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Abstract
Cardiogenesis is a complex developmental process involving multiple overlapping stages of cell fate specification, proliferation, differentiation, and morphogenesis. Precise spatiotemporal coordination between the different cardiogenic processes is ensured by intercellular signalling crosstalk and tissue-tissue interactions. Notch is an intercellular signalling pathway crucial for cell fate decisions during multicellular organismal development and is aptly positioned to coordinate the complex signalling crosstalk required for progressive cell lineage restriction during cardiogenesis. In this Review, we describe the role of Notch signalling and the crosstalk with other signalling pathways during the differentiation and patterning of the different cardiac tissues and in cardiac valve and ventricular chamber development. We examine how perturbation of Notch signalling activity is linked to congenital heart diseases affecting the neonate and adult, and discuss studies that shed light on the role of Notch signalling in heart regeneration and repair after injury.
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Shi Y, Li Y, Wang Y, Zhuang J, Wang H, Hu M, Mo X, Yue S, Chen Y, Fan X, Chen J, Cai W, Zhu X, Wan Y, Zhong Y, Ye X, Li F, Zhou Z, Dai G, Luo R, Ocorr K, Jiang Z, Li X, Zhu P, Wu X, Yuan W. The Functional Polymorphism R129W in the BVES Gene Is Associated with Sporadic Tetralogy of Fallot in the Han Chinese Population. Genet Test Mol Biomarkers 2019; 23:601-609. [PMID: 31386585 DOI: 10.1089/gtmb.2019.0085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: Tetralogy of Fallot (TOF) accounts for ∼10% of congenital heart disease cases. The blood vessel epicardial substance (BVES) gene has been reported to play a role in the function of adult hearts. However, whether allelic variants in BVES contribute to the risk of TOF and its possible mechanism remains unknown. Methods: The open reading frame of the BVES gene was sequenced using samples from 146 TOF patients and 100 unrelated healthy controls. qRT-PCR and western blot assays were used to confirm the expression of mutated BVES variants in the TOF samples. The online software Polyphen2 and SIFT were used to predict the deleterious effects of the observed allelic variants. The effects of these allelic variants on the transcriptional activities of genes were examined using dual-fluorescence reporter assays. Results: We genotyped four single nucleotide polymorphisms (SNPs) in the BVES gene from each of the 146 TOF patients. Among them, the minor allelic frequencies of c.385C>T (p.R129W) were 0.035% in TOF, but ∼0.025% in 100 controls and the Chinese Millionome Database. This allelic variant was predicted to be a potentially harmful alteration by the Polyphen2 and SIFT softwares. qRT-PCR and western blot analyses indicated that the expression of BVES in the six right ventricular outflow tract samples with the c.385C>T allelic variant was significantly downregulated. A dual-fluorescence reporter system showed that the c.385C>T allelic variant significantly decreased the transcriptional activity of the BVES gene and also decreased transcription from the GATA4 and NKX2.5 promoters. Conclusions: c.385C>T (p.R129W) is a functional SNP of the BVES gene that reduces the transcriptional activity of BVES in vitro and in vivo in TOF tissues. This subsequently affects the transcriptional activities of GATA4 and NKX2.5 related to TOF. These findings suggest that c.385C>T may be associated with the risk of TOF in the Han Chinese population.
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Affiliation(s)
- Yan Shi
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yongqing Li
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yuequn Wang
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jian Zhuang
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Heng Wang
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Min Hu
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiaoyang Mo
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shusheng Yue
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yu Chen
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiongwei Fan
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jimei Chen
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wanwan Cai
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiaolan Zhu
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yongqi Wan
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Ying Zhong
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiangli Ye
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Fang Li
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zuoqiong Zhou
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China.,Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guo Dai
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Rong Luo
- Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Karen Ocorr
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, California
| | - Zhigang Jiang
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiaoping Li
- Department of Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Chengdu, China
| | - Ping Zhu
- Department of Cardiac Surgery, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiushan Wu
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wuzhou Yuan
- State Key Lab of Development Biology of Freshwater Fish, Key Lab of MOE for Development Biology and Protein Chemistry, The Center for Heart Development, College of Life Sciences, Hunan Normal University, Changsha, China
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Dong HQ, Du YX. The study of copy number variations in the regions of PRKAB2 and PPM1K among congenital heart defects patients. ACTA ACUST UNITED AC 2019; 65:786-790. [PMID: 31340305 DOI: 10.1590/1806-9282.65.6.786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/27/2018] [Indexed: 11/22/2022]
Abstract
OBJECTIVE This study was to assess the genetic association of copy number variations in two genes (PRKAB2 and PPM1K) located in two regions (tetralogy of Fallot and ventricular septal defect) in a Chinese Han population. METHODS A total of 200 congenital heart disease patients (100 tetralogy of Fallot patients and 100 ventricular septal defect patients) and 100 congenital heart defect-free controls were recruited, and quantitative real-time PCR analysis was used to replicate the association of two copy number variations with congenital heart defects in a Chinese Han population. RESULTS One deletion at PRKAB2 and one duplication at PPM1K were found in two of the tetralogy of Fallot patients, respectively; while all these regions were duplicated in both ventricular septal defect patients and in the 100 congenital heart defects-free controls. CONCLUSIONS We replicated the copy number variations at the disease-candidate genes of PRKAB2 and PPM1K with tetralogy of Fallot in a Chinese Han population, and in patients with ventricular septal defect mutations in these two genes were not found. These results indicate the same molecular population genetics exist in these two genes with different ethnicity. This shows that these two genes are possibly specific pf tetralogy of Fallot candidates.
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Affiliation(s)
- Han-Quan Dong
- Department of Pneumology, Tianjin Children's Hospital, Tianjin, 300074-China
| | - Yue-Xin Du
- Department of Child Healthcare, Tianjin Municipal Women and Children health care center, Tianjin, 300070, China
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54
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Sewda A, Agopian AJ, Goldmuntz E, Hakonarson H, Morrow BE, Taylor D, Mitchell LE; Pediatric Cardiac Genomics Consortium. Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects. PLoS One 2019; 14:e0219926. [PMID: 31314787 DOI: 10.1371/journal.pone.0219926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/02/2019] [Indexed: 12/28/2022] Open
Abstract
Conotruncal heart defects (CTDs) are among the most common and severe groups of congenital heart defects. Despite evidence of an inherited genetic contribution to CTDs, little is known about the specific genes that contribute to the development of CTDs. We performed gene-based genome-wide analyses using microarray-genotyped and imputed common and rare variants data from two large studies of CTDs in the United States. We performed two case-parent trio analyses (N = 640 and 317 trios), using an extension of the family-based multi-marker association test, and two case-control analyses (N = 482 and 406 patients and comparable numbers of controls), using a sequence kernel association test. We also undertook two meta-analyses to combine the results from the analyses that used the same approach (i.e. family-based or case-control). To our knowledge, these analyses are the first reported gene-based, genome-wide association studies of CTDs. Based on our findings, we propose eight CTD candidate genes (ARF5, EIF4E, KPNA1, MAP4K3, MBNL1, NCAPG, NDFUS1 and PSMG3). Four of these genes (ARF5, KPNA1, NDUFS1 and PSMG3) have not been previously associated with normal or abnormal heart development. In addition, our analyses provide additional evidence that genes involved in chromatin-modification and in ribonucleic acid splicing are associated with congenital heart defects.
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55
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Petukhova L, Patel AV, Rigo RK, Bian L, Verbitsky M, Sanna-Cherchi S, Erjavec SO, Abdelaziz AR, Cerise JE, Jabbari A, Christiano AM. Integrative analysis of rare copy number variants and gene expression data in alopecia areata implicates an aetiological role for autophagy. Exp Dermatol 2019; 29:243-253. [PMID: 31169925 DOI: 10.1111/exd.13986] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 04/23/2019] [Accepted: 05/09/2019] [Indexed: 12/26/2022]
Abstract
Alopecia areata (AA) is a highly prevalent autoimmune disease that attacks the hair follicle and leads to hair loss that can range from small patches to complete loss of scalp and body hair. Our previous linkage and genome-wide association studies (GWAS) generated strong evidence for aetiological contributions from inherited genetic variants at different population frequencies, including both rare mutations and common polymorphisms. Additionally, we conducted gene expression (GE) studies on scalp biopsies of 96 patients and controls to establish signatures of active disease. In this study, we performed an integrative analysis on these two datasets to test the hypothesis that rare CNVs in patients with AA could be leveraged to identify drivers of disease in our AA GE signatures. We analysed copy number variants (CNVs) in a case-control cohort of 673 patients with AA and 16 311 controls independent of the case-control cohort of 96 research participants used in our GE study. Using an integrative computational analysis, we identified 14 genes whose expression levels were altered by CNVs in a consistent direction of effect, corresponding to gene expression changes in lesional skin of patients. Four of these genes were affected by CNVs in three or more unrelated patients with AA, including ATG4B and SMARCA2, which are involved in autophagy and chromatin remodelling, respectively. Our findings identified new classes of genes with potential contributions to AA pathogenesis.
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Affiliation(s)
- Lynn Petukhova
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Aakash V Patel
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Rachel K Rigo
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Li Bian
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Miguel Verbitsky
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Stephanie O Erjavec
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Alexa R Abdelaziz
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Jane E Cerise
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Ali Jabbari
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Angela M Christiano
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Genetics and Development, College of Physicians and Surgeons, Columbia University, New York, New York
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Park KB, Nam KE, Cho AR, Jang W, Kim M, Park JH. Effects of Copy Number Variations on Developmental Aspects of Children With Delayed Development. Ann Rehabil Med 2019; 43:215-223. [PMID: 31072088 PMCID: PMC6509583 DOI: 10.5535/arm.2019.43.2.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/19/2018] [Indexed: 11/06/2022] Open
Abstract
Objective To determine effects of copy number variations (CNV) on developmental aspects of children suspected of having delayed development. Methods A retrospective chart review was done for 65 children who underwent array-comparative genomic hybridization after visiting physical medicine & rehabilitation department of outpatient clinic with delayed development as chief complaints. Children were evaluated with Denver Developmental Screening Test II (DDST-II), Sequenced Language Scale for Infants (SELSI), or Preschool Receptive-Expressive Language Scale (PRES). A Mann-Whitney U test was conducted to determine statistical differences of developmental quotient (DQ), receptive language quotient (RLQ), and expressive language quotient (ELQ) between children with CNV (CNV(+) group, n=16) and children without CNV (CNV(–) group, n=37). Results Of these subjects, the average age was 35.1 months (mean age, 35.1±24.2 months). Sixteen (30.2%) patients had copy number variations. In the CNV(+) group, 14 children underwent DDST-II. In the CNV(–) group, 29 children underwent DDST-II. Among variables, gross motor scale was significantly (p=0.038) lower in the CNV(+) group compared with the CNV(–) group. In the CNV(+) group, 5 children underwent either SELSI or PRES. In the CNV(–) group, 27 children underwent above language assessment examination. Both RLQ and ELQ were similar between the two groups. Conclusion The gross motor domain in DQ was significantly lower in children with CNV compared to that in children without CNV. This result suggests that additional genetic factors contribute to this variability. Active detection of genomic imbalance could play a vital role when prominent gross motor delay is presented in children with delayed development.
