantly altered by the six variants (p < 0.05). The results of the electrophoretic mobility change assay and JASPAR database analysis showed that these variants generated or destroyed a series of possible transcription factor binding sites, resulting in changes in the CITED2 protein expression. We conclude that CITED2 promoter variants in TOF patients affect transcriptional activity and may be involved in the occurrence and progression of TOF. These findings may provide new insights into molecular pathogenesis and potential therapeutic insights in patients with TOF.
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Affiliation(s)
- Zhuo Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Huan-Xin Chen
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Hai-Tao Hou
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Xiu-Yun Yin
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
- School of Pharmacy, Drug Research & Development Center, Wannan Medical College, Wuhu 241002, China
| | - Qin Yang
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
| | - Guo-Wei He
- The Institute of Cardiovascular Diseases & Department Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin 300457, China
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6
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Althali NJ, Hentges KE. Genetic insights into non-syndromic Tetralogy of Fallot. Front Physiol 2022; 13:1012665. [PMID: 36277185 PMCID: PMC9582763 DOI: 10.3389/fphys.2022.1012665] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/13/2022] [Indexed: 10/17/2023] Open
Abstract
Congenital heart defects (CHD) include structural abnormalities of the heart or/and great vessels that are present at birth. CHD affects around 1% of all newborns worldwide. Tetralogy of Fallot (TOF) is the most prevalent cyanotic congenital cardiac abnormality, affecting three out of every 10,000 live infants with a prevalence rate of 5-10% of all congenital cardiac defects. The four hallmark characteristics of TOF are: right ventricular hypertrophy, pulmonary stenosis, ventricular septal defect, and overriding aorta. Approximately 20% of cases of TOF are associated with a known disease or chromosomal abnormality, with the remaining 80% of TOF cases being non-syndromic, with no known aetiology. Relatively few TOF patients have been studied, and little is known about critical causative genes for non-syndromic TOF. However, rare genetic variants have been identified as significant risk factors for CHD, and are likely to cause some cases of TOF. Therefore, this review aims to provide an update on well-characterized genes and the most recent variants identified for non-syndromic TOF.
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Affiliation(s)
- Nouf J. Althali
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
- Biology Department, Science College, King Khalid University, Abha, Saudi Arabia
| | - Kathryn E. Hentges
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, United Kingdom
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7
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He GW, Maslen CL, Chen HX, Hou HT, Bai XY, Wang XL, Liu XC, Lu WL, Chen XX, Chen WD, Xing QS, Wu Q, Wang J, Yang Q. Identification of Novel Rare Copy Number Variants Associated with Sporadic Tetralogy of Fallot and Clinical Implications. Clin Genet 2022; 102:391-403. [PMID: 35882632 DOI: 10.1111/cge.14201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. Highly penetrant copy number variants (CNVs) and genes related to the etiology of TOF likely exist with differences among populations. We aimed to identify CNV contributions to sporadic TOF cases in Han Chinese. Genomic DNA was extracted from peripheral blood in 605 subjects (303 sporadic TOF and 302 unaffected Han Chinese [Control] from cardiac centers in China and analyzed by genome-wide association study (GWAS). The GWAS results were compared to existing Database of Genetic Variants. These CNVs were further validated by qPCR. Bioinformatics analyses were performed with Protein-Protein Interaction (PPI) network and KEGG pathway enrichment. Across all chromosomes 119 novel "TOF-specific CNVs" were identified with prevalence of CNVs of 21.5% in chromosomes 1-20 and 37.0% including Chr21/22. In chromosomes 1-20, CNVs on 11q25 (encompasses genes ACAD8, B3GAT1, GLB1L2, GLB1L3, IGSF9B, JAM3, LOC100128239, LOC283177, MIR4697, MIR4697HG, NCAPD3, OPCML, SPATA19, THYN1, and VPS26B) and 14q32.33 (encompasses genes THYN1, OPCML, and NCAPD3) encompass genes most likely to be associated with TOF. Specific CNVs found on the chromosome 21 (6.3%) and 22(11.9%) were also identified in details. PPI network analysis identified the genes covering the specific CNVs related to TOF and the signaling pathways. This study for first time identified novel TOF-specific CNVs in the Han Chinese with higher frequency than in Caucasians and with 11q25 and 14q32.33 not reported in TOF of Caucasians. These novel CNVs identify new candidate genes for TOF and provide new insights into genetic basis of TOF.
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Affiliation(s)
- Guo-Wei He
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China.,Department of Surgery, Oregon Health and Science University, Portland, Oregon, USA
| | - Cheryl L Maslen
- Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Huan-Xin Chen
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Hai-Tao Hou
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Yan Bai
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiu-Li Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xiao-Cheng Liu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Wan-Li Lu
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Xin-Xin Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Wei-Dan Chen
- Guangzhou Women and Children Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Quan-Sheng Xing
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Qin Wu
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Jun Wang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- Institute of Cardiovascular Diseases & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Tianjin University & Chinese Academy of Medical Sciences, Tianjin, China
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8
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Yang L, Liu X, Chen Y, Shen B. An update on the CHDGKB for the systematic understanding of risk factors associated with non-syndromic congenital heart disease. Comput Struct Biotechnol J 2021; 19:5741-5751. [PMID: 34765091 PMCID: PMC8556603 DOI: 10.1016/j.csbj.2021.10.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 02/05/2023] Open
Abstract
The Congenital Heart Disease Genetic Knowledge Base (CHDGKB) was established in 2020 to provide comprehensive knowledge about the genetics and pathogenesis of non-syndromic CHD (NS-CHD). In addition to the genetic causes of NS-CHD, environmental factors such as maternal drug use and gene-environment interactions can also lead to CHD. There is a need to integrate this information into a platform for clinicians and researchers to better understand the overall risk factors associated with NS-CHD. The updated CHDGKB contains the genetic and non-genetic risk factors from over 4200 records from PubMed that was manually curated to include the information associated with NS-CHD. The current version of CHDGKB, named CHD-RF-KB (KnowledgeBase for non-syndromic Congenital Heart Disease-associated Risk Factors), is an important tool that allows users to evaluate the recurrence risk and prognosis of NS-CHD, to guide treatment and highlight the precautions of NS-CHD. In this update, we performed extensive functional analyses of the genetic and non-genetic risk information in CHD-RF-KB. These data can be used to systematically understand the heterogeneous relationship between risk factors and NS-CHD phenotypes.
