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Zhou Z, Jiao X, Gong P, Niu Y, Xu Z, Zhang G, Zhang Y, Qin J, Yang Z. Clinical features and underlying etiology of children with Lennox-Gastaut syndrome. J Neurol 2024; 271:5392-5401. [PMID: 39008035 DOI: 10.1007/s00415-024-12465-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 07/16/2024]
Abstract
OBJECTIVE Lennox-Gastaut Syndrome (LGS) is characterized by the presence of multiple seizure types and encompasses a heterogenous group of etiologies. The aim of our study was to evaluate the etiological profile of LGS and investigate seizure outcomes based on different clinical variables. METHODS The clinical features, neuroimaging findings, genetic testing and other testing results of LGS patients were systematically reviewed. The identifiable etiology was categorized as either acquired or nonacquired. Univariate and multivariate regression analyses were performed to explore the association between clinical variables and seizure outcome at the last follow-up. RESULTS We enrolled 156 patients diagnosed with LGS, of whom 66% were male. The mean age of patients was 34.2 months and the median follow-up duration was 29.5 months (interquartile range = 14-56.25 months). The initial seizure type was epileptic spasm in 61 patients, among which 33 of them met the criteria for infantile epileptic spasm syndrome. All patients underwent neuroimaging test, with 25% falling into the acquired structural category. Etiology could be identified in 84 individuals, including pathogenetic variants found in 34 out of 117 patients with nonacquired etiology. CHD2 mutations were most frequently observed among these pathogenetic variants. At the last follow-up, favorable outcomes were observed in 27 patients. The identification of etiology emerged as a significant determinant influencing LGS outcome; specifically, patients with unknown etiology had a higher likelihood of experiencing favorable outcomes compared to those with known cause (p = 0.041). Early onset age and longer epilepsy duration significantly increased the odds of an unfavorable outcome (p = 0.006 and 0.024). SIGNIFICANCE We present novel data on the clinical and etiological spectrum of LGS, with determined etiology observed in over half of the patients. Epileptic spasms were found to be more prevalent than tonic seizures as seizure onset types in LGS. The presence of a known etiology, earlier age at onset, and longer duration of epilepsy were associated with a poorer long-term epileptological outcome.
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Affiliation(s)
- Zongpu Zhou
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Xianru Jiao
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Pan Gong
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yue Niu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhao Xu
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Genfu Zhang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jiong Qin
- Department of Pediatrics, Peking University People's Hospital, Beijing, China
- Epilepsy Center, Peking University People's Hospital, Beijing, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University People's Hospital, Beijing, China.
- Epilepsy Center, Peking University People's Hospital, Beijing, China.
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Sun B, Liu L, Han L, Li Q, Wu Q, Hou J, Wang W, Ying W, Zhou Q, Qian F, Lu W, Wang X, Sun J. Novel Mutation in the Moesin (MSN) Gene Leads to Immunodeficiency with Epstein-Barr Virus (EBV) Infection and Dermatomyositis-Like Symptoms. J Clin Immunol 2024; 44:155. [PMID: 38922539 DOI: 10.1007/s10875-024-01755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024]
Abstract
PURPOSE Moesin (MSN) deficiency is a recently reported combined immunodeficiency, and few cases have been reported to date. We describe a Chinese patient with a novel mutation causing MSN deficiency and a novel phenotype. METHODS Clinical and immunological data were collected. Whole-exome sequencing was performed to identify gene mutations. MSN protein expression and T cell proliferation and activation were determined by flow cytometry. Cell migration was confirmed with a Transwell assay. Autoantibody levels were analyzed using antigen microarrays. RESULTS The patient was a 10-year-old boy who presented with recurrent fever, oral ulcers and dermatomyositis-like symptoms, such as periorbital edema, facial swelling, elevated creatine kinase levels, and abnormal electromyography and muscle biopsy results. Epstein-Barr virus (EBV) DNA was detected in the serum, cells and tissues of this patient. He further developed nasal-type NK/T-cell lymphoma. A novel hemizygous mutation (c.68 A > G, p.N23S) in the MSN gene was found. The immunological phenotype of this patient included persistent decreases in T and B lymphocyte counts but normal immunoglobulin IgG levels. The patient had attenuated MSN protein expression and impaired T-cell proliferation and migration. The proportions of Tfh cells and CD21low B cells in the patient were higher than those in the controls. Moreover, 82 IgG and 102 IgM autoantibodies were more abundant in the patient than in the healthy controls. CONCLUSIONS The novel mutation N23S is pathogenic and leads to a severe clinical phenotype. EBV infection, tumor, and dermatomyositis-like autoimmune symptoms may be associated with MSN deficiency, further expanding the understanding of the disease.
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Affiliation(s)
- Bijun Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Luyao Liu
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Lingli Han
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qifan Li
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qi Wu
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Jia Hou
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenjie Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenjing Ying
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qinhua Zhou
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Feng Qian
- Ministry of Education Key Laboratory of Contemporary Anthropology, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Wei Lu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, 200032, China.
| | - Jinqiao Sun
- Department of Clinical Immunology, Children's Hospital of Fudan University, National Children Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
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Li ZD, Li YC, Jing-Zhao, Wang JS, Xie XB. NR1H4 disease: rapidly progressing neonatal intrahepatic cholestasis and early death. Orphanet J Rare Dis 2024; 19:171. [PMID: 38641832 PMCID: PMC11027519 DOI: 10.1186/s13023-024-03166-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/30/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Clinical studies on progressive familial intrahepatic cholestasis (PFIC) type 5 caused by mutations in NR1H4 are limited. METHODS New patients with biallelic NR1H4 variants from our center and all patients from literature were retrospectively analyzed. RESULTS Three new patients were identified to be carrying five new variants. Liver phenotypes of our patients manifests as low-γ-glutamyl transferase cholestasis, liver failure and related complications. One patient underwent liver transplantation (LT) and survived, and two other patients died without LT. Nine other patients were collected through literature review. Twelve out of 13 patients showed neonatal jaundice, with the median age of onset being 7 days after birth. Reported clinical manifestations included cholestasis (13/13, 100%), elevated AFP (11/11, 100%), coagulopathy (11/11, 100%), hypoglycemia (9/13, 69%), failure to thrive (8/13, 62%), splenomegaly (7/13, 54%), hyperammonemia (7/13, 54%), and hepatomegaly (6/13, 46%). Six of 13 patients received LT at a median age of 6.2 months, and only one patient died of acute infection at one year after LT. Other 7 patients had no LT and died with a median age of 5 months (range 1.2-8). There were 8 patients with homozygous genotype and 5 patients with compound heterozygous genotype. In total, 13 different variants were detected, and 5 out of 12 single or multiple nucleotides variants were located in exon 5. CONCLUSIONS We identified three newly-diagnosed patients and five novel mutations. NR1H4-related PFIC typically cause progressive disease and early death. LT may be the only lifesaving therapy leading to cure.
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Affiliation(s)
- Zhong-Die Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Minhang District, 201102, Shanghai, China
| | - Yu-Chuan Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Minhang District, 201102, Shanghai, China
| | - Jing-Zhao
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Minhang District, 201102, Shanghai, China
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Minhang District, 201102, Shanghai, China
| | - Xin-Bao Xie
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, No. 399 Wanyuan Road, Minhang District, 201102, Shanghai, China.
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Dong X, Lu Y, Guo L, Li C, Ni Q, Wu B, Wang H, Yang L, Wu S, Sun Q, Zheng H, Zhou W, Wang S. PICOTEES: a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts. J Genet Genomics 2024; 51:243-251. [PMID: 37714454 DOI: 10.1016/j.jgg.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023]
Abstract
The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://birthdefectlab.cn:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lanting Guo
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Chuan Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Lin Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Songyang Wu
- The Third Research Institute of the Ministry of Public Security, Shanghai 200031, China
| | - Qi Sun
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Hao Zheng
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai 201102, China; Xiamen Campus of Children's Hospital of Fudan University, Xiamen, Fujian 361006, China.
| | - Shuang Wang
- Department of Bioinformatics, Hangzhou Nuowei Information Technology Co., Ltd, Hangzhou, Zhejiang 310000, China; Institutes for Systems Genetics, West China Hospital, Chengdu, Sichuan 610041, China; Shanghai Putuo People's Hospital, Tongji University, Shanghai 200060, China.