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Affiliation(s)
- Kee-Boem Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung Eun Nam
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ah-Ra Cho
- Department of Rehabilitation Medicine, St. Paul's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woori Jang
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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57
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Luyckx I, Kumar AA, Reyniers E, Dekeyser E, Vanderstraeten K, Vandeweyer G, Wünnemann F, Preuss C, Mazzella JM, Goudot G, Messas E, Albuisson J, Jeunemaitre X, Eriksson P, Mohamed SA, Kempers M, Salemink S, Duijnhouwer A, Andelfinger G, Dietz HC, Verstraeten A, Van Laer L, Loeys BL; MIBAVA Leducq Consortium. Copy number variation analysis in bicuspid aortic valve-related aortopathy identifies TBX20 as a contributing gene. Eur J Hum Genet 2019; 27:1033-43. [PMID: 30820038 DOI: 10.1038/s41431-019-0364-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/08/2019] [Accepted: 02/02/2019] [Indexed: 12/26/2022] Open
Abstract
Bicuspid aortic valve (BAV) is the most common congenital heart defect (CHD), affecting 1-2% of the population. BAV is associated with thoracic aortic aneurysms (TAAs). Deleterious copy number variations (CNVs) were found previously in up to 10% of CHD cases. This study aimed at unravelling the contribution of deleterious deletions or duplications in 95 unrelated BAV/TAA patients. Seven unique or rare CNVs were validated, harbouring protein-coding genes with a role in the cardiovascular system. Based on the presence of overlapping CNVs in patients with cardiovascular phenotypes in the DECIPHER database, the identification of similar CNVs in whole-exome sequencing data of 67 BAV/TAA patients and suggested topological domain involvement from Hi-C data, supportive evidence was obtained for two genes (DGCR6 and TBX20) of the seven initially validated CNVs. A rare variant burden analysis using next-generation sequencing data from 637 BAV/TAA patients was performed for these two candidate genes. This revealed a suggestive genetic role for TBX20 in BAV/TAA aetiology, further reinforced by segregation of a rare TBX20 variant with the phenotype within a BAV/TAA family. To conclude, our results do not confirm a significant contribution for deleterious CNVs in BAV/TAA as only one potentially pathogenic CNV (1.05%) was identified. We cannot exclude the possibility that BAV/TAA is occasionally attributed to causal CNVs though, or that certain CNVs act as genetic risk factors by creating a sensitised background for BAV/TAA. Finally, accumulative evidence for TBX20 involvement in BAV/TAA aetiology underlines the importance of this transcription factor in cardiovascular disease.
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58
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Xie Y, Ma A, Wang B, Peng R, Jing Y, Wang D, Finnell RH, Qiao B, Wang Y, Wang H, Zheng Y. Rare mutations of ADAM17 from TOFs induce hypertrophy in human embryonic stem cell-derived cardiomyocytes via HB-EGF signaling. Clin Sci (Lond) 2019; 133:225-38. [PMID: 30610007 DOI: 10.1042/CS20180842] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/22/2018] [Accepted: 01/03/2019] [Indexed: 12/31/2022]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic form of congenital heart defects (CHDs). The right ventricular hypertrophy is associated with the survival rate of patients with repaired TOF. However, very little is known concerning its genetic etiology. Based on mouse model studies, a disintergrin and metalloprotease 10/17 (ADAM10 and ADAM17) are the key enzymes for the NOTCH and ErbB pathways, which are critical pathways for heart development. Mutations in these two genes have not been previously reported in human TOF patients. In this study, we sequenced ADAM10 and ADAM17 in a Han Chinese CHD cohort comprised of 80 TOF patients, 286 other CHD patients, and 480 matched healthy controls. Three missense variants of ADAM17 were only identified in 80 TOF patients, two of which (Y42D and L659P) are novel and not found in the Exome Aggregation Consortium (ExAC) database. Point mutation knock-in (KI) and ADAM17 knock-out (KO) human embryonic stem cells (hESCs) were generated by CRISPR/Cas9 and programmed to differentiate into cardiomyocytes (CMs). Y42D or L659P KI cells or complete KO cells all developed hypertrophy with disorganized sarcomeres. RNA-seq results showed that phosphatidylinositide 3-kinases/protein kinase B (PI3K/Akt), which is downstream of epidermal growth factor receptor (EGFR) signaling, was affected in both ADAM17 KO and KI hESC-CMs. In vitro experiments showed that these two mutations are loss-of-function mutations in shedding heparin-binding EGF-like growth factor (HB-EGF) but not NOTCH signaling. Our results revealed that CM hypertrophy in TOF could be the result of mutations in ADAM17 which affects HB-EGF/ErbB signaling.
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Wu Y, Zhang J, Wang M, Yang L, Wang Y, Hu T, Liu A, Cheng Q, Fu Z, Zhang P, Cao L. Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects. J Cell Physiol 2019; 234:13544-13556. [PMID: 30635921 DOI: 10.1002/jcp.28033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022]
Abstract
Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.
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Affiliation(s)
- Yun Wu
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jingjing Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Mei Wang
- Department of Pathology, Nanjing Hospital of Traditional Chinese Medicine, The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Yang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yongmei Wang
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tao Hu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - An Liu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Qing Cheng
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Ziyi Fu
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pingyang Zhang
- Department of Echocardiography, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Li Cao
- Department of Ultrasonography, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
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Ji L, Hou H, Zhu K, Liu X, Liu Y, Wang Q, Li J, Liu H, Zhang Q, Lv J, Alexander R, Wang W, Li D. NOTCH1 Gene MicroRNA Target Variation and Ventricular Septal Defect Risk. OMICS 2019; 23:28-35. [PMID: 30629480 DOI: 10.1089/omi.2018.0171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Birth defects, the ventricular septal defect (VSD) in particular, have major public health significance. There is evidence that genetic factors play a role in VSD risk. We report here our findings on the relationship between VSD and microRNA (miRNA)-3691-3p target sequence single-nucleotide polymorphisms (SNPs) in the 3' untranslated region of the NOTCH1 gene. Functional SNPs in NOTCH1 target sequence were screened from the SNP database. A case-control study in a large Chinese Han population sample of 350 children with VSD and 430 healthy controls examined the association between rs6563 SNPs and VSD. NOTCH1 wild and mutant recombinant expression vectors were constructed by the luciferase reporter gene system. The effects of miRNA on gene regulatory effects were also analyzed. The allelic distributions at the locus rs6563 showed statistically significant susceptibility to VSD (odds ratio [OR] = 1.502, 95% confidence interval [CI] = 1.209-1.866, p < 0.001). Compared with the subjects with G/G genotype, individuals with G/A genotype or A/A genotype showed ORs 1.414 (95% CI = 1.047-1.908, p = 0.020) and 2.366 (95% CI = 1.430-3.914, p < 0.001), respectively. The miRNA-3691-3p reduced luciferase activity of the A allele. The rs6563G > A genetic variation appears to be associated with congenital VSD through gene regulatory effects of miR-3691-3p on the NOTCH1 gene. Further studies in other population samples are called for diagnostics and public health innovation in relation to birth defects.
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Affiliation(s)
- Long Ji
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Haifeng Hou
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China.,2 School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Kai Zhu
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Xuezhen Liu
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Yizhi Liu
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Qian Wang
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Jindong Li
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Huamin Liu
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Qianqian Zhang
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Jian Lv
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
| | - Rachel Alexander
- 2 School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Wei Wang
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China.,2 School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Dong Li
- 1 School of Public Health, Taishan Medical University, Tai'an, P.R. China
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61
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Verbitsky M, Westland R, Perez A, Kiryluk K, Liu Q, Krithivasan P, Mitrotti A, Fasel DA, Batourina E, Sampson MG, Bodria M, Werth M, Kao C, Martino J, Capone VP, Vivante A, Shril S, Kil BH, Marasà M, Zhang JY, Na YJ, Lim TY, Ahram D, Weng PL, Heinzen EL, Carrea A, Piaggio G, Gesualdo L, Manca V, Masnata G, Gigante M, Cusi D, Izzi C, Scolari F, van Wijk JAE, Saraga M, Santoro D, Conti G, Zamboli P, White H, Drozdz D, Zachwieja K, Miklaszewska M, Tkaczyk M, Tomczyk D, Krakowska A, Sikora P, Jarmoliński T, Borszewska-Kornacka MK, Pawluch R, Szczepanska M, Adamczyk P, Mizerska-Wasiak M, Krzemien G, Szmigielska A, Zaniew M, Dobson MG, Darlow JM, Puri P, Barton DE, Furth SL, Warady BA, Gucev Z, Lozanovski VJ, Tasic V, Pisani I, Allegri L, Rodas LM, Campistol JM, Jeanpierre C, Alam S, Casale P, Wong CS, Lin F, Miranda DM, Oliveira EA, Simões-E-Silva AC, Barasch JM, Levy B, Wu N, Hildebrandt F, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Zhang F, Hakonarson H, Papaioannou VE, Mendelsohn CL, Gharavi AG, Sanna-Cherchi S. The copy number variation landscape of congenital anomalies of the kidney and urinary tract. Nat Genet 2018; 51:117-127. [PMID: 30578417 PMCID: PMC6668343 DOI: 10.1038/s41588-018-0281-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/18/2018] [Indexed: 12/18/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are a major cause of pediatric kidney failure. We performed a genome-wide analysis of copy number variants (CNVs) in 2,824 cases and 21,498 controls. Affected individuals carried a significant burden of rare exonic (i.e. affecting coding regions) CNVs and were enriched for known genomic disorders (GD). Kidney anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; obstructive uropathy (OU) had a lower CNV burden and an intermediate prevalence of GD-CNVs; vesicoureteral reflux (VUR) had the fewest GD-CNVs but was enriched for novel exonic CNVs, particularly duplications. Six loci (1q21, 4p16.1-p16.3, 16p11.2, 16p13.11, 17q12, and 22q11.2) accounted for 65% of patients with GD-CNVs. Deletions at 17q12, 4p16.1-p16.3, and 22q11.2 were specific for KA; the 16p11.2 locus showed extensive pleiotropy. Using a multidisciplinary approach, we identified TBX6 as a driver for the CAKUT subphenotypes in the 16p11.2 microdeletion syndrome.
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Affiliation(s)
- Miguel Verbitsky
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.,Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Alejandra Perez
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Qingxue Liu
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Priya Krithivasan
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Adele Mitrotti
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - David A Fasel
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ekaterina Batourina
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Max Werth
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Charlly Kao
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Valentina P Capone
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Asaf Vivante
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Tel Hashomer and the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Byum Hee Kil
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Maddalena Marasà
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Young-Ji Na
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Tze Y Lim
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dina Ahram
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Patricia L Weng
- Department of Pediatric Nephrology, UCLA Medical Center and UCLA Medical Center-Santa Monica, Los Angeles, CA, USA
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alba Carrea
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Giorgio Piaggio
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Valeria Manca
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Giuseppe Masnata
- Department of Pediatric Urology, Azienda Ospedaliera Brotzu, Cagliari, Italy
| | - Maddalena Gigante
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Daniele Cusi
- National Research Council of Italy, Inst. Biomedical Technologies Milano Bio4dreams Scientific Unit, Milano, Italy
| | - Claudia Izzi
- Dipartimento Ostetrico-Ginecologico e Seconda Divisione di Nefrologia ASST, Spedali Civili e Presidio di Montichiari, Brescia, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia, Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia, Italy
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split, Croatia.,School of Medicine, University of Split, Split, Croatia
| | - Domenico Santoro
- Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Messina, Messina, Italy
| | - Giovanni Conti
- Department of Pediatric Nephrology, Azienda Ospedaliera Universitaria "G. Martino", Messina, Italy
| | - Pasquale Zamboli
- Division of Nephrology, University of Campania "Luigi Vanvitell", Naples, Italy
| | - Hope White
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Dorota Drozdz
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Zachwieja
- Department of Pediatric Nephrology and Hypertension, Dialysis Unit, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Miklaszewska
- Department of Pediatric Nephrology, Jagiellonian University Medical College, Krakow, Poland
| | - Marcin Tkaczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Daria Tomczyk
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Anna Krakowska
- Department of Pediatrics, Immunology and Nephrology, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Przemyslaw Sikora
- Department of Pediatric Nephrology Medical University of Lublin, Lublin, Poland
| | | | - Maria K Borszewska-Kornacka
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Robert Pawluch
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Maria Szczepanska
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | - Piotr Adamczyk
- Department of Pediatrics, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, Poland
| | | | - Grazyna Krzemien
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Szmigielska
- Department of Pediatrics and Nephrology, Medical University of Warsaw, Warsaw, Poland
| | - Marcin Zaniew
- Department of Pediatrics, University of Zielona Góra, Zielona Góra, Poland
| | - Mark G Dobson
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - John M Darlow
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Prem Puri
- National Children's Research Centre, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,National Children's Hospital Tallaght, Dublin, Ireland
| | - David E Barton
- Department of Clinical Genetics, Our Lady's Children's Hospital Crumlin, Dublin, Ireland.,University College Dublin UCD School of Medicine, Our Lady's Children's Hospital Crumlin, Dublin, Ireland
| | - Susan L Furth
- Departments of Pediatrics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Division of Nephrology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Bradley A Warady
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Division of Nephrology, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Zoran Gucev
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Vladimir J Lozanovski
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia.,University Clinic for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Velibor Tasic
- University Children's Hospital, Medical Faculty of Skopje, Skopje, Macedonia
| | - Isabella Pisani
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Lida M Rodas
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Josep M Campistol
- Renal Division, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, Inserm UMR 1163, Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Shumyle Alam
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Pasquale Casale
- Department of Pediatric Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.,Mount Sinai Medical Center, Kravis Children's Hospital, New York, NY, USA
| | - Craig S Wong
- Division of Pediatric Nephrology, University of New Mexico Children's Hospital, Albuquerque, NM, USA
| | - Fangming Lin
- Division of Pediatric Nephrology, Department of Pediatrics, Columbia University, New York, NY, USA
| | - Débora M Miranda
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Eduardo A Oliveira
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ana Cristina Simões-E-Silva
- Department of Pediatrics, Unit of Pediatric Nephrology, Interdisciplinary Laboratory of Medical Investigation, Faculty of Medicine, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Jonathan M Barasch
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Nan Wu
- Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Medical Research Center of Orthopedics, all at Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and NZOZ Center for Medical Genetics GENESIS, Poznan, Poland
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA.
| | - Cathy L Mendelsohn
- Department of Urology, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, NY, USA.