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Affiliation(s)
- Lan Yang
- Center of Prenatal Diagnosis, Wuxi Maternal and Child Health Hospital affiliated to Nanjing Medical University, Wuxi, China
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Xingyun Liu
- Center for Systems Biology, Soochow University, Suzhou 215006, China
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yalan Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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9
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Kim RW. Is There Any Clinical Utility to Genetic Testing for Patients With Congenital Heart Disease? Semin Thorac Cardiovasc Surg Pediatr Card Surg Annu 2021; 24:26-29. [PMID: 34116779 DOI: 10.1053/j.pcsu.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/11/2021] [Accepted: 04/19/2021] [Indexed: 11/11/2022]
Abstract
Genetic diagnosis is becoming increasingly sophisticated, with the ability to identify even fine differences in patients with a wide variety of congenital heart lesions. Although we have an incomplete understanding of the clinical consequences of most genetic findings, some categories of mutations can have important implications for disease recurrence and prognosis. Consideration of the biology underlying a genetic deficiency, when known, can be useful in the clinical management of some patients.
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Affiliation(s)
- Richard W Kim
- Pediatric and Congenital Cardiac Surgery, Guerin Congenital Heart Program, Smidt Heart Institute, Cedars- Sinai Medical Center, Los Angeles, California.
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10
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Page DJ, Miossec MJ, Williams SG, Monaghan RM, Fotiou E, Cordell HJ, Sutcliffe L, Topf A, Bourgey M, Bourque G, Eveleigh R, Dunwoodie SL, Winlaw DS, Bhattacharya S, Breckpot J, Devriendt K, Gewillig M, Brook JD, Setchfield KJ, Bu'Lock FA, O'Sullivan J, Stuart G, Bezzina CR, Mulder BJM, Postma AV, Bentham JR, Baron M, Bhaskar SS, Black GC, Newman WG, Hentges KE, Lathrop GM, Santibanez-Koref M, Keavney BD. Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot. Circ Res 2019; 124:553-563. [PMID: 30582441 DOI: 10.1161/circresaha.118.313250] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE Familial recurrence studies provide strong evidence for a genetic component to the predisposition to sporadic, nonsyndromic Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease phenotype. Rare genetic variants have been identified as important contributors to the risk of congenital heart disease, but relatively small numbers of TOF cases have been studied to date. OBJECTIVE We used whole exome sequencing to assess the prevalence of unique, deleterious variants in the largest cohort of nonsyndromic TOF patients reported to date. METHODS AND RESULTS Eight hundred twenty-nine TOF patients underwent whole exome sequencing. The presence of unique, deleterious variants was determined; defined by their absence in the Genome Aggregation Database and a scaled combined annotation-dependent depletion score of ≥20. The clustering of variants in 2 genes, NOTCH1 and FLT4, surpassed thresholds for genome-wide significance (assigned as P<5×10-8) after correction for multiple comparisons. NOTCH1 was most frequently found to harbor unique, deleterious variants. Thirty-one changes were observed in 37 probands (4.5%; 95% CI, 3.2%-6.1%) and included 7 loss-of-function variants 22 missense variants and 2 in-frame indels. Sanger sequencing of the unaffected parents of 7 cases identified 5 de novo variants. Three NOTCH1 variants (p.G200R, p.C607Y, and p.N1875S) were subjected to functional evaluation, and 2 showed a reduction in Jagged1-induced NOTCH signaling. FLT4 variants were found in 2.4% (95% CI, 1.6%-3.8%) of TOF patients, with 21 patients harboring 22 unique, deleterious variants. The variants identified were distinct to those that cause the congenital lymphoedema syndrome Milroy disease. In addition to NOTCH1, FLT4 and the well-established TOF gene, TBX1, we identified potential association with variants in several other candidates, including RYR1, ZFPM1, CAMTA2, DLX6, and PCM1. CONCLUSIONS The NOTCH1 locus is the most frequent site of genetic variants predisposing to nonsyndromic TOF, followed by FLT4. Together, variants in these genes are found in almost 7% of TOF patients.
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Affiliation(s)
- Donna J Page
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Matthieu J Miossec
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.).,Center for Bioinformatics and Integrative Biology, Faculty of Biological Sciences, Universidad Andrés Bello, Santiago, Chile (M.J.M.)
| | - Simon G Williams
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Richard M Monaghan
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Elisavet Fotiou
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
| | - Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | | | - Ana Topf
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, Montréal, QC, Canada (M.B.).,McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Guillaume Bourque
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Robert Eveleigh
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Sally L Dunwoodie
- Chain Reaction Program in Congenital Heart Disease Research, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia (S.L.D.).,Faculties of Medicine and Science, University of New South Wales, Sydney (S.L.D.).,Heart Centre for Children, The Children's Hospital at Westmead, Sydney, NSW (S.L.D.)
| | - David S Winlaw
- School of Child and Adolescent Health, Sydney Medical School, University of Sydney (D.S.W.).,Victor Chang Cardiac Research Institute, NSW, Australia (D.S.W.).,RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.)