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Wang X, Xiao T, Wang J, Wu B, Wang H, Lu Y, Wang Y, Chen B, Hu L, Cao Y, Zhang R, Cheng G, Wang L, Li Z, Dong X, Yang L, Zhou W. Clinical and genetic risk factors associated with neonatal severe hyperbilirubinemia: a case-control study based on the China Neonatal Genomes Project. Front Genet 2024; 14:1292921. [PMID: 38274110 PMCID: PMC10808734 DOI: 10.3389/fgene.2023.1292921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Objective: We aimed to investigate the clinical and genetic risk factors associated with neonatal severe unconjugated hyperbilirubinemia. Methods: This was a retrospective, 1:1 matched, case-control study. We included 614 neonates diagnosed with severe unconjugated hyperbilirubinemia (serum total bilirubin level ≥425 μmol/L or serum total bilirubin concentration that met exchange transfusion criteria) from the China Neonatal Genomes Project in Children's Hospital of Fudan University. Clinical exome sequencing data were analyzed using a data analysis pipeline of Children's Hospital of Fudan University. The factors associated with severe unconjugated hyperbilirubinemia were assessed using univariable and multivariable logistic regression analyses. Interaction analyses were examined between clinical and genetic risk factors. Results: ABO/Rh incompatibility hemolysis (odds ratio [OR] 3.36, 95% confidence interval [CI] 2.32-4.86), extravascular hemorrhage (OR 2.95, 95% CI 2.24-3.89), weight loss (OR 5.46, 95% CI 2.88-10.36), exclusive breastmilk feeding (OR 3.56, 95% CI 2.71-4.68), and the homozygous mutant of UGT1A1 211G>A (OR 2.35, 95% CI 1.54-3.59) were all identified as factors significantly associated with severe unconjugated hyperbilirubinemia. The presence of UGT1A1 211G>A mildly increased the risk of severe unconjugated hyperbilirubinemia caused by ABO/Rh incompatibility hemolysis (OR 3.98, 95% CI 2.19-7.23), although the effect is not statistically significant. Conclusion: ABO/Rh incompatibility hemolysis, extravascular hemorrhage, weight loss, exclusive breastmilk feeding, and the homozygous mutant of UGT1A1 211G>A were found to be risk factors for severe unconjugated hyperbilirubinemia. Clinical factors remain the most crucial and preventable determinants in managing severe unconjugated hyperbilirubinemia, with a minimal genetic contribution. The establishment of preconception care practices and the reinforcement of screening for the aforementioned risk factors are essential steps for preventing severe unconjugated hyperbilirubinemia.
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Affiliation(s)
- Xiao Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tiantian Xiao
- Chengdu Women’s and Children’s Central Hospital, The Affiliated Women’s and Children’s Hospital, School of Medicine, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jin Wang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bin Chen
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Zhihua Li
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Lin Yang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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Huang Z, Shen Q, Wu B, Wang H, Dong X, Lu Y, Cheng G, Wang L, Lu W, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen D, Yin Z, Yang L, Ni Q, Liu R, Li G, Zhang P, Qian Y, Peng X, Wang Y, Cao Y, Xu H, Hu L, Yang L, Zhou W. Genetic Spectrum of Congenital Anomalies of the Kidney and Urinary Tract in Chinese Newborn Genome Project. Kidney Int Rep 2023; 8:2376-2384. [PMID: 38025242 PMCID: PMC10658258 DOI: 10.1016/j.ekir.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Congenital anomalies of the kidney and urinary tract (CAKUT) corresponds to a spectrum of defects. Several large-cohort studies have used high-throughput sequencing to investigate the genetic risk of CAKUT during antenatal, childhood, and adulthood period. However, our knowledge of newborns with CAKUT is limited. Methods This multicenter retrospective cohort study explored the genetic spectrum of CAKUT in a Chinese neonatal cohort. Clinical data and whole exome sequencing (WES) data of 330 newborns clinically diagnosed with CAKUT were collected. WES data were analyzed for putative deleterious single nucleotide variants (SNVs) and potential disease-associated copy number variants (CNVs). Results In this study, pathogenic variants were identified in 61 newborns (18.5%, 61/330), including 35 patients (57.4%) with SNVs, 25 patients (41%) with CNVs, and 1 patient with both an SNV and a CNV. Genetic diagnosis rates were significantly higher in patients with extrarenal manifestations (P<0.001), especially in those with cardiovascular malformations (P<0.05). SNVs in genes related to syndromic disorders (CAKUT with extrarenal manifestations) were common, affecting 20 patients (57.1%, 20/35). KMT2D was the most common gene (5 patients) and 17q12 deletion was the most common CNV (4 patients). Patient 110 was detected with both a CNV (17q12 deletion) and an SNV (a homozygous variant of SLC25A13). Among the newborns with positive genetic results, 22 (36.1%, 22/61) patients may benefit from a molecular diagnosis and change in clinical management (including early multidisciplinary treatment, disease-specific follow-up, and familial genetic counseling). Conclusion This study shows the heterogeneous genetic etiologies in a Chinese CAKUT neonatal cohort by using WES. Patients with CAKUT who have extrarenal manifestations are more likely to harbor genetic diagnoses. Kabuki syndrome and 17q12 deletion syndrome were the most common genetic findings. Approximately 36.1% of the patients may benefit from molecular diagnoses and a change in clinical management.
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Affiliation(s)
- Zhelan Huang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Liping Chen
- Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wenqing Kang
- Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Long Li
- Department of Neonatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xinnian Pan
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiufen Wei
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | | | - Dongmei Chen
- Quanzhou Women and Children’s Hospital, Quanzhou, China
| | | | - Ling Yang
- Hainan Women and Children’s Medical Center, Haikou, China
| | - Qi Ni
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
- Xiamen Children’s Hospital, Xiamen, China
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Geng G, Hu W, Meng Y, Zhang H, Zhang H, Chen C, Zhang Y, Gao Z, Liu Y, Shi J. Vagus nerve stimulation for treating developmental and epileptic encephalopathy in young children. Front Neurol 2023; 14:1191831. [PMID: 37928141 PMCID: PMC10624125 DOI: 10.3389/fneur.2023.1191831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
Objective To investigate the clinical variables that might predict the outcome of developmental and epileptic encephalopathy (DEE) after vagus nerve stimulation (VNS) therapy and identify the risk factors for poor long-term outcome. Patients and methods We retrospectively studied 32 consecutive children with drug-resistant DEE who had undergone VNS surgery from April 2019 to July 2021, which were not suitable for corpus callosotomy. In spite of combining valproic acid, levetiracetam, lamotrigine, topiramate, etc. (standard anti-seizure medicine available in China) it has not been possible to effectively reduce seizures in the population we investigate (Cannabidiol and brivaracetam were not available in China). A responder was defined as a frequency reduction decrease > 50%. Seizure freedom was defined as freedom from seizures for at least 6 months. Sex, electroencephalograph (EEG) group, neurodevelopment, time lag, gene mutation, magnetic resonance imaging (MRI), and epilepsy syndrome were analyzed with Fisher's exact test, The age at onset and age at VNS therapy were analyzed with Kruskal-Wallis test, statistical significance was defined as p < 0.05. And used the effect size to correction. Results Among the 32 patients, the median age at VNS implantation was 4.7 years (range: 1-12 years). At the most recent follow-up, five children (15.6%) were seizure-free and 22 (68.8%) were responders. Univariate analysis demonstrated that the responders were significantly associated with mild development delay/intellectual disability (p = 0.044; phi coefficient = 0.357) and a multifocal EEG pattern (p = 0.022; phi coefficient = -0.405). Kaplan-Meier survival analyses demonstrated that a multifocal EEG pattern (p = 0.049) and DEE without epileptic spasm (ES) (p = 0.012) were statistically significant (p = 0.030). Multivariate analysis demonstrated that DEE with ES had significant predictive value for poor long-term outcome (p = 0.014, hazard ratio = 5.433, confidence interval = 1.402-21.058). Conclusions Our study suggested that VNS was a generally effective adjunct treatment for DEE. Although the predictive factors for VNS efficacy remain unclear, it should be emphasized that patients with ES are not suitable candidates for epilepsy surgery. Further investigations are needed to validate the present results.