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62
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Egloff M, Hervé B, Quibel T, Jaillard S, Le Bouar G, Uguen K, Saliou AH, Valduga M, Perdriolle E, Coutton C, Coston AL, Coussement A, Anselem O, Missirian C, Bretelle F, Prieur F, Fanget C, Muti C, Jacquemot MC, Beneteau C, Le Vaillant C, Vekemans M, Salomon LJ, Vialard F, Malan V. Diagnostic yield of chromosomal microarray analysis in fetuses with isolated increased nuchal translucency: a French multicenter study. Ultrasound Obstet Gynecol 2018; 52:715-721. [PMID: 29027723 DOI: 10.1002/uog.18928] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To determine the frequency and nature of copy number variants (CNVs) identified by chromosomal microarray analysis (CMA) in a large cohort of fetuses with isolated increased nuchal translucency thickness (NT) ≥ 3.5 mm. METHODS This was a retrospective, multicenter study, including 11 French hospitals, of data from the period between April 2012 and December 2015. In total, 720 fetuses were analyzed by rapid aneuploidy test and the fetuses identified as euploid underwent CMA. CNVs detected were evaluated for clinical significance and classified into five groups: pathogenic CNVs; benign CNVs; CNVs predisposing to neurodevelopmental disorders; variants of uncertain significance (VOUS); and CNVs not related to the phenotype (i.e. incidental findings). RESULTS In 121 (16.8%) fetuses, an aneuploidy involving chromosome 13, 18 or 21 was detected by rapid aneuploidy test and the remaining 599 fetuses were euploid. Among these, 53 (8.8%) had a CNV detected by CMA: 16/599 (2.7%) were considered to be pathogenic, including 11/599 (1.8%) that were cryptic (not visible by karyotyping); 7/599 (1.2%) were CNVs predisposing to neurodevelopmental disorders; and 8/599 (1.3%) were VOUS. Additionally, there was one (0.2%) CNV that was unrelated to the reason for referral diagnosis (i.e. an incidental finding) and the remaining 21 were benign CNVs, without clinical consequence. Interestingly, we identified five genomic imbalances of the 1q21.1 or 15q11.2 regions known to be associated with congenital heart defects. CONCLUSION Our study demonstrates the benefit of CMA in the etiological diagnosis of fetuses with isolated increased NT. It is worth noting that most (69%) of the detected pathogenic CNVs were cryptic. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- M Egloff
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - B Hervé
- Unité de Cytogénétique, CHI de Poissy St Germain, Poissy, France
- EA7404-GIG, UFR des Sciences de la Santé Simone Veil, UVSQ, Montigny-le-Bretonneux, France
| | - T Quibel
- Service de Gynécologie Obstétrique, CHI de Poissy St Germain, Poissy, France
| | - S Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU de Rennes, Rennes, France
| | - G Le Bouar
- Département de Gynécologie Obstétrique et Reproduction Humaine, CHU de Rennes, Rennes, France
| | - K Uguen
- Laboratoire de Cytogénétique, Cytologie et Biologie de la Reproduction, CHRU, Brest, France
| | - A-H Saliou
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU, Brest, France
| | - M Valduga
- Service de Génétique, CHRU Nancy-Brabois, Nancy, France
| | - E Perdriolle
- Service d'Obstétrique, CHRU Nancy-Brabois, Nancy, France
| | - C Coutton
- Laboratoire de Génétique Chromosomique, INSERM 1209, CNRS UMR 5309, CHU Grenoble Alpes, Institut Albert Bonniot, Université Grenoble Alpes, Grenoble, France
| | - A-L Coston
- Service de Gynécologie-Obstétrique et Médecine de la Reproduction, Hôpital Couple Enfant, Université Grenoble Alpes, CHU Grenoble Alpes, Grenoble, France
| | - A Coussement
- Laboratoire de Cytogénétique, Hôpital Cochin, APHP, Paris, France
| | - O Anselem
- Service de Gynécologie et Obstétrique de Port-Royal, Maternité Port-Royal, Groupe Hospitalier Cochin Broca Hôtel-Dieu, APHP, Paris, France
| | - C Missirian
- Département de Génétique Médicale, CHU Timone Enfants, APHM, Marseille, France
| | - F Bretelle
- Service de Gynécologie Obstétrique, CHU Nord, APHM, Marseille, France
| | - F Prieur
- Service de Génétique Clinique Chromosomique Moléculaire, CHU Saint-Etienne, Saint-Etienne, France
| | - C Fanget
- Service d'Obstétrique, CHU Saint-Etienne, Saint-Etienne, France
| | - C Muti
- Génétique Constitutionnelle, Laboratoire de Biologie, Centre Hospitalier de Versailles, Le Chesnay, France
| | - M-C Jacquemot
- Consultation de Diagnostic Prénatal, Service de Gynécologie Obstétrique, Centre Hospitalier de Versailles, Le Chesnay, France
| | - C Beneteau
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - C Le Vaillant
- Service de Gynécologie-Obstétrique, CHU de Nantes, Nantes, France
| | - M Vekemans
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
| | - L J Salomon
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
- Service d'Obstétrique, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - F Vialard
- Unité de Cytogénétique, CHI de Poissy St Germain, Poissy, France
- EA7404-GIG, UFR des Sciences de la Santé Simone Veil, UVSQ, Montigny-le-Bretonneux, France
| | - V Malan
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, APHP, Paris, France
- Sorbonne Paris Cité, Université Paris Descartes, Paris, France
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63
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Shi X, Cheng L, Jiao X, Chen B, Li Z, Liang Y, Liu W, Wang J, Liu G, Xu Y, Sun J, Fu Q, Lu Y, Chen S. Rare Copy Number Variants Identify Novel Genes in Sporadic Total Anomalous Pulmonary Vein Connection. Front Genet 2018; 9:559. [PMID: 30532766 PMCID: PMC6265481 DOI: 10.3389/fgene.2018.00559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022] Open
Abstract
Total anomalous pulmonary venous connection (TAPVC) is a rare congenital heart anomaly. Several genes have been associated TAPVC but the mechanisms remain elusive. To search novel CNVs and candidate genes, we screened a cohort of 78 TAPVC cases and 100 healthy controls for rare copy number variants (CNVs) using whole exome sequencing (WES). Then we identified pathogenic CNVs by statistical comparisons between case and control groups. After that, we identified altogether eight pathogenic CNVs of seven candidate genes (PCSK7, RRP7A, SERHL, TARP, TTN, SERHL2, and NBPF3). All these seven genes have not been described previously to be related to TAPVC. After network analysis of these candidate genes and 27 known pathogenic genes derived from the literature and publicly database, PCSK7 and TTN were the most important genes for TAPVC than other genes. Our study provides novel candidate genes potentially related to this rare congenital birth defect (CHD) which should be further fundamentally researched and discloses the possible molecular pathogenesis of TAPVC.
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Affiliation(s)
- Xin Shi
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Liangping Cheng
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - XianTing Jiao
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Chen
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zixiong Li
- Department of Medical Oncology, Bayi Hospital, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yulai Liang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Liu
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Wang
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gang Liu
- Medical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuejuan Xu
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Sun
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qihua Fu
- Medical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Lu
- Department of Cardiothoracic Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun Chen
- Department of Pediatric Cardiovascular, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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64
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Cantù C, Felker A, Zimmerli D, Prummel KD, Cabello EM, Chiavacci E, Méndez-Acevedo KM, Kirchgeorg L, Burger S, Ripoll J, Valenta T, Hausmann G, Vilain N, Aguet M, Burger A, Panáková D, Basler K, Mosimann C. Mutations in Bcl9 and Pygo genes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling. Genes Dev 2018; 32:1443-1458. [PMID: 30366904 PMCID: PMC6217730 DOI: 10.1101/gad.315531.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/22/2018] [Indexed: 12/31/2022]
Abstract
Bcl9 and Pygopus (Pygo) are obligate Wnt/β-catenin cofactors in Drosophila, yet their contribution to Wnt signaling during vertebrate development remains unresolved. Combining zebrafish and mouse genetics, we document a conserved, β-catenin-associated function for BCL9 and Pygo proteins during vertebrate heart development. Disrupting the β-catenin-BCL9-Pygo complex results in a broadly maintained canonical Wnt response yet perturbs heart development and proper expression of key cardiac regulators. Our work highlights BCL9 and Pygo as selective β-catenin cofactors in a subset of canonical Wnt responses during vertebrate development. Moreover, our results implicate alterations in BCL9 and BCL9L in human congenital heart defects.
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Affiliation(s)
- Claudio Cantù
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Anastasia Felker
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Dario Zimmerli
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Karin D Prummel
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Elena M Cabello
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Elena Chiavacci
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Kevin M Méndez-Acevedo
- Electrochemical Signaling in Development and Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin-Buch, Germany
| | - Lucia Kirchgeorg
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Sibylle Burger
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, 28911 Madrid, Spain
| | - Tomas Valenta
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - George Hausmann
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Nathalie Vilain
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Michel Aguet
- Swiss Institute for Experimental Cancer Research (ISREC), École Polytechnique Fédérale de Lausanne (EPFL), School of Life Sciences, 1015 Lausanne, Switzerland
| | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Daniela Panáková
- Electrochemical Signaling in Development and Disease, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin-Buch, Germany
- Deutsches Zentrum für Herz-Kreislauf-Forschung (DZHK), partner site Berlin, 10115 Berlin, Germany
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zürich, 8057 Zürich, Switzerland
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Mercer-Rosa L, Zhang X, Tanel RE, Rychik J, Fogel MA, Paridon SM, Goldmuntz E. Perioperative Factors Influence the Long-Term Outcomes of Children and Adolescents with Repaired Tetralogy of Fallot. Pediatr Cardiol 2018; 39:1433-9. [PMID: 29876584 DOI: 10.1007/s00246-018-1913-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/23/2018] [Indexed: 10/14/2022]
Abstract
Tetralogy of Fallot (TOF) often carries long-term seqüelae following surgical intervention. We hypothesized that early perioperative factors are associated with long-term adverse right ventricular (RV) remodeling, diminished exercise capacity, and increased morbidity. We conducted a retrospective cohort study of patients operated for TOF that underwent cardiac magnetic resonance imaging study (CMR), exercise stress test (EST), and detailed review of past medical history. Outcome variables included measures of RV size, and function, maximal work rate, and oxygen consumption, and interim hospitalizations, surgeries, and catheterizations. Thirty-nine subjects were included. Age at surgical repair was 0.3 ± 0.3 years and age at testing was 9.7 ± 1.4 years. On CMR, there was borderline RV dilation with moderate pulmonary insufficiency (PI) [RF 32% (8; 43)] and normal RV ejection fraction [60% (55; 67)]. On EST, there was low percent-predicted maximal oxygen consumption (77 ± 20%), and percent-predicted maximal work rate (84 ± 23%). On multivariable analysis, mechanical ventilation and Blalock-Taussig (BT) shunt prior to complete surgical repair were associated with the number of future hospitalizations. Duration of cardiopulmonary bypass and prior BT shunt were associated with future catheterizations. Prior BT shunt was a predictor of worse RVEF, while duration of mechanical ventilation and use of transannular patch were predictors of worse PI. Longer duration of mechanical ventilation (or LOS) was associated with worse maximal work rate. Surgical and perioperative factors may portend long-term RV remodeling and outcome in TOF. Further studies are warranted to explore these associations and potential underlying mechanisms.