| | - Shoumo Bhattacharya
- RDM Cardiovascular Medicine, Wellcome Centre for Human Genetics, University of Oxford (D.S.W., S.B.).,Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Jeroen Breckpot
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.).,Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - Koenraad Devriendt
- Center for Human Genetics, Catholic University Leuven, Belgium (S.B., J.B., K.D.)
| | - Marc Gewillig
- Pediatric and Congenital Cardiology, UZ Leuven (J.B., M.G.)
| | - J David Brook
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Kerry J Setchfield
- School of Life Sciences, University of Nottingham, Queen's Medical Centre (J.D.B., K.J.S.)
| | - Frances A Bu'Lock
- Congenital and Paediatric Cardiology, East Midlands Congenital Heart Centre and University of Leicester, Glenfield Hospital (F.A.B.)
| | - John O'Sullivan
- Adult Congenital and Paediatric Cardiac Unit, Freeman Hospital, Newcastle upon Tyne (J.O.)
| | - Graham Stuart
- University Hospitals Bristol NHS Foundation Trust, Bristol (G.S.)
| | - Connie R Bezzina
- Heart Center, Department of Clinical and Experimental Cardiology (C.R.B.), Academic Medical Center, Amsterdam, the Netherlands
| | - Barbara J M Mulder
- Department of Medical Biology (B.J.M.M.), Academic Medical Center, Amsterdam, the Netherlands
| | - Alex V Postma
- Department of Clinical Genetics (A.V.P.), Academic Medical Center, Amsterdam, the Netherlands
| | - James R Bentham
- Department of Paediatric Cardiology, Yorkshire Heart Centre, Leeds (J.R.B.)
| | - Martin Baron
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester (M.B.)
| | - Sanjeev S Bhaskar
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford, Manchester (S.S.B., G.C.B.)
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford (W.G.N.); and Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | | | - G Mark Lathrop
- McGill Genome Center, Montréal, QC, Canada (M.B., G.B., R.E., G.M.L.)
| | - Mauro Santibanez-Koref
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom (M.J.M., H.J.C., L.S., A.T., M.S.-K.)
| | - Bernard D Keavney
- From the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science Centre, University of Manchester, United Kingdom (D.J.P., S.G.W., R.M.M., E.F., B.D.K.)
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11
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Fan SH, Shen ZY, Xiao YM. Functional polymorphisms of the neuropilin 1 gene are associated with the risk of tetralogy of Fallot in a Chinese Han population. Gene 2018; 653:72-79. [PMID: 29432830 DOI: 10.1016/j.gene.2018.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/22/2018] [Accepted: 02/08/2018] [Indexed: 01/07/2023]
Abstract
Tetralogy of Fallot (TOF) is one of the most severe forms of cyanotic congenital heart disease (CHD) and is also the most common. Previous genome-wide association study (GWAS) and replication studies have suggested that a polymorphism in the neuropilin 1 (NRP1) gene is significantly associated with the risk of TOF. To further confirm the association between the NRP1 polymorphism and the risk of TOF and to identify additional positive functional single-nucleotide polymorphisms (SNPs) for TOF risk, we systematically screened for functional polymorphisms throughout the regulatory and coding regions of the NRP1 gene. A total of 11 functional SNPs in 747 Chinese Han individuals, including 314 TOF patients and 433 healthy controls, were genotyped using the MassARRAY system and GeneScan. The results revealed that the allelic and genotypic frequencies of the NRP1 polymorphism rs2228638 were strongly associated with the risk of TOF (p = 0.002 and 0.001, respectively). To increase the robustness of rs2228638 as a TOF risk SNP, we conducted a meta-analysis that combined published studies and our current case-control study. The meta-analysis showed that the T allele of the NRP1 polymorphism rs2228638 was significantly associated with an increased risk of TOF in the combined population, which included European and Chinese Han individuals [combined p < 0.00001, odds ratio (OR) = 1.53, 95% confidence interval (95% CI) = 1.35-1.73]. In addition, the association analysis suggested for the first time that there is a strong association between the allele distribution of rs10080 and susceptibility to TOF (p = 0.001). Our data provide further evidence of the association between NRP1 polymorphisms and TOF risk, and suggest that rs2228638 may be an excellent marker for TOF risk in European and Chinese Han populations.
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Affiliation(s)
- Sai-Hou Fan
- Department of Adult Cardiac Surgery Center, Shanghai Yodak Cardiothoracic Hospital, Shanghai, PR China
| | - Zhen-Ya Shen
- Department of cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Soochow University, Suzhou, Jiangsu, PR China.
| | - Yi-Min Xiao
- Department of Adult Cardiac Surgery Center, Shanghai Yodak Cardiothoracic Hospital, Shanghai, PR China
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12
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Cristo F, Inácio JM, de Almeida S, Mendes P, Martins DS, Maio J, Anjos R, Belo JA. Functional study of DAND5 variant in patients with Congenital Heart Disease and laterality defects. BMC MEDICAL GENETICS 2017; 18:77. [PMID: 28738792 PMCID: PMC5525210 DOI: 10.1186/s12881-017-0444-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/13/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Perturbations on the Left-Right axis establishment lead to laterality defects, with frequently associated Congenital Heart Diseases (CHDs). Indeed, in the last decade, it has been reported that the etiology of isolated cases of CHDs or cases of laterality defects with associated CHDs is linked with variants of genes involved in the Nodal signaling pathway. METHODS With this in mind, we analyzed a cohort of 38 unrelated patients with Congenital Heart Defects that can arise from initial perturbations in the formation of the Left-Right axis and 40 unrelated ethnically matched healthy individuals as a control population. Genomic DNA was extracted from buccal epithelial cells, and variants screening was performed by PCR and direct sequencing. A Nodal-dependent luciferase assay was conducted in order to determine the functional effect of the variant found. RESULTS In this work, we report two patients with a DAND5 heterozygous non-synonymous variant (c.455G > A) in the functional domain of the DAND5 protein (p.R152H), a master regulator of Nodal signaling. Patient 1 presents left isomerism, ventricular septal defect with overriding aorta and pulmonary atresia, while patient 2 presents ventricular septal defect with overriding aorta, right ventricular hypertrophy and pulmonary atresia (a case of extreme tetralogy of Fallot phenotype). The functional analysis assay showed a significant decrease in the activity of this variant protein when compared to its wild-type counterpart. CONCLUSION Altogether, our results provide new insight into the molecular mechanism of the laterality defects and related CHDs, priming for the first time DAND5 as one of multiple candidate determinants for CHDs in humans.