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Affiliation(s)
- Guifu Geng
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
- Department of Functional Neurosurgery, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Wandong Hu
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yao Meng
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
- Department of Functional Neurosurgery, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Huan Zhang
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Hongwei Zhang
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Chuanmei Chen
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yanqing Zhang
- Pediatric Health Care Institute, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Zaifen Gao
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Yong Liu
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
| | - Jianguo Shi
- Department of Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
- Department of Functional Neurosurgery, Children's Hospital Affiliated to Shandong University, Jinan Children's Hospital, Jinan, Shandong, China
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8
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Millevert C, Weckhuysen S. ILAE Genetic Literacy Series: Self-limited familial epilepsy syndromes with onset in neonatal age and infancy. Epileptic Disord 2023; 25:445-453. [PMID: 36939707 DOI: 10.1002/epd2.20026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 03/21/2023]
Abstract
The self-limited (familial) epilepsies with onset in neonates or infants, formerly called benign familial neonatal and/or infantile epilepsies, are autosomal dominant disorders characterized by neonatal- or infantile-onset focal motor seizures and the absence of neurodevelopmental complications. Seizures tend to remit during infancy or early childhood and are therefore called "self-limited". A positive family history for epilepsy usually suggests the genetic etiology, but incomplete penetrance and de novo inheritance occur. Here, we review the phenotypic spectrum and the genetic architecture of self-limited (familial) epilepsies with onset in neonates or infants. Using an illustrative case study, we describe important clues in recognition of these syndromes, diagnostic steps including genetic testing, management, and genetic counseling.
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Affiliation(s)
- Charissa Millevert
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Neurology, University Hospital, Antwerp, Belgium
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Neurology, University Hospital, Antwerp, Belgium
- μNEURO Research Centre of Excellence, University of Antwerp, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
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9
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Huang Z, Lu W, Zhang P, Lu Y, Chen L, Kang W, Yang L, Li G, Zhu J, Wu B, Zhou W, Wang H. Early onset critically ill infants with Schaaf-Yang syndrome: a retrospective study from the China neonatal genomes project and literature review. ANNALS OF TRANSLATIONAL MEDICINE 2023; 11:312. [PMID: 37404980 PMCID: PMC10316094 DOI: 10.21037/atm-22-4396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/19/2023] [Indexed: 07/06/2023]
Abstract
Background Schaaf-Yang syndrome (SYS) is a recently identified rare neurodevelopmental disorder characterized by neonatal hypotonia, feeding difficulty, joint contractures, autism spectrum disorder and development delay/intellectual disability. It is mainly caused by truncating variants in maternally imprinted gene MAGEL2 within the Prader-Willi syndrome critical region 15q11-q13. Clinical diagnosis of SYS is difficult for clinicians due to its rarity and highly variable phenotypes, while unique inheritance patterns also complicate genetic diagnosis. To date, no published papers have analyzed the clinical consequences and molecular changes in Chinese patients. Methods In this study, we retrospectively investigated the mutation spectrums and phenotypic features of 12 SYS infants. The data were from a cohort of critically ill infants from the China neonatal genomes project (CNGP), sponsored by Children's Hospital of Fudan University. We also reviewed relevant literature. Results Six previously reported mutations and six novel pathogenic variations of MAGEL2 were identified in 12 unrelated infants. Neonatal respiratory problems were the major complaint for hospitalization, which occurred in 91.7% (11/12) cases. All babies displayed feeding difficulties and a poor suck postnatally, and neonatal dystonia was present in 11 of the cases; joint contractures and multiple congenital defects were also observed. Interestingly, we found that 42.5% (57/134) of the reported SYS patients, including ours carried variants in the c.1996 site, particularly the c.1996dupC variant. The mortality rate was 17.2% (23/134), with the median age of death between 24 gestational weeks in fetuses and 1-month-old in infants. Respiratory failure was the leading cause of death in live-born patients (58.8%, 10/17), especially during the neonatal period. Conclusions Our findings expanded the genotype and phenotype spectrum of neonatal SYS patients. The results demonstrated that respiratory dysfunction was a typical characteristic among Chinese SYS neonates that should attract physicians' attention. The early identification of such disorders allows early intervention and can further provide genetic counseling as well as reproductive options for the affected families.
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Affiliation(s)
- Zhongwen Huang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases1, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liping Chen
- Department of Neonatology, Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wenqing Kang
- Department of Neonatology, Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases1, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jitao Zhu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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10
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Li M, Chen X, Chen H, Hu L, Cao Y, Cheng G, Wang L, Wu B, Lu W, Yang L, Zhou W. Genetic background and clinical characteristics of infantile hyperammonemia. Transl Pediatr 2023; 12:882-889. [PMID: 37305718 PMCID: PMC10248927 DOI: 10.21037/tp-22-359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/15/2023] [Indexed: 06/13/2023] Open
Abstract
Background This study was conducted to analyze the genetic spectrum and clinical characteristics of infantile hyperammonemia. Methods Between January 2016 and June 2020, we retrospectively enrolled infantile hyperammonemia patients with definitive genetic diagnosis at the Children's Hospital of Fudan University. Based on the age of hyperammonemia onset, patients were grouped into neonatal and post-neonatal subgroups to compare their genetic and clinical features. Results Collectively, 136 pathogenic or likely pathogenic variants of the 33 genes were identified. Fourteen genes were reported with hyperammonemia (42%, 14/33), with SLC25A13 and MUT being the top two detected genes. In contrast, 19 genes, which have not been previously reported with hyperammonemia, were detected (58%, 19/33), in which JAG1 and ABCC8 were the most frequently mutated genes. Compared with post-neonatal hyperammonemia, neonatal patients with hyperammonemia presented with higher rates of organic acidemia (P=0.001) and fatty acid oxidation disorder (P=0.006), but a lower rate of cholestasis (P<0.001). Patients with neonatal hyperammonemia had a higher ratio of peak plasma ammonia level ≥500 µmol/L (P=0.003) and were more likely to receive precision medicine (P=0.027); however, they had a refractory clinical course (P=0.001) and poorer prognosis than the infantile group. Conclusions There were significant differences in the genetic spectrum, clinical features, clinical course, and outcomes between infants with different hyperammonemia onset ages.