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Lin M, Zheng J, Peng R, Du L, Zheng Q, Lei T, Xie H. Prenatal diagnosis of chromosomal aberrations in fetuses with conotruncal heart defects by genome-wide high-resolution SNP array. J Matern Fetal Neonatal Med 2018; 33:1211-1217. [PMID: 30149741 DOI: 10.1080/14767058.2018.1517316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Objectives: To explore chromosomal variations, including copy number variations (CNVs), in fetuses with conotruncal heart defect (CTD).Methods: During a 5-year period, a total of 129 fetuses with ascertained CTDs were investigated for chromosomal abnormalities using quantitative fluorescence PCR (QF-PCR) and chromosomal microarray analysis (CMA). Fetuses were divided into two subgroups: benign group (with normal QF-PCR results and benign CNVs) and nonbenign group [with aneuploidies, nonbenign CNVs [pathogenic CNVs and CNVs of unknown significance (VOUS)]. Data on fetal structural malformations, chromosomal variations, and pregnancy outcomes were collected and compared.Results: Of the 129 cases, 17 were found to have common aneuploidies. In the remaining 112 cases with normal a QF-PCR result, pathogenic CNVs, CNVs of VOUS, and benign CNVs were identified in 5.3, 5.3, and 4.5%, respectively. Compared with benign group, fetuses in nonbenign group had a significantly higher rate of neurologic defects (13.8 versus 3.0%, p < .05), overall extracardiac anomalies (86.2 versus 45.0%, p < .05), and perinatal death (57.1 versus 18.4%, p < .05), whereas, no significant difference in that of associated cardiovascular anomalies was noted (48.2 versus 46.0%, p = .29). Among the extracardiac anomalies, thymus abnormalities were strongly associated with nonbenign CNVs (33.3 versus 1% of fetuses in benign group, p < .05).Conclusions: Pathogenic CNVs, in addition to chromosomal aneuploidies, contributed to the pathogenesis of CTD. The presence of associated extracardiac anomalies including thymus abnormalities correlated with a higher probability of nonbenign chromosomal variations, which was associated with an unfavorable outcome.
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Affiliation(s)
- Meifang Lin
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ju Zheng
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ruan Peng
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Liu Du
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Qiao Zheng
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ting Lei
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Hongning Xie
- Department of Ultrasonic Medicine and Fetal Medical Centre, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Luo S, Meng D, Li Q, Hu X, Chen Y, He C, Xie B, She S, Li Y, Fu C. Genetic Testing and Pregnancy Outcome Analysis of 362 Fetuses with Congenital Heart Disease Identified by Prenatal Ultrasound. Arq Bras Cardiol 2018; 111:571-577. [PMID: 30133550 PMCID: PMC6199505 DOI: 10.5935/abc.20180144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 04/11/2018] [Indexed: 11/27/2022] Open
Abstract
Background Congenital heart defects (CHD), as the most common congenital anomaly, have
been reported to be associated with chromosomal abnormalities. Currently,
patients with CHD are routinely offered karyotyping and chromosomal
microarray (CMA) testing, but the genotype-phenotype relationship has not
yet been fully established. Objective To determine the type and frequency of chromosomal abnormalities in fetuses
with CHD and to analyze pregnancy outcomes of fetuses with heart
abnormalities caused by different genetic factors. Methods A total of 362 cases of CHD were enrolled from 2009 to 2016. Detailed
ultrasound and laboratory examinations, including karyotyping and CMA, were
performed. Outcome was obtained from discharge summaries. Results Of the 362 fetuses, 220 were found with an isolated CHD, and 142 had CHD with
extracardiac anomaly. Among these 362 fetuses, 140 were identified with a
genetic cause, including 111 cases with aneuploidy, 10 cases with
abnormality of chromosomal structure by karyotyping and 19 cases with
pathogenic or likely pathogenic copy-number variations (CNVs) by CMA. The
detection rate is close to 38.7%. Only one (identified as trisomy 18
syndrome) in 140 positive cases resulted in perinatal death, with the others
being induced. The remaining 222 cases had negative results for both genetic
testing and of these cases, 56 resulted in induced labor, and 77 had natural
childbirth or caesarean births. The pregnancy outcome of the remaining 89
cases was uncertain. Conclusions Karyotyping and CMA are effective and accurate prenatal genetic techniques
for identifying fetal chromosomal abnormalities associated with cardiac
defects, and this can assist clinical doctors to perform appropriate genetic
counselling with regard to the etiology and outcome of CHD.
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Affiliation(s)
- Shiyu Luo
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Dahua Meng
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Qifei Li
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Xuehua Hu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Yuhua Chen
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Chun He
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Bobo Xie
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Shangyang She
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Yingfeng Li
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
| | - Chunyun Fu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Guangxi - China
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Ceyhan-Birsoy O, Miatkowski MM, Hynes E, Funke BH, Mason-Suares H. NGS testing for cardiomyopathy: Utility of adding RASopathy-associated genes. Hum Mutat 2018; 39:954-958. [PMID: 29696744 DOI: 10.1002/humu.23535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 12/28/2022]
Abstract
RASopathies include a group of syndromes caused by pathogenic germline variants in RAS-MAPK pathway genes and typically present with facial dysmorphology, cardiovascular disease, and musculoskeletal anomalies. Recently, variants in RASopathy-associated genes have been reported in individuals with apparently nonsyndromic cardiomyopathy, suggesting that subtle features may be overlooked. To determine the utility and burden of adding RASopathy-associated genes to cardiomyopathy panels, we tested 11 RASopathy-associated genes by next-generation sequencing (NGS), including NGS-based copy number variant assessment, in 1,111 individuals referred for genetic testing for hypertrophic cardiomyopathy (HCM) or dilated cardiomyopathy (DCM). Disease-causing variants were identified in 0.6% (four of 692) of individuals with HCM, including three missense variants in the PTPN11, SOS1, and BRAF genes. Overall, 36 variants of uncertain significance (VUSs) were identified, averaging ∼3VUSs/100 cases. This study demonstrates that adding a subset of the RASopathy-associated genes to cardiomyopathy panels will increase clinical diagnoses without significantly increasing the number of VUSs/case.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maya M Miatkowski
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts
| | - Birgit H Funke
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Heather Mason-Suares
- Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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69
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Sophocleous F, Milano EG, Pontecorboli G, Chivasso P, Caputo M, Rajakaruna C, Bucciarelli-Ducci C, Emanueli C, Biglino G. Enlightening the Association between Bicuspid Aortic Valve and Aortopathy. J Cardiovasc Dev Dis 2018; 5:E21. [PMID: 29671812 PMCID: PMC6023468 DOI: 10.3390/jcdd5020021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 04/16/2018] [Accepted: 04/16/2018] [Indexed: 12/11/2022] Open
Abstract
Bicuspid aortic valve (BAV) patients have an increased incidence of developing aortic dilation. Despite its importance, the pathogenesis of aortopathy in BAV is still largely undetermined. Nowadays, intense focus falls both on BAV morphology and progression of valvular dysfunction and on the development of aortic dilation. However, less is known about the relationship between aortic valve morphology and aortic dilation. A better understanding of the molecular pathways involved in the homeostasis of the aortic wall, including the extracellular matrix, the plasticity of the vascular smooth cells, TGFβ signaling, and epigenetic dysregulation, is key to enlighten the mechanisms underpinning BAV-aortopathy development and progression. To date, there are two main theories on this subject, i.e., the genetic and the hemodynamic theory, with an ongoing debate over the pathogenesis of BAV-aortopathy. Furthermore, the lack of early detection biomarkers leads to challenges in the management of patients affected by BAV-aortopathy. Here, we critically review the current knowledge on the driving mechanisms of BAV-aortopathy together with the current clinical management and lack of available biomarkers allowing for early detection and better treatment optimization.
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Affiliation(s)
- Froso Sophocleous
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
| | - Elena Giulia Milano
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Department of Medicine, Division of Cardiology, University of Verona, 37100 Verona, Italy.
| | - Giulia Pontecorboli
- Structural Interventional Cardiology Division, Department of Experimental and Clinical Medicine, University of Florence, 50100 Florence, Italy.
| | - Pierpaolo Chivasso
- Cardiac Surgery, University Hospitals Bristol, NHS Foundation Trust, Bristol BS2 8HW, UK.
| | - Massimo Caputo
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Cardiac Surgery, University Hospitals Bristol, NHS Foundation Trust, Bristol BS2 8HW, UK.
| | - Cha Rajakaruna
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Cardiac Surgery, University Hospitals Bristol, NHS Foundation Trust, Bristol BS2 8HW, UK.
| | - Chiara Bucciarelli-Ducci
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Cardiac Surgery, University Hospitals Bristol, NHS Foundation Trust, Bristol BS2 8HW, UK.
| | - Costanza Emanueli
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Cardiac Surgery, University Hospitals Bristol, NHS Foundation Trust, Bristol BS2 8HW, UK.
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK.
| | - Giovanni Biglino
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol BS2 89HW, UK.
- Cardiorespiratory Unit, Great Ormond Street Hospital for Children, NHS Foundation Trust, London WC1N 3JH, UK.
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70
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Lin S, Shi S, Zhou Y, Ji Y, Huang P, Wu J, Chen B, Luo Y. Intrauterine phenotypic features associated with 16p11.2 recurrent microdeletions. Prenat Diagn 2018. [PMID: 29514395 DOI: 10.1002/pd.5245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To investigate the detection rate of 16p11.2 recurrent microdeletions in fetuses with abnormal ultrasound findings and determine the common abnormal ultrasound findings in fetuses carrying the deletion. METHODS This study reviewed 2262 consecutive fetuses with abnormal ultrasound findings who underwent prenatal chromosomal microarray analysis between October 2014 and December 2016. Cases carrying the 16p11.2 recurrent microdeletion were further genetically analyzed, and their clinical features were reviewed. RESULTS The 16p11.2 recurrent microdeletion was identified in 12 fetuses, who had skeletal malformations (5/12), cardiovascular malformations (4/12), or isolated ultrasound markers (3/12). Approximately 0.5% (12/2262) of the fetuses with abnormal ultrasound findings harbored the deletion. The 5 fetuses with skeletal malformations displayed vertebral defects, particularly in the hemivertebra and butterfly vertebra. The detection rate of the 16p11.2 recurrent microdeletion was statistically significant (P < .05) among fetuses with skeletal malformations (3.6%, 5/140), fetuses with cardiovascular malformations (1.1%, 4/367), and fetuses with isolated ultrasound markers (0.4%, 3/702). CONCLUSION The most frequent ultrasound findings in fetuses with 16p11.2 recurrent microdeletions are skeletal malformations (particularly vertebral malformations), followed by cardiovascular malformations, and isolated ultrasound markers.
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Affiliation(s)
- Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Shanshan Shi
- Fetal Medicine Center, The First Affiliated Hospital, Jinan University, Guangzhou, People's Republic of China
| | - Yi Zhou
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yuanjun Ji
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Peizhi Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Jianzhu Wu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Baojiang Chen
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Yanmin Luo
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
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72
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Duran I, Tenney J, Warren CM, Sarukhanov A, Csukasi F, Skalansky M, Iruela-Arispe ML, Krakow D. NRP1 haploinsufficiency predisposes to the development of Tetralogy of Fallot. Am J Med Genet A 2018; 176:649-656. [PMID: 29363855 DOI: 10.1002/ajmg.a.38600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/16/2017] [Accepted: 12/12/2017] [Indexed: 01/13/2023]
Abstract
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect. It involves anatomical abnormalities that change the normal flow of blood through the heart resulting in low oxygenation. Although not all of the underlying causes of TOF are completely understood, the disease has been associated with varying genetic etiologies including chromosomal abnormalities and Mendelian disorders, but can also occur as an isolated defect. In this report, we describe a familial case of TOF associated with a 1.8 Mb deletion of chromosome 10p11. Among the three genes in the region one is Neuropilin1 (NRP1), a membrane co-receptor of VEGF that modulates vasculogenesis. Hemizygous levels of NRP1 resulted in a reduced expression at the transcriptional and protein levels in patient-derived cells. Reduction of NRP1 also lead to decreased function of its activity as a co-receptor in intermolecular VEGF signaling. These findings support that diminished levels of NRP1 contribute to the development of TOF, likely through its function in mediating VEGF signal and vasculogenesis.