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Affiliation(s)
- Fernando Cristo
- Stem Cells and Development Laboratory, CEDOC, NOVA Medical School / Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal.,Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal.,Biomedical Sciences, Universidade do Algarve, Faro, Portugal.,Regenerative Medicine Program, Biomedical and Medicine Sciences Department, Universidade do Algarve, Faro, Portugal
| | - José M Inácio
- Stem Cells and Development Laboratory, CEDOC, NOVA Medical School / Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Salomé de Almeida
- Medical Genetics Service, Centro Hospitalar Lisboa Central (CHLC), EPE, Lisboa, Portugal
| | - Patrícia Mendes
- Departamento Materno-Infantil, Centro Hospitalar do Algarve, EPE, Faro, Portugal
| | | | - José Maio
- Departamento Materno-Infantil, Centro Hospitalar do Algarve, EPE, Faro, Portugal
| | - Rui Anjos
- Hospital de Santa Cruz, Centro Hospitalar Lisboa Ocidental, Lisboa, Portugal
| | - José A Belo
- Stem Cells and Development Laboratory, CEDOC, NOVA Medical School / Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa, Portugal. .,NOVA Medical School
- Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Edifício CEDOC II, Rua Câmara Pestana n.° 6, 1150-082, Lisboa, Portugal.
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13
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Gao SJ, Zhang GF, Zhang RP. High CpG island methylation of p16 gene and loss of p16 protein expression associate with the development and progression of tetralogy of Fallot. J Genet 2017; 95:831-837. [PMID: 27994181 DOI: 10.1007/s12041-016-0697-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We examined CpG island methylation in p16 gene and its effect on p16 protein expression in tetralogy of Fallot (ToF) patients to explore its potential implications in the development and progression of ToF. The study subjects consisted of 75 healthy controls and 63 ToF patients recruited at Linyi People's Hospital between January 2012 and June 2014. The 4 mL of peripheral venous blood of each subject was obtained and saved in ethylene diamine tetraacetic acid (EDTA) tubes. Methylation-specific polymerase chain reaction (MSP) was employed to detect CpG island methylation in p16 promoter region andWestern blotting was used to detect p16 expression of all subjects. Real-time fluorescence quantitative polymerase chain reaction (FQ-PCR) was performed to test p16 mRNA expression. The results showed that p16-methylation rates in ToF group were significantly higher than the control group (ToF group, 58.73%; control group, 13.33%; P < 0.001). Remarkably, Western blotting and FQ-PCR results derived from RVOT revealed that p16 protein expression was significantly lower in ToF group compared tothe control group (0.76 ± 0.21 versus 2.31 ± 0.35; P < 0.001), and p16 gene expression was also markedly decreased in ToF group (1.212 ± 0.152 versus 1.346 ± 0.191, P < 0.001). Additionally, our analysis suggested that CpG island methylation in p16 promoters in ToF patients was negatively correlated with p16 protein and gene expression (both P < 0.05). Our study reports that high CpG island methylation of p16 gene and loss of p16 protein expression associate with the development and progression of ToF, which may have significant therapeutic applications for ToF.
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Affiliation(s)
- Si-Ju Gao
- Department of Pediatrics, Linyi People's Hospital, No. 27, Jiefang Dong Road, Linyi 276003, People's Republic of China.
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14
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Cabral R, Pires R, Anjos R, Branco CC, Maciel P, Mota-Vieira L. Genealogical and molecular analysis of a family-based cohort of congenital heart disease patients from the São Miguel Island (Azores, Portugal). Ann Hum Biol 2016; 43:547-553. [PMID: 26568276 DOI: 10.3109/03014460.2015.1119888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Congenital heart disease (CHD) is one common birth malformation, accounting for ∼30% of total congenital abnormalities. AIM Considering the unknown role of consanguinity in causing CHD, this study hypothesised that consanguineous unions and/or familial aggregation may be frequent in the Azorean Island of São Miguel (Portugal). To that end, a retrospective observational study was performed based on genealogical and molecular analyses. SUBJECTS AND METHODS The study enrolled 112 CHD patients from São Miguel Island, which allowed the assessment of type of family (simplex or multiplex), parental consanguinity and grandparental endogamy. Based on 15 STR markers, inbreeding coefficients (FIS) in the CHD cohort and healthy control group (n = 114) were estimated. RESULTS Multiplex families were 37.6% (n = 41/109), a rate considerably higher than previously described in the literature (< 15%). Moreover, 9.2% (n = 10/109) of the CHD families were consanguineous, mostly derived from third cousin unions, and 20.2% (n = 22/109) presented full grandparental endogamy. Higher FIS values were found in patients with parental consanguinity (0.0371) and patent ductus arteriosus (0.0277). CONCLUSION This study analysed several genealogical and genetic features related with CHD, revealing the presence of parental consanguinity and extensive familial aggregation in the CHD patients from São Miguel Island.