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Affiliation(s)
- Mengyao Li
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xiang Chen
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Huiyao Chen
- Clinical Genetic Center, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Clinical Genetic Center, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wei Lu
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Clinical Genetic Center, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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11
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Chen X, Chen Y, Yan K, Chen H, Qin Q, Yang L, Liu B, Cheng G, Cao Y, Wu B, Dong X, Qiao Z, Zhou W. Genetic background of idiopathic neurodevelopmental delay patients with significant brain deviation volume. Chin Med J (Engl) 2023; 136:807-814. [PMID: 36806579 PMCID: PMC10150856 DOI: 10.1097/cm9.0000000000002297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Significant brain volume deviation is an essential phenotype in children with neurodevelopmental delay (NDD), but its genetic basis has not been fully characterized. This study attempted to analyze the genetic factors associated with significant whole-brain deviation volume (WBDV). METHODS We established a reference curve based on 4222 subjects ranging in age from the first postnatal day to 18 years. We recruited only NDD patients without acquired etiologies or positive genetic results. Cranial magnetic resonance imaging (MRI) and clinical exome sequencing (2742 genes) data were acquired. A genetic burden test was performed, and the results were compared between patients with and without significant WBDV. Literature review analyses and BrainSpan analysis based on the human brain developmental transcriptome were performed to detect the potential role of genetic risk factors in human brain development. RESULTS We recruited a total of 253 NDD patients. Among them, 26 had significantly decreased WBDV (<-2 standard deviations [SDs]), and 14 had significantly increased WBDV (>+2 SDs). NDD patients with significant WBDV had higher rates of motor development delay (49.8% [106/213] vs . 75.0% [30/40], P = 0.003) than patients without significant WBDV. Genetic burden analyses found 30 genes with an increased allele frequency of rare variants in patients with significant WBDV. Analyses of the literature further demonstrated that these genes were not randomly identified: burden genes were more related to the brain development than background genes ( P = 1.656e -9 ). In seven human brain regions related to motor development, we observed burden genes had higher expression before 37-week gestational age than postnatal stages. Functional analyses found that burden genes were enriched in embryonic brain development, with positive regulation of synaptic growth at the neuromuscular junction, positive regulation of deoxyribonucleic acid templated transcription, and response to hormone, and these genes were shown to be expressed in neural progenitors. Based on single cell sequencing analyses, we found TUBB2B gene had elevated expression levels in neural progenitor cells, interneuron, and excitatory neuron and SOX15 had high expression in interneuron and excitatory neuron. CONCLUSION Idiopathic NDD patients with significant brain volume changes detected by MRI had an increased prevalence of motor development delay, which could be explained by the genetic differences characterized herein.
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Affiliation(s)
- Xiang Chen
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yuxi Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Kai Yan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Huiyao Chen
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Qian Qin
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Bo Liu
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Xinran Dong
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Zhongwei Qiao
- Department of Radiology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200433, China
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12
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Xiao T, Dong X, Lu Y, Zhou W. High-Resolution and Multidimensional Phenotypes Can Complement Genomics Data to Diagnose Diseases in the Neonatal Population. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:204-215. [PMID: 37197647 PMCID: PMC10110825 DOI: 10.1007/s43657-022-00071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 05/19/2023]
Abstract
Advances in genomic medicine have greatly improved our understanding of human diseases. However, phenome is not well understood. High-resolution and multidimensional phenotypes have shed light on the mechanisms underlying neonatal diseases in greater details and have the potential to optimize clinical strategies. In this review, we first highlight the value of analyzing traditional phenotypes using a data science approach in the neonatal population. We then discuss recent research on high-resolution, multidimensional, and structured phenotypes in neonatal critical diseases. Finally, we briefly introduce current technologies available for the analysis of multidimensional data and the value that can be provided by integrating these data into clinical practice. In summary, a time series of multidimensional phenome can improve our understanding of disease mechanisms and diagnostic decision-making, stratify patients, and provide clinicians with optimized strategies for therapeutic intervention; however, the available technologies for collecting multidimensional data and the best platform for connecting multiple modalities should be considered.
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Affiliation(s)
- Tiantian Xiao
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Department of Neonatology, Chengdu Women’s and Children’s Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610000 China
| | - Xinran Dong
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
| | - Wenhao Zhou
- Division of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai, 201102 China
- Center for Molecular Medicine, Pediatric Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102 China
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13
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Wang H, Xiao F, Qian Y, Wu B, Dong X, Lu Y, Cheng G, Wang L, Yan K, Yang L, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen D, Yin Z, Yang L, Ni Q, Liu R, Li G, Zhang P, Li X, Peng X, Wang Y, Chen H, Ma X, Liu F, Cao Y, Huang G, Zhou W. Genetic architecture in neonatal intensive care unit patients with congenital heart defects: a retrospective study from the China Neonatal Genomes Project. J Med Genet 2023; 60:247-253. [PMID: 35595280 DOI: 10.1136/jmedgenet-2021-108354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/02/2022] [Indexed: 11/03/2022]
Abstract
BACKGROUND Congenital heart defects (CHDs) are the most common type of birth defects. The genetic aetiology of CHD is complex and incompletely understood. The overall distribution of genetic causes in patients with CHD from neonatal intensive care units (NICUs) needs to be studied. METHODS CHD cases were extracted from the China Neonatal Genomes Project (2016-2021). Next-generation sequencing results and medical records were retrospectively evaluated to note the frequency of genetic diagnosis and the respective patient outcomes. RESULTS In total, 1795 patients were included. The human phenotype ontology term of atrial septal defect, patent ductus arteriosus and ventricular septal defect account for a large portion of the CHD subtype. Co-occurring extracardiac anomalies were observed in 35.1% of patients. 269 of the cases received genetic diagnoses that could explain the phenotype of CHDs, including 172 copy number variations and 97 pathogenic variants. The detection rate of trio-whole-exome sequencing was higher than clinical exome sequencing (21.8% vs 14.5%, p<0.05). Further follow-up analysis showed the genetic diagnostic rate was higher in the deceased group than in the surviving group (29.0% vs 11.9%, p<0.05). CONCLUSION This is the largest cohort study to explore the genetic spectrum of patients with CHD in the NICU in China. Our findings may benefit future work on improving genetic screening and counselling for NICU patients with CHD.
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Affiliation(s)
- Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Kai Yan
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liping Chen
- Department of Neonatology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Wenqing Kang
- Department of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, China
| | - Long Li
- Department of Neonatology, The People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China
| | - Xinnian Pan
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Qiufen Wei
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Deyi Zhuang
- Department of Pediatrics, Xiamen Children's Hospital, Xiamen, Fujian, China
| | - Dongmei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, China
| | - Zhaoqing Yin
- Department of Neonatology, The People's Hospital of Dehong, Dehong, Yunnan, China
| | - Ling Yang
- Department of Neonatology, Hainan Women and Children's Medical Center, Haikou, Hainan, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xu Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaojing Ma
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Fang Liu
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoying Huang
- Cardiovascular Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China .,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China .,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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14
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Zhu J, Li W, Yu S, Lu W, Xu Q, Wang S, Qian Y, Guo Q, Xu S, Wang Y, Zhang P, Zhao X, Ni Q, Liu R, Li X, Wu B, Zhou S, Wang H. Further delineation of EBF3-related syndromic neurodevelopmental disorder in twelve Chinese patients. Front Pediatr 2023; 11:1091532. [PMID: 36937983 PMCID: PMC10020332 DOI: 10.3389/fped.2023.1091532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) have heterogeneity in both clinical characteristics and genetic factors. EBF3 is a recently discovered gene associated with a syndromic form of NDDs characterized by hypotonia, ataxia and facial features. In this study, we report twelve unrelated individuals with EBF3 variants using next-generation sequencing. Five missense variants (four novel variants and one known variant) and seven copy number variations (CNVs) of EBF3 gene were identified. All of these patients exhibited developmental delay/intellectual disability. Ataxia was observed in 33% (6/9) of the patients, and abnormal muscle tone was observed in 55% (6/11) of the patients. Aberrant MRI reports were noted in 64% (7/11) of the patients. Four novel missense variants were all located in the DNA-binding domain. The pathogenicity of these variants was validated by in vitro experiments. We found that the subcellular protein localization of the R152C and F211L mutants was changed, and the distribution pattern of the R163G mutant was changed from even to granular. Luciferase assay results showed that the four EBF3 mutants' transcriptional activities were all significantly decreased (p < 0.01). Our study further expanded the gene mutation spectrum of EBF3-related NDD.