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Affiliation(s)
- Ivan Duran
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Jessica Tenney
- Department of Pediatrics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Carmen M Warren
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California
| | - Anna Sarukhanov
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Fabiana Csukasi
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Mark Skalansky
- Department of Pediatrics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
| | - Maria L Iruela-Arispe
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California
| | - Deborah Krakow
- Department of Orthopedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California.,Department of Human Genetics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California
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73
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Sanna-Cherchi S, Westland R, Ghiggeri GM, Gharavi AG. Genetic basis of human congenital anomalies of the kidney and urinary tract. J Clin Invest 2018; 128:4-15. [PMID: 29293093 DOI: 10.1172/jci95300] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The clinical spectrum of congenital anomalies of the kidney and urinary tract (CAKUT) encompasses a common birth defect in humans that has significant impact on long-term patient survival. Overall, data indicate that approximately 20% of patients may have a genetic disorder that is usually not detected based on standard clinical evaluation, implicating many different mutational mechanisms and pathogenic pathways. In particular, 10% to 15% of CAKUT patients harbor an unsuspected genomic disorder that increases risk of neurocognitive impairment and whose early recognition can impact clinical care. The emergence of high-throughput genomic technologies is expected to provide insight into the common and rare genetic determinants of diseases and offer opportunities for early diagnosis with genetic testing.
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Affiliation(s)
- Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
| | - Rik Westland
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Department of Pediatric Nephrology, VU University Medical Center, Amsterdam, Netherlands
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto Giannina Gaslini, Genoa, Italy
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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74
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Shanshen E, Rosenberg J, Van Bergen AH. Identification of Novel Congenital Heart Disease Candidate Genes Using Chromosome Microarray. Pediatr Cardiol 2018; 39:148-59. [PMID: 28993849 DOI: 10.1007/s00246-017-1741-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 09/16/2017] [Indexed: 10/18/2022]
Abstract
While the majority of patients have isolated heart disease, congenital heart disease (CHD) may be associated with other congenital anomalies or syndromes. Our institution utilizes chromosomal microarray (CMA) to identify chromosomal abnormalities, specifically copy number variations (CNVs). While CNVs have been associated with CHD, their direct impact on cardiac development remains unclear. This study sought to identify potential novel CHD candidate genes by comparing CNVs present in our institution's CHD population with those already recognized in the literature. A list of candidate genes was compiled from recent medical literature that utilized CMA. Records from neonatal cases at our institution over 10 years were reviewed. Genes identified from CMAs were compared with those reported in the literature and cross-referenced with the Online Mendelian Inheritance in Man catalog. We identified 375 CNVs reported in patients with CHD. At our institution between 2005 and 2015, 307 neonates with CHD had CMA. Of these, 77 patients (25%) had CNVs containing 832 unique candidate genes. 49 patients (16%) had isolated CHD with 353 candidate genes expressed within the CNVs, many of which were previously reported. However, there were 16 unique candidate genes identified that have been expressed with heart structure of the mouse knock-out models. Our findings demonstrate a high incidence of abnormal genes identified by CMA in CHD patients, including many CNVs of "unknown clinical significance". We conclude that a portion of these CNVs (including 16 genes expressed in the heart of the mouse knock-out models) could be candidate genes involved in CHD pathogenesis.
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75
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Lansdon LA, Darbro BW, Petrin AL, Hulstrand AM, Standley JM, Brouillette RB, Long A, Mansilla MA, Cornell RA, Murray JC, Houston DW, Manak JR. Identification of Isthmin 1 as a Novel Clefting and Craniofacial Patterning Gene in Humans. Genetics 2018; 208:283-296. [PMID: 29162626 PMCID: PMC5753863 DOI: 10.1534/genetics.117.300535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/20/2017] [Indexed: 12/26/2022] Open
Abstract
Orofacial clefts are one of the most common birth defects, affecting 1-2 per 1000 births, and have a complex etiology. High-resolution array-based comparative genomic hybridization has increased the ability to detect copy number variants (CNVs) that can be causative for complex diseases such as cleft lip and/or palate. Utilizing this technique on 97 nonsyndromic cleft lip and palate cases and 43 cases with cleft palate only, we identified a heterozygous deletion of Isthmin 1 in one affected case, as well as a deletion in a second case that removes putative 3' regulatory information. Isthmin 1 is a strong candidate for clefting, as it is expressed in orofacial structures derived from the first branchial arch and is also in the same "synexpression group" as fibroblast growth factor 8 and sprouty RTK signaling antagonist 1a and 2, all of which have been associated with clefting. CNVs affecting Isthmin 1 are exceedingly rare in control populations, and Isthmin 1 scores as a likely haploinsufficiency locus. Confirming its role in craniofacial development, knockdown or clustered randomly interspaced short palindromic repeats/Cas9-generated mutation of isthmin 1 in Xenopus laevis resulted in mild to severe craniofacial dysmorphologies, with several individuals presenting with median clefts. Moreover, knockdown of isthmin 1 produced decreased expression of LIM homeobox 8, itself a gene associated with clefting, in regions of the face that pattern the maxilla. Our study demonstrates a successful pipeline from CNV identification of a candidate gene to functional validation in a vertebrate model system, and reveals Isthmin 1 as both a new human clefting locus as well as a key craniofacial patterning gene.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pediatrics
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
| | - Benjamin W Darbro
- Department of Pediatrics
- Interdisciplinary Graduate Program in Genetics
| | - Aline L Petrin
- Department of Pediatrics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | | | | | | | | | - Robert A Cornell
- Interdisciplinary Graduate Program in Genetics
- Department of Anatomy and Cell Biology, and
| | - Jeffrey C Murray
- Department of Pediatrics
- Department of Biology
- Department of Anatomy and Cell Biology, and
- Interdisciplinary Graduate Program in Genetics
- College of Dentistry, University of Iowa, Iowa 52242 and
| | | | - J Robert Manak
- Department of Pediatrics,
- Department of Biology
- Interdisciplinary Graduate Program in Genetics
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76
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Wang HD, Liu L, Wu D, Li T, Cui CY, Zhang LZ, Wang CZ. Clinical and molecular cytogenetic analyses of four families with 1q21.1 microdeletion or microduplication. J Gene Med 2017; 19. [PMID: 28220983 PMCID: PMC5413856 DOI: 10.1002/jgm.2948] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 02/04/2023] Open
Abstract
Background Little information is available regarding the penetrance of 1q21.1 copy number variants (CNVs). In the present study, we explored the clinical significance of 1q21.1 microdeletion or microduplication. Methods In four families, chromosome karyotype was analyzed using G‐banding karyotype analysis technology. CNVs were detected using array‐comparative genomic hybridization (aCGH) and then a quantitative polymerase chain reaction (qPCR) was used to validate candidate CNVs. Sequence signature in the breakpoint region was analyzed using University of California Santa Cruz (UCSC) databases. Results Except for karyotype 45, XX, der (13, 14) (q10, q10) in the mother (I2) of family 2, the karyotype was normal in all other members of the four families. In the mother (I2) and fetus (II2) of family 1, in newborn (II1) of family 2 and in fetus (II1) of family 3, there was 1.22‐Mb heterozygous microdeletion in the chromosome 1q21.1q21.2 region. The child (II1) of family 4 had a 1.46‐Mb heterozygous microduplication in the chromosome 1q21.1q21.2 region. The results of the qPCR were consistent with that of aCGH. There was large number of low copy repeats (LCRs) in the breakpoint region found by analysis of the UCSC database, and multiple LCRs were matched with sequences in the chromosome 1 short‐arm region. Conclusions 1q21.1 microdeletion and microduplication exhibit a variety of clinical manifestations and the specificity of their clinical features is not high. The penetrance of the distal 1q21.1 microdeletion may be affected by other factors in the present study. In summary, we report the discovery of a new distal 1q21.1 microduplication, which enriches the CNV spectrum in the 1q21.1 region and is conducive to prenatal genetic counseling.
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Affiliation(s)
- Hong-Dan Wang
- Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Lin Liu
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Dong Wu
- Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Tao Li
- Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Cun-Ying Cui
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Lian-Zhong Zhang
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Cheng-Zeng Wang
- Department of Ultrasound, the Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou, China
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77
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Jin ZB, Li Z, Liu Z, Jiang Y, Cai XB, Wu J. Identification of de novo germline mutations and causal genes for sporadic diseases using trio-based whole-exome/genome sequencing. Biol Rev Camb Philos Soc 2017; 93:1014-1031. [PMID: 29154454 DOI: 10.1111/brv.12383] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 09/28/2017] [Accepted: 10/10/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome or whole-exome sequencing (WGS/WES) of the affected proband together with normal parents (trio) is commonly adopted to identify de novo germline mutations (DNMs) underlying sporadic cases of various genetic disorders. However, our current knowledge of the occurrence and functional effects of DNMs remains limited and accurately identifying the disease-causing DNM from a group of irrelevant DNMs is complicated. Herein, we provide a general-purpose discussion of important issues related to pathogenic gene identification based on trio-based WGS/WES data. Specifically, the relevance of DNMs to human sporadic diseases, current knowledge of DNM biogenesis mechanisms, and common strategies or software tools used for DNM detection are reviewed, followed by a discussion of pathogenic gene prioritization. In addition, several key factors that may affect DNM identification accuracy and causal gene prioritization are reviewed. Based on recent major advances, this review both sheds light on how trio-based WGS/WES technologies can play a significant role in the identification of DNMs and causal genes for sporadic diseases, and also discusses existing challenges.
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Affiliation(s)
- Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
| | - Xue-Bi Cai
- Division of Ophthalmic Genetics, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, 325027, China.,State Key Laboratory of Ophthalmology Optometry and Vision Science, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325000, China
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78
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Liu L, Wang HD, Cui CY, Qin YY, Fan TB, Peng BT, Zhang LZ, Wang CZ. Whole exome sequencing identifies novel mutation in eight Chinese children with isolated tetralogy of Fallot. Oncotarget 2017; 8:106976-106988. [PMID: 29291004 PMCID: PMC5739789 DOI: 10.18632/oncotarget.22202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022] Open
Abstract
Background Tetralogy of Fallot is the most common cyanotic congenital heart disease. However, its pathogenesis remains to be clarified. The purpose of this study was to identify the genetic variants in Tetralogy of Fallot by whole exome sequencing. Methods Whole exome sequencing was performed among eight small families with Tetralogy of Fallot. Differential single nucleotide polymorphisms and small InDels were found by alignment within families and between families and then were verified by Sanger sequencing. Tetralogy of Fallot-related genes were determined by analysis using Gene Ontology /pathway, Online Mendelian Inheritance in Man, PubMed and other databases. Results A total of sixteen differential single nucleotide polymorphisms loci and eight differential small InDels were discovered. The sixteen differential single nucleotide polymorphisms loci were located on Chr 1, 2, 4, 5, 11, 12, 15, 22 and X. Among the sixteen single nucleotide polymorphisms loci, six has not been reported. The eight differential small InDels were located on Chr 2, 4, 9, 12, 17, 19 and X, whereas of the eight differential small InDels, two has not been reported. Analysis using Gene Ontology /pathway, Online Mendelian Inheritance in Man, PubMed and other databases revealed that PEX5, NACA, ATXN2, CELA1, PCDHB4 and CTBP1 were associated with Tetralogy of Fallot. Conclusions Our findings identify PEX5, NACA, ATXN2, CELA1, PCDHB4 and CTBP1 mutations as underlying genetic causes of isolated tetralogy of Fallot.
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Affiliation(s)
- Lin Liu
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Hong-Dan Wang
- Institute of Medical Genetics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Cun-Ying Cui
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Yun-Yun Qin
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Tai-Bing Fan
- Children's Heart Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Bang-Tian Peng
- Children's Heart Center, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Lian-Zhong Zhang
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou 450003, China
| | - Cheng-Zeng Wang
- Department of Ultrasound, The Affiliated Cancer Hospital, Zhengzhou University, Zhengzhou 450008, China
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79
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McBride KL, Ware SM. Modifying Mendel Redux: Unbiased Approaches Can Find Modifiers. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.117.001891. [PMID: 29025762 DOI: 10.1161/circgenetics.117.001891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kim L McBride
- From the Center for Cardiovascular Research (K.L.M.) and Department of Pediatrics, College of Medicine (K.L.M.), Nationwide Children's Hospital, Ohio State University, Columbus; and Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.).
| | - Stephanie M Ware
- From the Center for Cardiovascular Research (K.L.M.) and Department of Pediatrics, College of Medicine (K.L.M.), Nationwide Children's Hospital, Ohio State University, Columbus; and Departments of Pediatrics and Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis (S.M.W.)