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Affiliation(s)
- Rita Cabral
- a Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE , São Miguel Island, Azores , Portugal
| | - Renato Pires
- a Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE , São Miguel Island, Azores , Portugal.,b Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa , Portugal
| | - Rui Anjos
- c Department of Pediatric Cardiology , Hospital of Santa Cruz , Carnaxide , Portugal
| | - Claudia C Branco
- a Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE , São Miguel Island, Azores , Portugal.,b Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa , Portugal.,d Instituto Gulbenkian de Ciência , Oeiras , Portugal , and
| | - Paula Maciel
- e Department of Pediatrics , Hospital of Divino Espírito Santo of Ponta Delgada, EPE , São Miguel Island, Azores , Portugal
| | - Luisa Mota-Vieira
- a Molecular Genetics and Pathology Unit, Hospital of Divino Espírito Santo of Ponta Delgada, EPE , São Miguel Island, Azores , Portugal.,b Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa , Portugal.,d Instituto Gulbenkian de Ciência , Oeiras , Portugal , and
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15
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Kheirollahi M, Khosravi F, Ashouri S, Ahmadi A. Existence of mutations in the homeodomain-encoding region of NKX2.5 gene in Iranian patients with tetralogy of Fallot. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2016; 21:24. [PMID: 27904570 PMCID: PMC5122105 DOI: 10.4103/1735-1995.179893] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/03/2016] [Accepted: 02/17/2016] [Indexed: 12/21/2022]
Abstract
Background: Tetralogy of Fallot (TOF), the most common cyanotic heart defect and one of the most common congenital heart diseases, occurs mostly sporadically and nonsyndromically. The underlying molecular genetic mechanism is not known. Therefore, the existence of mutations in the homeodomain-encoding region of NKX2.5 gene in Iranian patients with tetralogy of Fallot is evaluated. Materials and Methods: In the present study, we analyzed the peripheral blood samples of27 patients in order to find any mutation in the 180 bp homeodomain-encoding region of NKX2.5 gene, which is known to be involved in heart development and diseases. DNA was extracted and all the samples were amplified by polymerase chain reaction (PCR) and sequenced. Results: Twenty-seven patients were included in the study. Twenty-five of them were infants and children (6 days to 11 years of age), one was a teenager (14-years of age), and another was a 33-year-old man [mean ± standard deviation (SD): 5.80 ± 3.90 years]. Thirteen patents were males (mean ± SD: 6.587077 ± 5.02 years) and 14 were females (mean ± SD: 5.0726 ± 2.81 years). One synonymous variant, i.e., c.543G>A was identified in one patient. Conclusion: Mutations in the homeodomain-encoding region of NKX2.5 gene may not have an outstanding role in etiology of tetralogy of Fallot patients in Iran.
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Affiliation(s)
- Majid Kheirollahi
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan, Iran; Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Saeideh Ashouri
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan, Iran
| | - Alireza Ahmadi
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan, Iran
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16
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Mlynarski EE, Xie M, Taylor D, Sheridan MB, Guo T, Racedo SE, McDonald-McGinn DM, Chow EWC, Vorstman J, Swillen A, Devriendt K, Breckpot J, Digilio MC, Marino B, Dallapiccola B, Philip N, Simon TJ, Roberts AE, Piotrowicz M, Bearden CE, Eliez S, Gothelf D, Coleman K, Kates WR, Devoto M, Zackai E, Heine-Suñer D, Goldmuntz E, Bassett AS, Morrow BE, Emanuel BS. Rare copy number variants and congenital heart defects in the 22q11.2 deletion syndrome. Hum Genet 2016; 135:273-85. [PMID: 26742502 DOI: 10.1007/s00439-015-1623-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022]
Abstract
The 22q11.2 deletion syndrome (22q11DS; velocardiofacial/DiGeorge syndrome; VCFS/DGS; MIM #192430; 188400) is the most common microdeletion syndrome. The phenotypic presentation of 22q11DS is highly variable; approximately 60-75 % of 22q11DS patients have been reported to have a congenital heart defect (CHD), mostly of the conotruncal type, and/or aortic arch defect. The etiology of the cardiac phenotypic variability is not currently known for the majority of patients. We hypothesized that rare copy number variants (CNVs) outside the 22q11.2 deleted region may modify the risk of being born with a CHD in this sensitized population. Rare CNV analysis was performed using Affymetrix SNP Array 6.0 data from 946 22q11DS subjects with CHDs (n = 607) or with normal cardiac anatomy (n = 339). Although there was no significant difference in the overall burden of rare CNVs, an overabundance of CNVs affecting cardiac-related genes was detected in 22q11DS individuals with CHDs. When the rare CNVs were examined with regard to gene interactions, specific cardiac networks, such as Wnt signaling, appear to be overrepresented in 22q11DS CHD cases but not 22q11DS controls with a normal heart. Collectively, these data suggest that CNVs outside the 22q11.2 region may contain genes that modify risk for CHDs in some 22q11DS patients.