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Affiliation(s)
- Jitao Zhu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhui Li
- Neurology Department, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Sha Yu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qiong Xu
- Department of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qiufang Guo
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Suzhen Xu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xuemei Zhao
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xu Li
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
| | - Shuizhen Zhou
- Neurology Department, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Correspondence: Bingbing Wu Shuizhen Zhou Huijun Wang
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15
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Overcoming the Pitfalls of Next-Generation Sequencing-Based Molecular Diagnosis of Shwachman-Diamond Syndrome. J Mol Diagn 2022; 24:1240-1253. [PMID: 36162759 DOI: 10.1016/j.jmoldx.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 07/30/2022] [Accepted: 09/09/2022] [Indexed: 01/13/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is the second most common cause of exocrine pancreatic insufficiency, and 90% of patients carry mutations in the SBDS gene, the most common being the c.183_184delinsCT and c.258+2T>C variants. However, precise detection of these most contributory variants by conventional short-read next-generation sequencing data analysis is limited because of the SBDS/SBDSP1 highly homologous sequences. In this study, an efficient approach was established to infer the haplotype of SBDS based on the expectation-maximization algorithm. The workflow was retrospectively applied to detect the two most common SBDS variants in a Chinese SDS high-risk cohort, and a systematic comparison of variant detection results was performed between the workflow and conventional next-generation sequencing analysis based on Sanger sequencing validation. Among the Chinese SDS high-risk cohort (n = 47) and their available parents (n = 64), the established workflow improved the diagnostic rate for these two variants by 27.7% (95% CI, 15.6%-42.6%) compared with conventional analysis. For overall variant detection, the established workflow achieved 100% (95% CI, 92.5%-100%) concordance with Sanger sequencing, whereas conventional analysis showed only 65.8% accuracy; these results included 25.2% with missed variant calls, 7.2% with diagnosed but inaccurate variant calls, and 1.8% with false-positive calls. With its favorable result in both SDS patient diagnosis and carrier detection performance, the provided workflow showed its potential in clinical application for SDS molecular diagnosis.
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16
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Dong X, Xiao T, Chen B, Lu Y, Zhou W. Precision medicine via the integration of phenotype-genotype information in neonatal genome project. FUNDAMENTAL RESEARCH 2022; 2:873-884. [PMID: 38933389 PMCID: PMC11197532 DOI: 10.1016/j.fmre.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
The explosion of next-generation sequencing (NGS) has enabled the widespread use of genomic data in precision medicine. Currently, several neonatal genome projects have emerged to explore the advantages of NGS to diagnose or screen for rare genetic disorders. These projects have made remarkable achievements, but still the genome data could be further explored with the assistance of phenotype collection. In contrast, longitudinal birth cohorts are great examples to record and apply phenotypic information in clinical studies starting at the neonatal period, especially the trajectory analyses for health development or disease progression. It is obvious that efficient integration of genotype and phenotype benefits not only the clinical management of rare genetic disorders but also the risk assessment of complex diseases. Here, we first summarize the recent neonatal genome projects as well as some longitudinal birth cohorts. Then, we propose two simplified strategies by integrating genotypic and phenotypic information in precision medicine based on current studies. Finally, research collaborations, sociological issues, and future perspectives are discussed. How to maximize neonatal genomic information to benefit the pediatric population remains an area in need of more research and effort.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Tiantian Xiao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610066, China
| | - Bin Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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17
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Xiao H, Zhang JT, Dong XR, Lu YL, Wu BB, Wang HJ, Zhao ZY, Yang L, Zhou WH. Secondary genomic findings in the 2020 China Neonatal Genomes Project participants. World J Pediatr 2022; 18:687-694. [PMID: 35727495 DOI: 10.1007/s12519-022-00558-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 04/19/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND During next generation sequencing (NGS) data interpretation in critically ill newborns, there is a potential for recognizing and reporting secondary findings (SFs). Early awareness of SFs may provide clues for disease prevention. In this study, we assessed the frequency of SFs in the China Neonatal Genomes Project (CNGP) participants. METHODS A total of 2020 clinical exome sequencing (CES) datasets were screened for variants from a list of 59 genes recommended by the American College of Medical Genetics and Genomics (ACMG) for secondary findings reporting v2.0 (ACMG SF v2.0). Identified variants were classified according to the evidence-based guidelines reached by a joint consensus of the ACMG and the Association for Molecular Pathology (AMP). RESULTS Among the 2020 CES datasets, we identified 23 ACMG-reportable genes in 61 individuals, resulting in an overall frequency of SFs at 3.02%. A total of 53 unique variants were identified, including 35 pathogenic and 18 likely pathogenic variants. The common disease categories of SFs associated were cardiovascular and cancer disease. The SF results affected the medical management and follow-up strategy in 49 (80.3%) patients. CONCLUSIONS We presented the frequency of SFs and their impact on clinical management strategies in CNGP participants. Our study demonstrated that SFs have important practical value in disease prevention and intervention at an early stage.
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Affiliation(s)
- Hui Xiao
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Jian-Tao Zhang
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xin-Ran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yu-Lan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Bing-Bing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Hui-Jun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Zheng-Yan Zhao
- Department of Child Health Care, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lin Yang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China. .,Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, China.
| | - Wen-Hao Zhou
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China. .,Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China.
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18
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Chen J, Zhang P, Peng M, Liu B, Wang X, Du S, Lu Y, Mu X, Lu Y, Wang S, Wu Y. An additional whole-exome sequencing study in 102 panel-undiagnosed patients: A retrospective study in a Chinese craniosynostosis cohort. Front Genet 2022; 13:967688. [PMID: 36118902 PMCID: PMC9481236 DOI: 10.3389/fgene.2022.967688] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Craniosynostosis (CRS) is a disease with prematurely fused cranial sutures. In the last decade, the whole-exome sequencing (WES) was widely used in Caucasian populations. The WES largely contributed in genetic diagnosis and exploration on new genetic mechanisms of CRS. In this study, we enrolled 264 CRS patients in China. After a 17-gene-panel sequencing designed in the previous study, 139 patients were identified with pathogenic/likely pathogenic (P/LP) variants according to the ACMG guideline as positive genetic diagnosis. WES was then performed on 102 patients with negative genetic diagnosis by panel. Ten P/LP variants were additionally identified in ten patients, increasing the genetic diagnostic yield by 3.8% (10/264). The novel variants in ANKH, H1-4, EIF5A, SOX6, and ARID1B expanded the mutation spectra of CRS. Then we designed a compatible research pipeline (RP) for further exploration. The RP could detect all seven P/LP SNVs and InDels identified above, in addition to 15 candidate variants found in 13 patients with worthy of further study. In sum, the 17-gene panel and WES identified positive genetic diagnosis for 56.4% patients (149/264) in 16 genes. At last, in our estimation, the genetic testing strategy of “Panel-first” saves 24.3% of the cost compared with “WES only”, suggesting the “Panel-first” is an economical strategy.