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80
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Rodríguez F, Vallejos C, Giraudo F, Unanue N, Hernández MI, Godoy P, Célis S, Martín-Arenas R, Palomares-Bralo M, Heath KE, López MT, Cassorla F. Copy number variants of Ras/MAPK pathway genes in patients with isolated cryptorchidism. Andrology 2017; 5:923-930. [PMID: 28914499 DOI: 10.1111/andr.12390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 01/02/2023]
Abstract
Cryptorchidism is the most common congenital disorder in boys, but the cause for most cases remains unknown. Patients with Noonan Syndrome are characterized by a typical face, growth retardation, congenital heart defects, learning disabilities and cryptorchidism. Copy number variations of Ras/MAPK pathway genes are unusual in patients with several clinical features of Noonan Syndrome; however, they have not been studied in patients with only one feature of this condition, such as cryptorchidism. Our aim was to determine whether patients with isolated cryptorchidism exhibit Ras/MAPK pathway gene copy number variations (CNVs). Fifty-nine patients with isolated cryptorchidism and negative for mutations in genes associated with Noonan Syndrome were recruited. Determination of Ras/MAPK pathway gene CNVs was performed by Comparative Genome Hybridization array. A CNV was identified in two individuals, a ~175 kb microduplication at 3p25.2, partially including RAF1. A similar RAF1 microduplication has been observed in a patient with testicular aplasia. This suggests that some patients with isolated cryptorchidism may harbor Ras/MAPK pathway gene CNVs.
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Affiliation(s)
- F Rodríguez
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - C Vallejos
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - F Giraudo
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - N Unanue
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - M I Hernández
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
| | - P Godoy
- Pediatric Service, Hospital Base San José, Osorno, Chile
| | - S Célis
- Pediatric Urology Department, Hospital Clínico San Borja - Arriarán, Santiago, Chile
| | - R Martín-Arenas
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, UAM and CIBERER, ISCIII, Madrid, Spain
| | - M Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, UAM and CIBERER, ISCIII, Madrid, Spain
| | - K E Heath
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, UAM and CIBERER, ISCIII, Madrid, Spain
| | - M T López
- Pediatric Urology Department, Hospital Clínico San Borja - Arriarán, Santiago, Chile
| | - F Cassorla
- Institute of Maternal and Child Research, School of Medicine, University of Chile, Santiago, Chile
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81
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Kardon G, Ackerman KG, McCulley DJ, Shen Y, Wynn J, Shang L, Bogenschutz E, Sun X, Chung WK. Congenital diaphragmatic hernias: from genes to mechanisms to therapies. Dis Model Mech 2017; 10:955-970. [PMID: 28768736 PMCID: PMC5560060 DOI: 10.1242/dmm.028365] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Congenital diaphragmatic hernias (CDHs) and structural anomalies of the diaphragm are a common class of congenital birth defects that are associated with significant morbidity and mortality due to associated pulmonary hypoplasia, pulmonary hypertension and heart failure. In ∼30% of CDH patients, genomic analyses have identified a range of genetic defects, including chromosomal anomalies, copy number variants and sequence variants. The affected genes identified in CDH patients include transcription factors, such as GATA4, ZFPM2, NR2F2 and WT1, and signaling pathway components, including members of the retinoic acid pathway. Mutations in these genes affect diaphragm development and can have pleiotropic effects on pulmonary and cardiac development. New therapies, including fetal endoscopic tracheal occlusion and prenatal transplacental fetal treatments, aim to normalize lung development and pulmonary vascular tone to prevent and treat lung hypoplasia and pulmonary hypertension, respectively. Studies of the association between particular genetic mutations and clinical outcomes should allow us to better understand the origin of this birth defect and to improve our ability to predict and identify patients most likely to benefit from specialized treatment strategies.
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Affiliation(s)
- Gabrielle Kardon
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Kate G Ackerman
- Departments of Pediatrics (Critical Care) and Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David J McCulley
- Department of Pediatrics, University of Wisconsin, Madison, WI 53792, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Linshan Shang
- Departments of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Bogenschutz
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Xin Sun
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wendy K Chung
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
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82
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Abstract
Congenital heart disease is diagnosed in 0.4% to 5% of live births and presents unique challenges to the pediatric anesthesiologist. Furthermore, advances in surgical management have led to improved survival of those patients, and many adult anesthesiologists now frequently take care of adolescents and adults who have previously undergone surgery to correct or palliate congenital heart lesions. Knowledge of abnormal heart development on the molecular and genetic level extends and improves the anesthesiologist's understanding of congenital heart disease. In this article, we aim to review current knowledge pertaining to genetic alterations and their cellular effects that are involved in the formation of congenital heart defects. Given that congenital heart disease can currently only occasionally be traced to a single genetic mutation, we highlight some of the difficulties that researchers face when trying to identify specific steps in the pathogenetic development of heart lesions.
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Affiliation(s)
- Benjamin Kloesel
- From the Department of Anesthesia, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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83
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Hanchard NA, Umana LA, D'Alessandro L, Azamian M, Poopola M, Morris SA, Fernbach S, Lalani SR, Towbin JA, Zender GA, Fitzgerald-Butt S, Garg V, Bowman J, Zapata G, Hernandez P, Arrington CB, Furthner D, Prakash SK, Bowles NE, McBride KL, Belmont JW. Assessment of large copy number variants in patients with apparently isolated congenital left-sided cardiac lesions reveals clinically relevant genomic events. Am J Med Genet A 2017; 173:2176-2188. [PMID: 28653806 DOI: 10.1002/ajmg.a.38309] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 04/18/2017] [Accepted: 05/06/2017] [Indexed: 12/30/2022]
Abstract
Congenital left-sided cardiac lesions (LSLs) are a significant contributor to the mortality and morbidity of congenital heart disease (CHD). Structural copy number variants (CNVs) have been implicated in LSL without extra-cardiac features; however, non-penetrance and variable expressivity have created uncertainty over the use of CNV analyses in such patients. High-density SNP microarray genotyping data were used to infer large, likely-pathogenic, autosomal CNVs in a cohort of 1,139 probands with LSL and their families. CNVs were molecularly confirmed and the medical records of individual carriers reviewed. The gene content of novel CNVs was then compared with public CNV data from CHD patients. Large CNVs (>1 MB) were observed in 33 probands (∼3%). Six of these were de novo and 14 were not observed in the only available parent sample. Associated cardiac phenotypes spanned a broad spectrum without clear predilection. Candidate CNVs were largely non-recurrent, associated with heterozygous loss of copy number, and overlapped known CHD genomic regions. Novel CNV regions were enriched for cardiac development genes, including seven that have not been previously associated with human CHD. CNV analysis can be a clinically useful and molecularly informative tool in LSLs without obvious extra-cardiac defects, and may identify a clinically relevant genomic disorder in a small but important proportion of these individuals.
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Affiliation(s)
- Neil A Hanchard
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.,USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Luis A Umana
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Lisa D'Alessandro
- Division of Cardiology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Mahshid Azamian
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Mojisola Poopola
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Shaine A Morris
- Division of Cardiology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Susan Fernbach
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Seema R Lalani
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Jeffrey A Towbin
- Pediatric Cardiology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Gloria A Zender
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, Ohio
| | - Sara Fitzgerald-Butt
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, Ohio.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Vidu Garg
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, Ohio.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Jessica Bowman
- Heart Center, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Gladys Zapata
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.,USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Patricia Hernandez
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.,USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Cammon B Arrington
- Division of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Siddharth K Prakash
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Neil E Bowles
- Division of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Kim L McBride
- Center for Cardiovascular Research, Nationwide Children's Hospital, Columbus, Ohio.,Heart Center, Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - John W Belmont
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.,USDA/ARS/Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas
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84
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Kahlert A, Hoff K, Hitz M. Genetik der angeborenen Herzfehler. MED GENET-BERLIN 2017; 29:248-56. [DOI: 10.1007/s11825-017-0131-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Zusammenfassung
Strukturelle Herzfehler sind eine der häufigsten menschlichen Fehlbildungen. Es lassen sich mehrere morphologische Gruppen unterscheiden, wobei auch Überlappungen mit verschiedenen Formen der Kardiomyopathien, unter anderem mit der Non-Compaction Kardiomyopathie, beobachtet werden. Zum jetzigen Zeitpunkt liegt nur ein sehr eingeschränktes Verständnis der zugrunde liegenden genetischen Ursachen vor. Dies liegt zum einen an einer „komplexen Genetik“, bei welcher häufig reduzierte Penetranz und variable Expressivität vorliegen, zum anderen aber auch an heterogenen Literaturangaben, bei denen nur unzureichende genetische Evidenzen bestehen. Der Fokus dieses Reviews ist es, anhand von stringenten Evidenzkriterien die bekannten Gene für strukturelle Herzfehler darzustellen. Speziell durch die Nutzung von Next Generation Sequencing (NGS) können zunehmend mehr relevante genetische Zusammenhänge geklärt werden. Dies gilt nicht nur für die Validierung von Genotyp-Phänotyp-Assoziationen, sondern auch für die Identifizierung neuer Gene für angeborene Herzfehler (AHF), was besonders wegen des seltenen Vorkommens rekurrenter AHF-assoziierter Mutationen im gleichen Gen in Zukunft notwendig sein wird. Um dieses Ziel zu erreichen, ist es notwendig, große deutschlandweite oder internationale Studien zu etablieren und bereits publizierte Datensätze öffentlich zugänglich zu machen. Dies sollte auch für diagnostische Datensätze gelten. Mit einem derartigen Ansatz könnte nicht nur eine Gen-Panel-Diagnostik, sondern auch die Eingruppierung der Herzfehler in therapeutische Subgruppen erreicht werden.
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85
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Zhang J, Liang D, Cheng Q, Cao L, Wu Y, Wang Y, Han S, Yu Z, Cui X, Xu T, Ma D, Hu P, Xu Z. Peptidomic Analysis of Fetal Heart Tissue for Identification of Endogenous Peptides Involved in Tetralogy of Fallot. DNA Cell Biol 2017; 36:451-461. [PMID: 28304193 DOI: 10.1089/dna.2017.3647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Qing Cheng
- Department of Obstetrics, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Li Cao
- Department of Ultrasound, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yun Wu
- Department of Ultrasound, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Shuping Han
- Department of Pediatrics, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhangbin Yu
- Department of Pediatrics, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Tianhui Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, China
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86
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Garfinkel AM, Khokha MK. An interspecies heart-to-heart: Using Xenopus to uncover the genetic basis of congenital heart disease. Curr Pathobiol Rep 2017; 5:187-96. [PMID: 29082114 DOI: 10.1007/s40139-017-0142-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Given the enormous impact congenital heart disease has on child health, it is imperative that we improve our understanding of the disease mechanisms that underlie patient phenotypes and clinical outcomes. This review will outline the merits of using the frog model, Xenopus, as a tool to study human cardiac development and left-right patterning mechanisms associated with congenital heart disease. RECENT FINDINGS Patient-driven gene discovery continues to provide new insight into the mechanisms of congenital heart disease, and by extension, patient phenotypes and outcomes. By identifying gene variants in CHD patients, studies in Xenopus have elucidated the molecular mechanisms of how these candidate genes affect cardiac development, both cardiogenesis as well as left-right patterning, which can have a major impact on cardiac morphogenesis. Xenopus has also proved to be a useful screening tool for the biological relevance of identified patient-mutations, and ongoing investigations continue to illuminate disease mechanisms. SUMMARY Analyses in model organisms can help to elucidate the disease mechanisms underlying CHD patient phenotypes. Using Xenopus to disentangle the genotype-phenotype relationships of well-known and novel disease genes could enhance the ability of physicians to efficaciously treat patients and predict clinical outcomes, ultimately improving quality of life and survival rates of patients born with congenital heart disease.
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Wu XL, Li R, Fu F, Pan M, Han J, Yang X, Zhang YL, Li FT, Liao C. Chromosome microarray analysis in the investigation of children with congenital heart disease. BMC Pediatr 2017; 17:117. [PMID: 28472932 PMCID: PMC5418813 DOI: 10.1186/s12887-017-0863-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our study was aimed to explore the clinical implication of chromosome microarray analysis (CMA) in genetically etiological diagnosis of children with congenital heart disease (CHD). METHODS A total of 104 children with CHD with or without multiple congenital anomalies (MCA) or intellectual disabilities/developmental delay (ID/DD) but normal karyotype were investigated using Affymetrix CytoScan HD array. RESULT Pathogenic copy number variations (PCNVs) were identified in 29 children (27.9%). The detection rates in children with simple CHD and complex CHD were 31.1% (19/61) and 23.2% (10/43), respectively. The detection rates of PCNVs were 17.9% (7/39), 20% (5/25), 63.2% (12/19) and 23.8% (5/21) in isolated CHD, CHD plus MCA, CHD plus ID/DD, CHD plus MCA and ID/DD, respectively. The PCNVs rate of CHD plus ID/DD was significantly higher than that of isolated CHD. Two genomic loci including 15q11.2 deletion and 1q43-q44 deletion were considered as CHD locus. The DVL1, SKI, STIM1, CTNNA3 and PLN were identified as candidate genes associated with CHD phenotypes. CONCLUSION CMA can increase the diagnostic rate and improve the etiological diagnosis in children with CHD. We suggest CMA as a first-tier test in children with CHD, especially in children with CHD plus ID/DD.