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Affiliation(s)
- Elisabeth E Mlynarski
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael Xie
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Molly B Sheridan
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Silvia E Racedo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3584, Utrecht, The Netherlands
| | - Ann Swillen
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University of Leuven, 3000, Leuven, Belgium
| | | | - Bruno Marino
- Lorillard Spencer Cenci Foundation and Department of Pediatrics, La Sapienza University of Rome, 00165, Rome, Italy
| | | | - Nicole Philip
- Department of Medical Genetics, Timone Children's Hospital, AP-HM and University of Mediterranee, 13005, Marseille, France
| | - Tony J Simon
- Department of Psychiatry and Behavioral Sciences, M.I.N.D. Institute, University of California, Sacramento, CA, 95817, USA
| | - Amy E Roberts
- Department of Cardiology and Division of Genetics, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Małgorzata Piotrowicz
- Department of Genetics, Research Institute, Polish Mother's Memorial Hospital, 93-338, Lodz, Poland
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Stephan Eliez
- Office Médico- Pédagogique Research Unit, Department of Psychiatry, University of Geneva School of Medicine, 1211, Geneva 8, Switzerland
| | - Doron Gothelf
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, 52621, Tel Aviv, Israel
| | - Karlene Coleman
- Marcus Autism Center, Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, and Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Molecular Medicine, University of Rome La Sapienza, 00185, Rome, Italy
| | - Elaine Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Damian Heine-Suñer
- Genetics Department, Hospital Universitari Son Espases, 07020, Palma de Mallorca, Spain
| | - Elizabeth Goldmuntz
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health and Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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17
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Lahm H, Schön P, Doppler S, Dreßen M, Cleuziou J, Deutsch MA, Ewert P, Lange R, Krane M. Tetralogy of Fallot and Hypoplastic Left Heart Syndrome - Complex Clinical Phenotypes Meet Complex Genetic Networks. Curr Genomics 2015; 16:141-58. [PMID: 26069455 PMCID: PMC4460219 DOI: 10.2174/1389202916666150303232520] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 01/06/2023] Open
Abstract
In many cases congenital heart disease (CHD) is represented by a complex phenotype and
an array of several functional and morphological cardiac disorders. These malformations will be
briefly summarized in the first part focusing on two severe CHD phenotypes, hypoplastic left heart
syndrome (HLHS) and tetralogy of Fallot (TOF). In most cases of CHD the genetic origin remains
largely unknown, though the complexity of the clinical picture strongly argues against a dysregulation which can be attributed
to a single candidate gene but rather suggests a multifaceted polygenetic origin with elaborate interactions. Consistent
with this idea, genome-wide approaches using whole exome sequencing, comparative sequence analysis of multiplex
families to identify de novo mutations and global technologies to identify single nucleotide polymorphisms, copy
number variants, dysregulation of the transcriptome and epigenetic variations have been conducted to obtain information
about genetic alterations and potential predispositions possibly linked to the occurrence of a CHD phenotype. In the second
part of this review we will summarize and discuss the available literature on identified genetic alterations linked to
TOF and HLHS.
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Affiliation(s)
- Harald Lahm
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Patric Schön
- Department of Paediatric Cardiology and Congenital Heart Defects, German Heart Center Munich, Technische Universität München, D-80636 Munich, Germany
| | - Stefanie Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Martina Dreßen
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Julie Cleuziou
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Marcus-André Deutsch
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany
| | - Peter Ewert
- Department of Paediatric Cardiology and Congenital Heart Defects, German Heart Center Munich, Technische Universität München, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich Heart Alliance, D-80636 Munich, Germany; ; DZHK (German Center for Cardiovascular Research) - partner site Munich Heart Alliance, Munich, Germany
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18
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Tonni G, Bellotti M, Palmisano M, Alesi V, Bertoli M, Bonasoni MP. 408 kb 15q11.2 microduplication by array comparative genomic hybridization in a fetus presenting with exomphalos, micrognathia, tetralogy of Fallot and normal karyotype: a genetic counseling dilemma in paternal carrier status. Congenit Anom (Kyoto) 2015; 55:65-70. [PMID: 25109822 DOI: 10.1111/cga.12078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/29/2014] [Indexed: 12/21/2022]
Abstract
Exomphalos may be associated with chromosomal abnormalities and syndromes. Severe exomphalos (herniation of liver, midgut and spleen) associated with increased nuchal translucency was seen at first trimester screening test. Karyotype by chorionic villus sampling showed normal male fetus. Follow up scan at 16 and 18 weeks of gestation confirmed the severe exomphalos and detected micrognathia and tetralogy of Fallot. Array comparative genomic hybridization (a-CGH) further demonstrated a 408 kb 15q11.2 microduplication, with the father-to-be as healthy carrier. This is the first case of an association between 15q11.2 micorduplication and fetal sonographic anomalies. Genetic counseling for estimation of recurrent risk of congenital anomalies is discussed.
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Affiliation(s)
- Gabriele Tonni
- Department of Obstetrics and Gynecology, Prenatal Diagnostic Service, Guastalla Civil Hospital, AUSL Reggio Emilia, Guastalla, Italy
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Mason SE, Lipshultz SE, Kaushal S, Fisher S. The implication of coronary artery malformations and congenital heart disease on cardiomyopathy. PROGRESS IN PEDIATRIC CARDIOLOGY 2014. [DOI: 10.1016/j.ppedcard.2014.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Heart failure in congenital heart disease: the role of genes and hemodynamics. Pflugers Arch 2014; 466:1025-35. [DOI: 10.1007/s00424-014-1447-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 01/07/2014] [Indexed: 12/28/2022]
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Digilio MC, Luca AD, Lepri F, Guida V, Ferese R, Dentici ML, Angioni A, Marino B, Dallapiccola B. JAG1 mutation in a patient with deletion 22q11.2 syndrome and tetralogy of Fallot. Am J Med Genet A 2013; 161A:3133-6. [PMID: 23956173 DOI: 10.1002/ajmg.a.36148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Accepted: 06/21/2013] [Indexed: 11/09/2022]
Abstract
Deletion 22q11.2 (del22q11.2) syndrome, also known as DiGeorge/Velo-cardio-facial syndrome (DG/VCFS), and Alagille syndrome are genetic disorders characteristically associated with congenital heart defects (CHDs). We report on a patient with tetralogy of Fallot (TOF) and clinical features of DG/VCFS, hemizygous for del22q11.2 and heterozygous for the 2810G > A (p.Arg937Gln) mutation in the JAG1 gene associated with Alagille syndrome. The clinical features of del22q11.2 syndrome are present in the patient, including facial anomalies, typical TOF, speech delay with hypernasal voice, and learning difficulties. TOF and mild hepatic involvement, consisting of slightly elevated aminotransferase conjugated bilirubin levels, were the only features of Alagille syndrome in our patient. The anatomic type of TOF displayed no distinctive recognizable pattern for either DG/VCFS or Alagille syndrome. It is likely that hemizygosity of the TBX1 gene was causally related to TOF in this patient, although a synergistic pathogenic role of the JAG1 gene mutation in causing the heart defect cannot be excluded. JAG1 mutations have been previously detected in patients with nonsyndromic TOF and recent molecular evidence supports the cumulative effect of multiple genetic defects in the etiology of human malformations. We hypothesize that a similar mechanism could be present in this patient with del22q11.2 syndrome associated with a JAG1 missense mutation acting as possible modifier factor for TOF.