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Affiliation(s)
- Jieyi Chen
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Fudan University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Meifang Peng
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics & Endocrinology, Shanghai Ninth People’s Hospital, State Key Laboratory of Medical Genomics, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiao Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
| | - Siyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yao Lu
- School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiongzheng Mu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Pediatrics Research Institute, Children’s Hospital of Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
| | - Yingzhi Wu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Yingzhi Wu, ; Sijia Wang, ; Yulan Lu,
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19
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Li ZD, Abuduxikuer K, Wang L, Hao CZ, Zhang J, Wang MX, Li LT, Qiu YL, Xie XB, Lu Y, Wang JS. Defining pathogenicity of NOTCH2 variants for diagnosis of Alagille syndrome type 2 using a large cohort of patients. Liver Int 2022; 42:1836-1848. [PMID: 35567760 DOI: 10.1111/liv.15292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/09/2022] [Accepted: 05/09/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Alagille syndrome (ALGS) type 2 caused by mutations in NOTCH2 has genotypic and phenotypic heterogeneity. Diagnosis in some atypical patients with isolated hepatic presentation could be missed. METHODS Using 2087 patients with paediatric liver manifestations, NOTCH2 allele frequencies, in-silico prediction, protein domains and clinical features were analysed to define the pathogenicity of NOTCH2 variants for diagnosis of ALGS type 2. RESULTS Among 2087 patients with paediatric liver manifestations, significantly more NOTCH2 variants were absent in gnomAD in patients with elevated γ-glutamyltransferase (GGT) (p = .041). Significantly more NOTCH2 variants which were absent in gnomAD were located in protein functional domains (p = .038). When missense variants were absent in gnomAD and predicted to be pathogenic by at least three out of seven in-silico tools, they were found to be significantly associated with liver manifestations with elevated GGT (p = .003). Comparing this to patients with likely benign (LB) variants, the patients with likely-pathogenic (LP) variants have significantly more liver manifestations with elevated GGT (p = .0001). Significantly more patients with LP variants had extra-hepatic phenotypes of ALGS compared with those patients with LB variants (p = .0004). CONCLUSION When NOTCH2 variants are absent in gnomAD, null variants and missense variants which were predicted to be pathogenic by at least three in-silico tools could be considered pathogenic in patients with high GGT chronic liver diseases.
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Affiliation(s)
- Zhong-Die Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Kuerbanjiang Abuduxikuer
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Li Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Chen-Zhi Hao
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Jing Zhang
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Meng-Xuan Wang
- Department of Pediatrics, Jinshan Hospital, Fudan University, Shanghai, China
| | - Li-Ting Li
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yi-Ling Qiu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Xin-Bao Xie
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Lu
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China
| | - Jian-She Wang
- The Center for Pediatric Liver Diseases, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defect, Shanghai, China
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20
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Chromosomal abnormalities related to fever of unknown origin in a Chinese pediatric cohort and literature review. Orphanet J Rare Dis 2022; 17:292. [PMID: 35897075 PMCID: PMC9327306 DOI: 10.1186/s13023-022-02444-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fever of unknown origin (FUO) has been difficult to diagnose in pediatric clinical practice. With the gradual change in the disease spectrum, genetic factors have received increasing attention. Limited studies have shown an association between FUO and chromosomal abnormalities. In this study, we investigated the clinical and genetic characteristics of patients with FUO presenting with chromosomal abnormalities in a Chinese pediatric cohort. RESULTS Chromosomal abnormalities were detected in 5.5% (8/145) of the patients with FUO. Six patients with inflammatory fever presented with pharyngitis/amygdalitis (4/6), oral aphthous ulcer (2/6), digestive symptoms (3/6), developmental delay (4/6) and elevated C-reactive protein levels (6/6) during fever. These patients were often considered to have systemic inflammatory diseases, such as Behcet's disease or systemic juvenile idiopathic arthritis. Trisomy 8, 7q11.23 dup, 3p26.3-p26.1 del/17q12 dup, 22q11.21 del, and 6q23.3-q24.1 del were identified in patients with inflammatory fever. The TNFAIP3 gene was included in the 6q23.3-q24.1 deletion fragment. Two patients with central fever were characterized by facial anomalies, developmental delay, seizures and no response to antipyretic drugs and were identified as carrying the de novo 18q22.3-q23 del. By performing a literature review, an additional 19 patients who had FUO and chromosomal abnormalities were identified. Trisomy 8, 6q23.2-q24.3 del and 18q22.3-q23 del were reported to present as fever, similar to the findings of our study. CONCLUSIONS We emphasized the important role of detecting chromosomal abnormalities in patients with FUO, especially in patients with systemic inflammatory manifestations or developmental delay. Identifying chromosomal abnormalities may change the diagnosis and management of patients with FUO.
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21
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Xiao T, Wang J, Wang H, Mei H, Dong X, Lu Y, Cheng G, Wang L, Hu L, Lu W, Ni Q, Li G, Zhang P, Qian Y, Li X, Peng X, Wang Y, Shen C, Chen G, Dou YL, Cao Y, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen DM, Yin Z, Wang J, Yang L, Wu B, Zhou W. Aetiology and outcomes of prolonged neonatal jaundice in tertiary centres: data from the China Neonatal Genome Project. Arch Dis Child Fetal Neonatal Ed 2022; 108:fetalneonatal-2021-323413. [PMID: 35851034 DOI: 10.1136/archdischild-2021-323413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/22/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To investigate the distribution of aetiologies and outcomes in neonates with prolonged neonatal jaundice. DESIGN An observational study. SETTING Multiple tertiary centres from the China Neonatal Genome Project. PATIENTS Term infants with jaundice lasting more than 14 days or preterm infants with jaundice lasting more than 21 days were recruited between 1 June 2016 and 30 June 2020. MAIN OUTCOME MEASURES Aetiology and outcomes were recorded from neonates with prolonged unconjugated hyperbilirubinaemia (PUCHB) and prolonged conjugated hyperbilirubinaemia (PCHB). RESULTS A total of 939 neonates were enrolled, and known aetiologies were identified in 84.1% of neonates (790 of 939). Among 411 neonates with PCHB, genetic disorders (27.2%, 112 of 411) were the leading aetiologies. There were 8 deceased neonates, 19 neonates with liver failure and 12 with neurodevelopmental delay. Among 528 neonates with PUCHB, a genetic aetiology was identified in 2 of 219 neonates (0.9%) who showed disappearance of jaundice within 4 weeks of age and in 32 of 309 neonates (10.4%) with persistent jaundice after 4 weeks of age. A total of 96 of 181 neonates (53.0%) who received genetic diagnoses had their clinical diagnosis modified as a result of the genetic diagnoses. CONCLUSION Known aetiologies were identified in approximately 80% of neonates in our cohort, and their overall outcomes were favourable. Genetic aetiology should be considered a priority in neonates with PCHB or the persistence of jaundice after 4 weeks of age. Moreover, genetic data can modify the clinical diagnosis and guide disease management, potentially improving outcomes.
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Affiliation(s)
- Tiantian Xiao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Hongfang Mei
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Qi Ni
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Gang Li
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Yanyan Qian
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Xu Li
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Xiaomin Peng
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Yao Wang
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Chun Shen
- Department of Pediatric Surgery, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Gong Chen
- Department of Pediatric Surgery, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Ya-Lan Dou
- Department of Clinical Epidemiology and Clinical Trial Unit, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liping Chen
- Department of Neonatology, Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Wenqing Kang
- Department of Neonatology, Children's Hospital of Zhengzhou University, Zhengzhou, China
| | - Long Li
- Department of Neonatology, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang, China
| | - Xinnian Pan
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiufen Wei
- Department of Neonatology, Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Deyi Zhuang
- Department of Pediatrics, Xiamen Children's Hospital, Xiamen, China
| | - Dong-Mei Chen
- Department of Neonatal Intensive Care Unit, Quanzhou Maternity and Children's Hospital, Quanzhou, China
| | - Zhaoqing Yin
- Department of Neonatology, The People's Hospital of Dehong, Yunnan, China
| | - Jianshe Wang
- The Centre for Pediatric Liver Diseases, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Centre for Molecular Medicine, Children's Hospital of Fudan University,National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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22
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Phenotypic and Genotypic Spectrum of Early-Onset Developmental and Epileptic Encephalopathies-Data from a Romanian Cohort. Genes (Basel) 2022; 13:genes13071253. [PMID: 35886038 PMCID: PMC9322987 DOI: 10.3390/genes13071253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Early-onset developmental epileptic encephalopathy (DEE) refers to an age-specific, diverse group of epilepsy syndromes with electroclinical anomalies that are associated with severe cognitive, behavioral, and developmental impairments. Genetic DEEs have heterogeneous etiologies. This study includes 36 Romanian patients referred to the Regional Centre for Medical Genetics Dolj for genetic testing between 2017 and 2020. The patients had been admitted to and clinically evaluated at Doctor Victor Gomoiu Children’s Hospital and Prof. Dr. Alexandru Obregia Psychiatry Hospital in Bucharest. Panel testing was performed using the Illumina® TruSight™ One “clinical exome” (4811 genes), and the analysis focused on the known genes reported in DEEs and clinical concordance. The overall diagnostic rate was 25% (9/36 cases). Seven cases were diagnosed with Dravet syndrome (likely pathogenic/pathogenic variants in SCN1A) and two with Genetic Epilepsy with Febrile Seizures Plus (SCN1B). For the diagnosed patients, seizure onset was <1 year, and the seizure type was generalized tonic-clonic. Four additional plausible variants of unknown significance in SCN2A, SCN9A, and SLC2A1 correlated with the reported phenotype. Overall, we are reporting seven novel variants. Comprehensive clinical phenotyping is crucial for variant interpretation. Genetic assessment of patients with severe early-onset DEE can be a powerful diagnostic tool for clinicians, with implications for the management and counseling of the patients and their families.