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Affiliation(s)
- Xiao-li Wu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Yong-ling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fa-tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
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Abstract
Congenital heart disease is the most common birth defect, and because of major advances in medical and surgical management, there are now more adults living with congenital heart disease (CHD) than children. Until recently, the cause of the majority of CHD was unknown. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. This review will focus on the evidence for genetic causes underlying CHD and discuss data supporting both monogenic and complex genetic mechanisms underlying CHD. The discoveries from CHD genetic studies draw attention to biological pathways that simultaneously open the door to a better understanding of cardiac development and affect clinical care of patients with CHD. Finally, we address clinical genetic evaluation of patients and families affected by CHD.
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Affiliation(s)
- Samir Zaidi
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT
| | - Martina Brueckner
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT.
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89
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Bianca I, Geraci G, Gulizia MM, Egidy Assenza G, Barone C, Campisi M, Alaimo A, Adorisio R, Comoglio F, Favilli S, Agnoletti G, Carmina MG, Chessa M, Sarubbi B, Mongiovì M, Russo MG, Bianca S, Canzone G, Bonvicini M, Viora E, Poli M. Consensus Document of the Italian Association of Hospital Cardiologists (ANMCO), Italian Society of Pediatric Cardiology (SICP), and Italian Society of Gynaecologists and Obstetrics (SIGO): pregnancy and congenital heart diseases. Eur Heart J Suppl 2017; 19:D256-D292. [PMID: 28751846 PMCID: PMC5526477 DOI: 10.1093/eurheartj/sux032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The success of cardiac surgery over the past 50 years has increased numbers and median age of survivors with congenital heart disease (CHD). Adults now represent two-thirds of patients with CHD; in the USA alone the number is estimated to exceed 1 million. In this population, many affected women reach reproductive age and wish to have children. While in many CHD patients pregnancy can be accomplished successfully, some special situations with complex anatomy, iatrogenic or residual pathology are associated with an increased risk of severe maternal and fetal complications. Pre-conception counselling allows women to come to truly informed choices. Risk stratification tools can also help high-risk women to eventually renounce to pregnancy and to adopt safe contraception options. Once pregnant, women identified as intermediate or high risk should receive multidisciplinary care involving a cardiologist, an obstetrician and an anesthesiologist with specific expertise in managing this peculiar medical challenge. This document is intended to provide cardiologists working in hospitals where an Obstetrics and Gynecology Department is available with a streamlined and practical tool, useful for them to select the best management strategies to deal with a woman affected by CHD who desires to plan pregnancy or is already pregnant.
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Affiliation(s)
- Innocenzo Bianca
- Pediatric Cardiology Unit, Maternity and Neonatal Department, ARNAS Garibaldi, Catania, Italy
| | - Giovanna Geraci
- Cardiology Department, PO Cervello, Az. Osp. Riuniti Villa Sofia-Cervello, Via Trabucco, 180, 90146 Palermo, Italy
| | - Michele Massimo Gulizia
- Cardiology Department, Ospedale Garibaldi-Nesima, Azienda di Rilievo Nazionale e Alta Specializzazione ‘Garibaldi’, Catania, Italy
| | - Gabriele Egidy Assenza
- Pediatric Cardiology and Adult Congenital Heart Program, Azienda Ospedaliera-Universitaria Sant’Orsola-Malpighi, Bologna, Itlay
| | - Chiara Barone
- Genetics Unit, Maternity and Neonatal Department, ARNAS Garibaldi, Catania, Italy
| | - Marcello Campisi
- Pediatric Cardiology Unit, Maternity and Neonatal Department, ARNAS Garibaldi, Catania, Italy
| | - Annalisa Alaimo
- Pediatric Cardiology Department, PO Di Cristina, ARNAS Civico, Palermo, Italy
| | - Rachele Adorisio
- Pediatric Cardiology Department, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Francesca Comoglio
- SCDU 2, Dipartimento di Scienze Chirurgiche (Surgical Sciences Department), Università di Torino, Italy
| | - Silvia Favilli
- Pediatric Cardiology Department, Azienda-Ospedalliero-Universitaria Meyer, Firenze, Italy
| | - Gabriella Agnoletti
- Pediatric Cardiology Department, Ospedale Regina Margherita, Città della Salute e della Scienza, Torino, Italy
| | - Maria Gabriella Carmina
- Cardiology Department, PO Cervello, Az. Osp. Riuniti Villa Sofia-Cervello, Via Trabucco, 180, 90146 Palermo, Italy
| | - Massimo Chessa
- Pediatric and Adult Congenital Heart Centre, IRCCS-Policlinico San Donato Milanese San Donato Milanese (MI), Italy
| | - Berardo Sarubbi
- Pediatric Cardiology and Cardiology SUN, Seconda Università di Napoli, AORN dei Colli, Ospedale Monaldi, Napoli, Italy
| | - Maurizio Mongiovì
- Pediatric Cardiology Department, PO Di Cristina, ARNAS Civico, Palermo, Italy
| | - Maria Giovanna Russo
- Pediatric Cardiology and Cardiology SUN, Seconda Università di Napoli, AORN dei Colli, Ospedale Monaldi, Napoli, Italy
| | - Sebastiano Bianca
- Genetics Unit, Maternity and Neonatal Department, ARNAS Garibaldi, Catania, Italy
| | - Giuseppe Canzone
- Women and Children Health Department, Ospedale S. Cimino, Termini Imerese (PA), Italy
| | - Marco Bonvicini
- Pediatric Cardiology and Adult Congenital Heart Program, Azienda Ospedaliera-Universitaria Sant’Orsola-Malpighi, Bologna, Itlay
| | - Elsa Viora
- Echography and Prenatal Diagnosis Centre, Obstetrics and Gynaecology Department, Città della Salute e della Scienza di Torino, Italy
| | - Marco Poli
- Intensive Cardiac Therapy Department, Ospedale Sandro Pertini, Roma, Italy
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90
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Capone VP, Morello W, Taroni F, Montini G. Genetics of Congenital Anomalies of the Kidney and Urinary Tract: The Current State of Play. Int J Mol Sci 2017; 18:E796. [PMID: 28398236 DOI: 10.3390/ijms18040796] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/29/2017] [Accepted: 04/07/2017] [Indexed: 01/13/2023] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) are the most frequent form of malformation at birth and represent the cause of 40–50% of pediatric and 7% of adult end-stage renal disease worldwide. The pathogenesis of CAKUT is based on the disturbance of normal nephrogenesis, secondary to environmental and genetic causes. Often CAKUT is the first clinical manifestation of a complex systemic disease, so an early molecular diagnosis can help the physician identify other subtle clinical manifestations, significantly affecting the management and prognosis of patients. The number of sporadic CAKUT cases explained by highly penetrant mutations in a single gene may have been overestimated over the years and a genetic diagnosis is missed in most cases, hence the importance of identifying new genetic approaches which can help unraveling the vast majority of unexplained CAKUT cases. The aim of our review is to clarify the current state of play and the future perspectives of the genetic bases of CAKUT.
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91
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Edvardson S, Prunetti L, Arraf A, Haas D, Bacusmo JM, Hu JF, Ta-Shma A, Dedon PC, de Crécy-Lagard V, Elpeleg O. tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy. Eur J Hum Genet 2017; 25:545-551. [PMID: 28272532 DOI: 10.1038/ejhg.2017.30] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/01/2017] [Accepted: 02/07/2017] [Indexed: 11/09/2022] Open
Abstract
Post-transcriptional tRNA modifications are numerous and require a large set of highly conserved enzymes in humans and other organisms. In yeast, the loss of many modifications is tolerated under unstressed conditions; one exception is the N6-threonyl-carbamoyl-adenosine (t6A) modification, loss of which causes a severe growth phenotype. Here we aimed at a molecular diagnosis in a brother and sister from a consanguineous family who presented with global developmental delay, failure to thrive and a renal defect manifesting in proteinuria and hypomagnesemia. Using exome sequencing, the patients were found to be homozygous for the c.974G>A (p.(Arg325Gln)) variant of the KAE1 gene. KAE1 is a constituent of the KEOPS complex, a five-subunit complex that catalyzes the second biosynthetic step of t6A in the cytosol. The yeast KAE1 allele carrying the equivalent mutation did not rescue the t6A deficiency of the kae1Δ yeast strain as efficiently as the WT allele; furthermore, t6A levels quantified by LC-MS/MS were lower in the kae1Δ strain which was complemented by the mutation than in the kae1Δ strain, which was complemented by the WT allele. We conclude that homozygosity for c.974G>A (p.(Arg325Gln)) in KAE1 likely exerts its pathogenic effect by perturbing t6A synthesis, thereby interfering with global protein production. This is the first report of t6A biosynthesis defect in human. KAE1 joins the growing list of cytoplasmic tRNA modification enzymes, all associated with severe neurological disorders.
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Affiliation(s)
- Simon Edvardson
- Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel.,Pediatric Neurology Unit, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Laurence Prunetti
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetic Institute, University of Florida, Gainesville, FL, USA
| | - Aiman Arraf
- Hebrew University School of Medicine, Jerusalem, Israel
| | - Drago Haas
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetic Institute, University of Florida, Gainesville, FL, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetic Institute, University of Florida, Gainesville, FL, USA
| | - Jennifer F Hu
- Center for Environmental Health Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Asas Ta-Shma
- Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter C Dedon
- Center for Environmental Health Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences and Genetic Institute, University of Florida, Gainesville, FL, USA
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
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92
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Xie HM, Werner P, Stambolian D, Bailey-Wilson JE, Hakonarson H, White PS, Taylor DM, Goldmuntz E. Rare copy number variants in patients with congenital conotruncal heart defects. Birth Defects Res 2017; 109:271-295. [PMID: 28398664 DOI: 10.1002/bdra.23609] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/22/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Previous studies using different cardiac phenotypes, technologies and designs suggest a burden of large, rare or de novo copy number variants (CNVs) in subjects with congenital heart defects. We sought to identify disease-related CNVs, candidate genes, and functional pathways in a large number of cases with conotruncal and related defects that carried no known genetic syndrome. METHODS Cases and control samples were divided into two cohorts and genotyped to assess each subject's CNV content. Analyses were performed to ascertain differences in overall CNV prevalence and to identify enrichment of specific genes and functional pathways in conotruncal cases relative to healthy controls. RESULTS Only findings present in both cohorts are presented. From 973 total conotruncal cases, a burden of rare CNVs was detected in both cohorts. Candidate genes from rare CNVs found in both cohorts were identified based on their association with cardiac development or disease, and/or their reported disruption in published studies. Functional and pathway analyses revealed significant enrichment of terms involved in either heart or early embryonic development. CONCLUSION Our study tested one of the largest cohorts specifically with cardiac conotruncal and related defects. These results confirm and extend previous findings that CNVs contribute to disease risk for congenital heart defects in general and conotruncal defects in particular. As disease heterogeneity renders identification of single recurrent genes or loci difficult, functional pathway and gene regulation network analyses appear to be more informative. Birth Defects Research 109:271-295, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Hongbo M Xie
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Petra Werner
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Dwight Stambolian
- Department of Ophthalmology and Human Genetics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joan E Bailey-Wilson
- Statistical Genetics Section, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - Hakon Hakonarson
- The Center for Applied Genomics, Department of Pediatrics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter S White
- Division of Biomedical Informatics, Cincinnati Children's Hospital, Department of Biomedical Informatics, University of Cincinnati, Cincinnati, Ohio
| | - Deanne M Taylor
- The Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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93
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Rice AM, McLysaght A. Dosage sensitivity is a major determinant of human copy number variant pathogenicity. Nat Commun 2017; 8:14366. [PMID: 28176757 DOI: 10.1038/ncomms14366] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/20/2016] [Indexed: 01/22/2023] Open
Abstract
Human copy number variants (CNVs) account for genome variation an order of magnitude larger than single-nucleotide polymorphisms. Although much of this variation has no phenotypic consequences, some variants have been associated with disease, in particular neurodevelopmental disorders. Pathogenic CNVs are typically very large and contain multiple genes, and understanding the cause of the pathogenicity remains a major challenge. Here we show that pathogenic CNVs are significantly enriched for genes involved in development and genes that have greater evolutionary copy number conservation across mammals, indicative of functional constraints. Conversely, genes found in benign CNV regions have more variable copy number. These evolutionary constraints are characteristic of genes in pathogenic CNVs and can only be explained by dosage sensitivity of those genes. These results implicate dosage sensitivity of individual genes as a common cause of CNV pathogenicity. These evolutionary metrics suggest a path to identifying disease genes in pathogenic CNVs. Copy number variants (CNVs) cause significant genomic variation in humans and may be benign or may cause disease. Here, the authors show that pathogenic CNVs are evolutionarily constrained compared with benign, pointing to dosage sensitivity as a potential cause of disease.