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Preuss C, Andelfinger G. Genetics of Heart Failure in Congenital Heart Disease. Can J Cardiol 2013; 29:803-10. [DOI: 10.1016/j.cjca.2013.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 01/09/2023] Open
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de Denus S, Kantor PF. Pharmacogenomics and heart failure in congenital heart disease. Can J Cardiol 2013; 29:779-85. [PMID: 23790550 DOI: 10.1016/j.cjca.2013.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 01/11/2023] Open
Abstract
Congenital heart disease (CHD) constitutes a lifelong challenge in heart failure management. Current therapy is based mainly on physiologic principles extrapolated from the management of left ventricular failure in adult populations with either ischemic or nonischemic cardiomyopathy. However, there is good evidence of genomic variability in the origin and progression of CHD that suggests the need for a individualized approach to treatment. The developing science of pharmacogenomics presents an opportunity for CHD management broadly, and especially in the context of heart failure. There is growing evidence that individualizing drug therapy for these patients might be beneficial, and that prediction of response to therapy might be possible by incorporating genomic data into the treatment algorithm for individual patients.
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Affiliation(s)
- Simon de Denus
- Faculty of Pharmacy, Université de Montréal, Montreal Heart Institute, Montreal, Québec, Canada
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Palomino Doza J, Topf A, Bentham J, Bhattacharya S, Cosgrove C, Brook JD, Granados-Riveron J, Bu'Lock FA, O'Sullivan J, Stuart AG, Parsons J, Relton C, Goodship J, Henderson DJ, Keavney B. Low-frequency intermediate penetrance variants in the ROCK1 gene predispose to Tetralogy of Fallot. BMC Genet 2013; 14:57. [PMID: 23782575 PMCID: PMC3734041 DOI: 10.1186/1471-2156-14-57] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 06/05/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Epidemiological studies indicate a substantial excess familial recurrence of non-syndromic Tetralogy of Fallot (TOF), implicating genetic factors that remain largely unknown. The Rho induced kinase 1 gene (ROCK1) is a key component of the planar cell polarity signalling pathway, which plays an important role in normal cardiac development. The aim of this study was to investigate the role of genetic variation in ROCK1 on the risk of TOF. RESULTS ROCK1 was sequenced in a discovery cohort of 93 non-syndromic TOF probands to identify rare variants. TagSNPs were selected to capture commoner variation in ROCK1. Novel variants and TagSNPs were genotyped in a discovery cohort of 458 TOF cases and 1331 healthy controls, and positive findings were replicated in a further 209 TOF cases and 1290 healthy controls. Association between genotypes and TOF was assessed using LAMP.A rare SNP (c.807C > T; rs56085230) discovered by sequencing was associated with TOF risk (p = 0.006) in the discovery cohort. The variant was also significantly associated with the risk of TOF in the replication cohort (p = 0.018). In the combined cohorts the odds ratio for TOF was 2.61 (95% CI 1.58-4.30); p < 0.0001. The minor allele frequency of rs56085230 in the cases was 0.02, and in the controls it was 0.007. The variant accounted for 1% of the population attributable risk (PAR) of TOF. We also found significant association with TOF for an uncommon TagSNP in ROCK1, rs288979 (OR 1.64 [95% CI 1.15-2.30]; p = 1.5x10⁻⁵). The minor allele frequency of rs288979 in the controls was 0.043, and the variant accounted for 11% of the PAR of TOF. These association signals were independent of each other, providing additional internal validation of our result. CONCLUSIONS Low frequency intermediate penetrance (LFIP) variants in the ROCK1 gene predispose to the risk of TOF.
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Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16. Nat Genet 2013; 45:822-4. [PMID: 23708191 PMCID: PMC3793630 DOI: 10.1038/ng.2637] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/12/2013] [Indexed: 12/15/2022]
Abstract
We carried out a genome-wide association study (GWAS) of congenital heart disease (CHD). Our discovery cohort comprised 1,995 CHD cases and 5,159 controls, and included patients from each of the three major clinical CHD categories (septal, obstructive and cyanotic defects). When all CHD phenotypes were considered together, no regions achieved genome-wide significant association. However, a region on chromosome 4p16, adjacent to the MSX1 and STX18 genes, was associated (P=9.5×10−7) with the risk of ostium secundum atrial septal defect (ASD) in the discovery cohort (N=340 cases), and this was replicated in a further 417 ASD cases and 2520 controls (replication P=5.0×10−5; OR in replication cohort 1.40 [95% CI 1.19-1.65]; combined P=2.6×10−10). Genotype accounted for ~9% of the population attributable risk of ASD.