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23
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Zhu Y, Hu L, Yang L, Wang L, Lu Y, Dong X, Xiao T, Xu Z, Wu B, Zhou W. Association Between Expanded Genomic Sequencing Combined With Hearing Screening and Detection of Hearing Loss Among Newborns in a Neonatal Intensive Care Unit. JAMA Netw Open 2022; 5:e2220986. [PMID: 35816303 PMCID: PMC9274323 DOI: 10.1001/jamanetworkopen.2022.20986] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
IMPORTANCE Hearing loss is a global social burden. Early identification of hearing loss missed by newborn hearing screening tests in the neonatal intensive care unit is crucial. OBJECTIVE To assess the association between expanded genomic sequencing combined with hearing screening and detection of hearing loss as well as improvement in the neonatal intensive care unit. DESIGN, SETTING, AND PARTICIPANTS This cohort study was performed between August 8, 2016, and December 31, 2020, among 8078 newborns admitted to the neonatal intensive care unit of the Children's Hospital of Fudan University in Shanghai, China. Follow-up for hearing status was performed via telephone interviews between September 1 and November 30, 2021. EXPOSURES A hearing screening test and the expanded genomic sequencing targeting 2742 genes were administered to each patient. Those who failed the hearing screening test or had positive genetic findings were referred for diagnostic audiometry at a median of 3 months of age. MAIN OUTCOMES AND MEASURES The primary outcome was hearing loss missed by hearing screening test. Secondary outcomes were genetic findings and benefits associated with the expanded genomic sequencing for clinical management of patients in the neonatal intensive care unit. RESULTS Of 8078 patients (4666 boys [57.8%]; median age, 6.3 days [IQR, 3.0-12.0 days]), 52 of 240 (21.7%) received a diagnosis of hearing loss. Expanded genomic sequencing combined with hearing screening was associated with a 15.6% increase (7 of 45 patients) in cases of diagnosed hearing loss that were missed by hearing screening. Of the 52 patients with hearing loss, genetic factors were identified for 39 patients (75.0%); GJB2 and SLC26A4 were the most common genes identified. Patients with genetic findings experienced a more severe degree of hearing loss than those without genetic findings (21 profound, 4 severe, 7 moderate, and 7 mild vs 2 severe, 4 moderate, and 7 mild; P = .005), with more bilateral hearing loss (39 of 39 [100%] vs 9 of 13 [69.2%]; P = .003). Clinical management strategies were changed for patients who underwent genomic sequencing combined with hearing screening. CONCLUSIONS AND RELEVANCE This study suggests that expanded genomic sequencing combined with hearing screening may be effective at detecting hearing loss among patients in the neonatal intensive care unit.
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Affiliation(s)
- Yunqian Zhu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tiantian Xiao
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Zhengmin Xu
- Department of Otolaryngology–Head and Neck Surgery, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
- Key Laboratory of Neonatal Diseases, Ministry of Health, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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Hu C, He L, Li H, Ding Y, Zhang K, Li D, Zhu G, Wu B, Xu X, Xu Q. Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China. Genes (Basel) 2022; 13:genes13061010. [PMID: 35741772 PMCID: PMC9222325 DOI: 10.3390/genes13061010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 12/03/2022] Open
Abstract
Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder in which genetics play a major role. Molecular diagnosis may lead to a more accurate prognosis, improved clinical management, and potential treatment of the condition. Both copy number variations (CNVs) and single nucleotide variations (SNVs) have been reported to contribute to the genetic etiology of ASD. The effectiveness and validity of clinical targeted panel sequencing (CTPS) designed to analyze both CNVs and SNVs can be evaluated in different ASD cohorts. CTPS was performed on 573 patients with the diagnosis of ASD. Medical records of positive CTPS cases were further reviewed and analyzed. Additional medical examinations were performed for a group of selective cases. Positive molecular findings were confirmed by orthogonal methods. The overall positive rate was 19.16% (109/569) in our cohort. About 13.89% (79/569) and 4.40% (25/569) of cases had SNVs only and CNVs only findings, respectively, while 0.9% (5/569) of cases had both SNV and CNV findings. For cases with SNVs findings, the SHANK3 gene has the greatest number of reportable variants, followed by gene MYT1L. Patients with MYT1L variants share common and specific clinical characteristics. We found a child with compound heterozygous SLC26A4 variants had an enlarged vestibular aqueduct syndrome and autistic phenotype. Our results showed that CTPS is an effective molecular diagnostic tool for ASD. Thorough clinical and genetic evaluation of ASD can lead to more accurate diagnosis and better management of the condition.
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Affiliation(s)
- Chunchun Hu
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Linlin He
- Pediatric Department, Suining Central Hospital, Suining 629000, China;
| | - Huiping Li
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Yanhua Ding
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Kaifeng Zhang
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Dongyun Li
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Guoqing Zhu
- Pediatric Department, Binzhou Peoples’ Hospital, Binzhou 256600, China;
| | - Bingbing Wu
- Clinical Genetic Center, Children’s Hospital of Fudan University, Shanghai 201102, China;
| | - Xiu Xu
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
| | - Qiong Xu
- Department of Child Health Care, Children’s Hospital of Fudan University, Shanghai 201102, China; (C.H.); (H.L.); (Y.D.); (K.Z.); (D.L.); (X.X.)
- Correspondence:
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Yang L, Mei H, Lu Y, Zhou W. Reply. J Pediatr 2022; 245:252-253. [PMID: 35346716 DOI: 10.1016/j.jpeds.2022.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Affiliation(s)
| | | | | | - Wenhao Zhou
- Clinical Genetic Center; Department of Neonatology; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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The Benefit of Multigene Panel Testing for the Diagnosis and Management of the Genetic Epilepsies. Genes (Basel) 2022; 13:genes13050872. [PMID: 35627257 PMCID: PMC9141259 DOI: 10.3390/genes13050872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
With the increasing use of genetic testing in pediatric epilepsy, it is important to describe the diagnostic outcomes as they relate to clinical care. The goal of this study was to assess the diagnostic yield and impact on patient care of genetic epilepsy panel testing. We conducted a retrospective chart review of patients at the Children’s Hospital of Eastern Ontario (CHEO) who had genetic testing between the years of 2013–2020. We identified 227 patients that met criteria for inclusion. The majority of patients had their testing performed as “out-of-province” tests since province-based testing during this period was limited. The diagnostic yield for multi-gene epilepsy panel testing was 17% (39/227) and consistent with the literature. Variants of unknown significance (VUS) were reported in a significant number of undiagnosed individuals (77%; 128/163). A higher diagnostic rate was observed in patients with a younger age of onset of seizures (before one year of age; 32%; 29/90). A genetic diagnosis informed prognosis, recurrence risk counselling and expedited access to resources in all those with a diagnosis. A direct change in clinical management as a result of the molecular diagnosis was evident for 9% (20/227) of patients. The information gathered in this study provides evidence of the clinical benefits of genetic testing in epilepsy and serves as a benchmark for comparison with the current provincial Ontario Epilepsy Genetic Testing Program (OEGTP) that began in 2020.