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94
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Blue GM, Humphreys D, Szot J, Major J, Chapman G, Bosman A, Kirk EP, Sholler GF, Harvey RP, Dunwoodie SL, Winlaw DS. The promises and challenges of exome sequencing in familial, non-syndromic congenital heart disease. Int J Cardiol 2016; 230:155-163. [PMID: 27989580 DOI: 10.1016/j.ijcard.2016.12.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/30/2016] [Accepted: 12/11/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Exome sequencing is an established strategy to identify causal variants in families with two or more members affected by congenital heart disease (CHD). This unbiased approach, in which both rare and common variants are identified, makes it suitable to research complex, heterogeneous diseases such as CHD. METHODS AND RESULTS Exome sequencing was performed on two affected members of a three generation family with atrial septal defects (ASD), suggesting a dominant inheritance pattern. Variants were filtered using two bioinformatics pipelines and prioritised according to in silico prediction programs. Segregation studies and functional analyses were used to assess co-segregation with disease and effects on protein function, respectively. Following the data and in silico analyses, ten candidate variants were prioritised. Of these, SRPK2 (c.2044C>T[p.Arg682Trp]) and NOTCH1 (c.3835C>T[p.Arg1279Cys]), co-segregated with disease in the family; however, previous functional analyses on SRPK2 make this an unlikely candidate. Functional analyses in the variant (c.3835C>T[p.Arg1279Cys]) of the known CHD gene NOTCH1 demonstrated a non-significant decrease in signalling activity. CONCLUSION This study demonstrates both the potential, as well as the challenges, of applying exome sequencing to complex diseases such as CHD. While in silico evidence and segregation analyses in the NOTCH1 p.Arg1279Cys variant are highly suggestive of pathogenicity, the minimal change in signalling capacity suggests that other variants may be required for CHD development. This study highlights the difficulties of applying exome sequencing in familial, non-syndromic CHD in the clinical environment and a cautionary note in the interpretation of apparently causal abnormalities in silico without supportive functional data.
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Affiliation(s)
- Gillian M Blue
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - David Humphreys
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Justin Szot
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Joelene Major
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Gavin Chapman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Alexis Bosman
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia
| | - Edwin P Kirk
- Department of Medical Genetics, Sydney Children's Hospital, Sydney, Australia; School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Gary F Sholler
- The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia
| | - Richard P Harvey
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia; School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, Australia
| | - David S Winlaw
- Kids Heart Research, The Children's Hospital at Westmead, Sydney, Australia; The Heart Centre for Children, The Children's Hospital at Westmead, Sydney, Australia; Sydney Medical School, University of Sydney, Australia.
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95
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Sukenik-Halevy R, Sukenik S, Koifman A, Alpert Y, Hershkovitz R, Levi A, Biron-Shental T. Clinical aspects of prenatally detected congenital heart malformations and the yield of chromosomal microarray analysis. Prenat Diagn 2016; 36:1185-1191. [PMID: 27794172 DOI: 10.1002/pd.4954] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The yield of chromosomal microarray analysis (CMA) for prenatally detected congenital heart defects (CHD) is 6.6% to 19.2%. We evaluated the yield of CMA in cases of prenatally detected CHD in regard to specific clinical characteristics. METHODS Data from 192 cases of CHD including type, clinical and familial background, workup performed during the pregnancy, and pregnancy outcomes were collected. RESULTS Fetal echocardiography was performed in all cases; 61.4% of CHD were suspected by ultrasound. There was a positive family history (FH) in 15.7%. Abnormal nuchal translucency or umbilical cord anomalies were detected in 1.7% and 5.9%, respectively, and 55.1% were isolated cases. In 11 of 96 cases in which genetic testing was performed, karyotype and CMA were abnormal (11.5%). The detection rate of CMA (performed in 72 cases) was 9.7%. The yield of CMA was similar in simple cases, isolated cases, and cases with a positive FH. CMA was abnormal in 7.3% of ventricular septal defect cases. CONCLUSION Most cases of prenatally detected CHD had no additional extra-cardiac, sonographic findings suggesting increased risk for CHD. The yield of CMA testing was significant in all clinical scenarios including simple heart malformations, isolated cases, and cases with a positive FH. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Rivka Sukenik-Halevy
- Department of OBGYN, Meir Medical Center, Kfar Saba, Israel.,Genetics Institute, Meir Medical Center, Kfar Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shay Sukenik
- Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Arie Koifman
- Ben Gurion University of the Negev, Beer Sheva, Israel.,Genetics Institute, Soroka Medical Center, Beer Sheva, Israel
| | - Yoav Alpert
- Department of OBGYN, Meir Medical Center, Kfar Saba, Israel
| | - Reli Hershkovitz
- Ben Gurion University of the Negev, Beer Sheva, Israel.,Ultrasound Unit, Soroka Medical Center, Beer Sheva, Israel
| | - Alex Levi
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Cardiology, Meir Medical Center, Kfar Saba, Israel
| | - Tal Biron-Shental
- Department of OBGYN, Meir Medical Center, Kfar Saba, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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96
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Szczałuba K, Demkow U. Array comparative genomic hybridization and genomic sequencing in the diagnostics of the causes of congenital anomalies. J Appl Genet 2017; 58:185-98. [PMID: 27858254 DOI: 10.1007/s13353-016-0376-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
The aim of this review is to provide the current state of knowledge about the usefulness of modern genetic technologies in uncovering the causality of isolated and multiple congenital anomalies. Array comparative genomic hybridization and next-generation sequencing have revolutionized the clinical approach to patients with these phenotypes. Both technologies enable early diagnosis, especially in clinically challenging newborn populations, and help to uncover genetic defects associated with various phenotypes. The application of both complementary methods could assist in identifying many variants that may simultaneously be involved in the development of a number of isolated or multiple congenital anomalies. Both technologies carry serious variant misinterpretation risks as well. Therefore, the methods of variant classification and accessible variant databases are mentioned. A useful strategy of clinical genetic testing with the application of both methodologies is presented. Finally, future directions and challenges are briefly commented on in this review.
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97
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Mak CCY, Chow PC, Liu APY, Chan KYK, Chu YWY, Mok GTK, Leung GKC, Yeung KS, Chau AKT, Lowther C, Scherer SW, Marshall CR, Bassett AS, Chung BHY. De novo large rare copy-number variations contribute to conotruncal heart disease in Chinese patients. NPJ Genom Med 2016; 1:16033. [PMID: 29263819 PMCID: PMC5685312 DOI: 10.1038/npjgenmed.2016.33] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/02/2016] [Accepted: 08/05/2016] [Indexed: 01/05/2023] Open
Abstract
Conotruncal heart anomalies (CTDs) are particularly prevalent congenital heart diseases (CHD) in Hong Kong. We surveyed large (>500 kb), rare (<1% frequency in controls) copy-number variations (CNVs) in Chinese patients with CTDs to identify potentially disease-causing variations. Adults who tested negative for 22q11.2 deletions were recruited from the adult CHD clinic in Hong Kong. Using a stringent calling criteria, high-confidence CNV calls were obtained, and a large control set comprising 3,987 Caucasian and 1,945 Singapore Chinese subjects was used to identify rare CNVs. Ten large rare CNVs were identified, and 3 in 108 individuals were confirmed to harbour de novo CNVs. All three patients were syndromic with a more complex phenotype, and each of these CNVs overlapped regions likely to be important in CHD. One was a 611 kb deletion at 17p13.3, telomeric to the Miller-Dieker syndrome (MDS) critical region, overlapping the NXN gene. Another was a 5 Mb deletion at 13q33.3, within a previously described critical region for CHD. A third CNV, previously unreported, was a large duplication at 2q22.3 overlapping the ZEB2 gene. The commonly reported 1q21.1 recurrent duplication was not observed in this Chinese cohort. We provide detailed phenotypic and genotypic descriptions of large rare genic CNVs that may represent CHD loci in the East Asian population. Larger samples of Chinese origin will be required to determine whether the genome-wide distribution differs from that found in predominantly European CHD cohorts.
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Affiliation(s)
- Christopher C Y Mak
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak Cheong Chow
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Anthony P Y Liu
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kelvin Y K Chan
- Department of Obstetrics and Gynecology, Queen Mary Hospital, Hong Kong, China
| | - Yoyo W Y Chu
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gary T K Mok
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gordon K C Leung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kit San Yeung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Adolphus K T Chau
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chelsea Lowther
- The Clinical Genetics Research Program at The Centre for Addiction and Mental Health, The Dalglish Family 22q Clinic at The University Health Network, and The Department of Psychiatry at The University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne S Bassett
- The Clinical Genetics Research Program at The Centre for Addiction and Mental Health, The Dalglish Family 22q Clinic at The University Health Network, and The Department of Psychiatry at The University of Toronto, Toronto, ON, Canada
| | - Brian H Y Chung
- Department of Paediatrics & Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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Abstract
Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD. These include de novo and inherited variants at established (chromosome 22q11.2), emerging (chromosome 1q21.1), and novel loci across the genome. Variable expression of rare CNVs provides support for the notion of a genetic spectrum of CHD that crosses traditional anatomic classification boundaries. Clinical genetic testing using genome-wide technologies (e.g., chromosomal microarray analysis) is increasingly employed in prenatal, paediatric and adult settings. CNV discoveries in CHD have translated to changes to clinical management, prognostication and genetic counselling. The convergence of findings at individual gene and at pathway levels is shedding light on the mechanisms that govern human cardiac morphogenesis. These clinical and research advances are helping to inform whole-genome sequencing, the next logical step in delineating the genetic architecture of CHD.
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99
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Del Viso F, Huang F, Myers J, Chalfant M, Zhang Y, Reza N, Bewersdorf J, Lusk CP, Khokha MK. Congenital Heart Disease Genetics Uncovers Context-Dependent Organization and Function of Nucleoporins at Cilia. Dev Cell 2016; 38:478-92. [PMID: 27593162 PMCID: PMC5021619 DOI: 10.1016/j.devcel.2016.08.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/07/2016] [Accepted: 08/08/2016] [Indexed: 01/21/2023]
Abstract
Human genomics is identifying candidate genes for congenital heart disease (CHD), but discovering the underlying mechanisms remains challenging. In a patient with CHD and heterotaxy (Htx), a disorder of left-right patterning, we previously identified a duplication in Nup188. However, a mechanism to explain how a component of the nuclear pore complex (NPC) could cause Htx/CHD was undefined. Here, we show that knockdown of Nup188 or its binding partner Nup93 leads to a loss of cilia during embryonic development while leaving NPC function largely intact. Many data, including the localization of endogenous Nup188/93 at cilia bases, support their direct role at cilia. Super-resolution imaging of Nup188 shows two barrel-like structures with dimensions and organization incompatible with an NPC-like ring, arguing against a proposed "ciliary pore complex." We suggest that the nanoscale organization and function of nucleoporins are context dependent in a way that is required for the structure of the heart.
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Affiliation(s)
- Florencia Del Viso
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Jordan Myers
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Madeleine Chalfant
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Nooreen Reza
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
| | - C Patrick Lusk
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
| | - Mustafa K Khokha
- Program in Vertebrate Developmental Biology, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA.
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100
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Affiliation(s)
- Patrice Bouvagnet
- From Laboratoire Cardiogénétique, INMG, CNRS UMR 5310, INSERM U1217 and Université Lyon 1, Lyon, France and Laboratoire Cardiogénétique, Hospices Civils de Lyon, Lyon, France.
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