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Hendriks WJAJ, Pulido R. Protein tyrosine phosphatase variants in human hereditary disorders and disease susceptibilities. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1673-96. [PMID: 23707412 DOI: 10.1016/j.bbadis.2013.05.022] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 12/18/2022]
Abstract
Reversible tyrosine phosphorylation of proteins is a key regulatory mechanism to steer normal development and physiological functioning of multicellular organisms. Phosphotyrosine dephosphorylation is exerted by members of the super-family of protein tyrosine phosphatase (PTP) enzymes and many play such essential roles that a wide variety of hereditary disorders and disease susceptibilities in man are caused by PTP alleles. More than two decades of PTP research has resulted in a collection of PTP genetic variants with corresponding consequences at the molecular, cellular and physiological level. Here we present a comprehensive overview of these PTP gene variants that have been linked to disease states in man. Although the findings have direct bearing for disease diagnostics and for research on disease etiology, more work is necessary to translate this into therapies that alleviate the burden of these hereditary disorders and disease susceptibilities in man.
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Affiliation(s)
- Wiljan J A J Hendriks
- Department of Cell Biology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Abstract
Congenital heart disease (CHD) is the most common congenital anomaly in newborn babies. Cardiac malformations have been produced in multiple experimental animal models, by perturbing selected molecules that function in the developmental pathways involved in myocyte specification, differentiation, or cardiac morphogenesis. In contrast, the precise genetic, epigenetic, or environmental basis for these perturbations in humans remains poorly understood. Over the past few decades, researchers have tried to bridge this knowledge gap through conventional genome-wide analyses of rare Mendelian CHD families, and by sequencing candidate genes in CHD cohorts. Although yielding few, usually highly penetrant, disease gene mutations, these discoveries provided 3 notable insights. First, human CHD mutations impact a heterogeneous set of molecules that orchestrate cardiac development. Second, CHD mutations often alter gene/protein dosage. Third, identical pathogenic CHD mutations cause a variety of distinct malformations, implying that higher order interactions account for particular CHD phenotypes. The advent of contemporary genomic technologies including single nucleotide polymorphism arrays, next-generation sequencing, and copy number variant platforms are accelerating the discovery of genetic causes of CHD. Importantly, these approaches enable study of sporadic cases, the most common presentation of CHD. Emerging results from ongoing genomic efforts have validated earlier observations learned from the monogenic CHD families. In this review, we explore how continued use of these technologies and integration of systems biology is expected to expand our understanding of the genetic architecture of CHD.
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Affiliation(s)
- Akl C Fahed
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Cordell HJ, Töpf A, Mamasoula C, Postma AV, Bentham J, Zelenika D, Heath S, Blue G, Cosgrove C, Granados Riveron J, Darlay R, Soemedi R, Wilson IJ, Ayers KL, Rahman TJ, Hall D, Mulder BJM, Zwinderman AH, van Engelen K, Brook JD, Setchfield K, Bu'Lock FA, Thornborough C, O'Sullivan J, Stuart AG, Parsons J, Bhattacharya S, Winlaw D, Mital S, Gewillig M, Breckpot J, Devriendt K, Moorman AFM, Rauch A, Lathrop GM, Keavney BD, Goodship JA. Genome-wide association study identifies loci on 12q24 and 13q32 associated with tetralogy of Fallot. Hum Mol Genet 2013; 22:1473-81. [PMID: 23297363 PMCID: PMC3596849 DOI: 10.1093/hmg/dds552] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We conducted a genome-wide association study to search for risk alleles associated with Tetralogy of Fallot (TOF), using a northern European discovery set of 835 cases and 5159 controls. A region on chromosome 12q24 was associated (P = 1.4 × 10(-7)) and replicated convincingly (P = 3.9 × 10(-5)) in 798 cases and 2931 controls [per allele odds ratio (OR) = 1.27 in replication cohort, P = 7.7 × 10(-11) in combined populations]. Single nucleotide polymorphisms in the glypican 5 gene on chromosome 13q32 were also associated (P = 1.7 × 10(-7)) and replicated convincingly (P = 1.2 × 10(-5)) in 789 cases and 2927 controls (per allele OR = 1.31 in replication cohort, P = 3.03 × 10(-11) in combined populations). Four additional regions on chromosomes 10, 15 and 16 showed suggestive association accompanied by nominal replication. This study, the first genome-wide association study of a congenital heart malformation phenotype, provides evidence that common genetic variation influences the risk of TOF.
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Affiliation(s)
- Heather J Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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Gelb BD, Seidman CE. The Good SHP2 Association: a porthole into the genetics of congenital heart disease. ACTA ACUST UNITED AC 2012; 5:271-3. [PMID: 22715277 DOI: 10.1161/circgenetics.112.963215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
PURPOSE OF REVIEW Advances in genomics have paved the way for personalized medicine applications. This review will discuss new discoveries in genomics and pharmacogenomics in children with congenital heart disease (CHD) and the application towards the development of new diagnostics, disease risk predictions, and optimizing response to drugs and surgery. RECENT FINDINGS Recent advances have identified common and rare variants associated with complex CHD using next-generation sequencing and genotyping technology. Next-generation sequencing is now being used not only for clinical genetic testing but also for noninvasive prenatal testing of fetal DNA in maternal serum to diagnose genetic conditions like fetal aneuploidies as early as the first trimester. This approach is not only more accurate but also safer than invasive maternal screening tests. This technology may also help in noninvasive diagnosis of transplant rejection. As genetic variations that influence the response to surgery in CHD are identified, this can guide decision-making surrounding optimum type and timing of surgery. Drug choice and dosing are being increasingly influenced by knowledge of pharmacogenetic and pharmacodynamic variations. Age-related and maturation-related changes in drug pharmacokinetics make it crucial to perform pediatric-targeted pharmacogenetic studies to enable the incorporation of age into genotype-guided drug dosing algorithms. SUMMARY Rapid genomic and pharmacogenomic discovery are guiding the development of more sensitive screening and diagnostic tests for CHD as well as development of safer and more effective drugs. This needs to be paralleled by the development of strategies to support rapid translation of emerging genomic knowledge to patient care.
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