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Shawahna R, Zaid L. Caring for women with epilepsy in Palestine: A qualitative study of the current status. Epilepsy Behav 2022; 130:108689. [PMID: 35398722 DOI: 10.1016/j.yebeh.2022.108689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/26/2022] [Accepted: 03/26/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE This qualitative study was conducted to explore the current status of caring for women with epilepsy (WWE) in the Palestinian healthcare system. METHODS This study used an explorative qualitative design. A purposive sampling technique was used to recruit the participants. Semi-structured in-depth interviews were conducted with neurologists (n = 6), gynecologists (n = 5), psychiatrists (n = 3), an internist (n = 1), and clinical pharmacists (n = 5). The interpretive description methodology was used to thematically analyze the qualitative data. RESULTS A total of 745 min (12.4 h) of interview time were analyzed. The qualitative data collected in this study were categorized under 3 major themes and multiple subthemes. The 3 major themes were: (1) diagnosis and care for patients with epilepsy, (2) general issues in caring for patients with epilepsy, and (3) consideration of women's issues in the pharmacotherapy of epilepsy. Formally adopted protocols/criteria for the diagnosis and care for WWE were lacking. CONCLUSION Findings of this qualitative study showed a need to formally adopt uniform guidelines that can guide the diagnosis and care of WWE in the Palestinian healthcare system. The findings of this study might be informative to healthcare providers, decision-makers in healthcare authorities, WWE, and patient advocacy groups who could be interested in improving and benchmarking healthcare services provided to WWE. Future studies are still needed to quantitatively measure adherence to the international guidelines in caring for WWE.
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Affiliation(s)
- Ramzi Shawahna
- Department of Physiology, Pharmacology and Toxicology, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine; An-Najah BioSciences Unit, Centre for Poisons Control, Chemical and Biological Analyses, An-Najah National University, Nablus, Palestine.
| | - Lina Zaid
- Master of Pharmacology Program, Faculty of Graduate Studies, An-Najah National University, Nablus, Palestine
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Simkin D, Ambrosi C, Marshall KA, Williams LA, Eisenberg J, Gharib M, Dempsey GT, George AL, McManus OB, Kiskinis E. 'Channeling' therapeutic discovery for epileptic encephalopathy through iPSC technologies. Trends Pharmacol Sci 2022; 43:392-405. [PMID: 35427475 PMCID: PMC9119009 DOI: 10.1016/j.tips.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 02/26/2022] [Accepted: 03/01/2022] [Indexed: 12/16/2022]
Abstract
Induced pluripotent stem cell (iPSC) and gene editing technologies have revolutionized the field of in vitro disease modeling, granting us access to disease-pertinent human cells of the central nervous system. These technologies are particularly well suited for the study of diseases with strong monogenic etiologies. Epilepsy is one of the most common neurological disorders in children, with approximately half of all genetic cases caused by mutations in ion channel genes. These channelopathy-associated epilepsies are clinically diverse, mechanistically complex, and hard to treat. Here, we review the genetic links to epilepsy, the opportunities and challenges of iPSC-based approaches for developing in vitro models of channelopathy-associated disorders, the available tools for effective phenotyping of iPSC-derived neurons, and discuss the potential therapeutic approaches for these devastating diseases.
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Affiliation(s)
- Dina Simkin
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Kelly A Marshall
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Jordyn Eisenberg
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mennat Gharib
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Clinical and Genetic Etiologies of Neonatal Unconjugated Hyperbilirubinemia in the China Neonatal Genomes Project. J Pediatr 2022; 243:53-60.e9. [PMID: 34953813 DOI: 10.1016/j.jpeds.2021.12.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 11/09/2021] [Accepted: 12/13/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To investigate the clinical and genetic causes of neonatal unconjugated hyperbilirubinemia. STUDY DESIGN We included 1412 neonates diagnosed with unconjugated hyperbilirubinemia (total serum bilirubin >95 percentile for age), from the China Neonatal Genomes Project between August 2016 and September 2019, in the current study. Clinical data and targeted panel sequencing data on 2742 genes including known unconjugated hyperbilirubinemia genes were analyzed. RESULTS Among the 1412 neonates with unconjugated hyperbilirubinemia, 37% had severe unconjugated hyperbilirubinemia, with total serum bilirubin levels that met the recommendations for exchange transfusion. Known clinical causes were identified for 68% of patients. The most common clinical cause in the mild unconjugated hyperbilirubinemia group was infection (17%) and in the severe group was combined factors (21%, with infection combined with extravascular hemorrhage the most common). A genetic variant was observed in 55 participants (4%), including 45 patients with variants in genes associated with unconjugated hyperbilirubinemia and 10 patients with variants that were regarded as additional genetic findings. Among the 45 patients identified with unconjugated hyperbilirubinemia-related variants, the genes were mainly associated with enzyme deficiencies, metabolic/biochemical disorders, and red blood cell membrane defects. G6PD and UGT1A1 variants, were detected in 34 of the 45 patients (76%). CONCLUSIONS Known clinical causes, which varied with bilirubin levels, were identified in approximately two-thirds of the patients. Genetic findings were identified in 4% of the patients, including in patients with an identified clinical cause, with G6PD and UGT1A1 being the most common genes in which variants were detected.
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30
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Ni Q, Chen X, Zhang P, Yang L, Lu Y, Xiao F, Wu B, Wang H, Zhou W, Dong X. Systematic estimation of cystic fibrosis prevalence in Chinese and genetic spectrum comparison to Caucasians. Orphanet J Rare Dis 2022; 17:129. [PMID: 35313924 PMCID: PMC8935702 DOI: 10.1186/s13023-022-02279-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cystic fibrosis (CF) is a common, life-threatening genetic disease in Caucasians but rarely reported in Chinese population. The prevalence and population-specific genetic spectrum of CF in China needs to be systematically estimated and compared with Caucasians.
Materials and methods We reviewed 30,951 exome-sequencing samples, including 20,909 pediatric patient samples and 10,042 parent samples, from Chinese Children's Rare Disease Genetic Testing Clinical Collaboration System (CCGT). After the in-lab filtration process, 477 candidate variants of CFTR gene were left and 53 variants were manually curated as pathogenic/likely-pathogenic (P/LP). These P/LP variants were adopted to estimate CF prevalence in three methods: the carrier frequency method, the permutation-combinations method and the Bayesian framework method. Allele frequencies of the 477 CFTR variants were compared with non-Finland European (NFE) and East Asian (EAS) from gnomAD database. To investigate the haplotype structure difference of CFTR, another 2067 whole-genome-sequencing samples from CCGT and 195 NFE from 1000 genome project were analyzed by Shapeit4 software. Result With the 53 manually curated P/LP variants in CFTR gene, we excluded individuals identified or suspected with CF and their parents in our cohorts and estimated the Chinese CF prevalence is approximately 1/128,434. Only 21 (39.6%) of the 53 variants were included in Caucasian specific CF screening panels, resulting in significantly under-estimation of CF prevalence in our children cohort (1/143,171 vs. 1/1,387,395, P = 5e−24) and parent’s cohort (1/110,127 vs. 1/872,437, P = 7e−10). The allele frequencies of six pathogenic variants (G970D, D979A, M469V, G622D, L88X, 1898+5G->T) were significantly higher in our cohorts compared with gnomAD-NFE population (all P-value < 0.1). Haplotype analysis showed more haplotype diversity in Chinese compared to Caucasians. In addition, G970D and F508del were founder mutation of Chinese and Caucasians with two SNPs (rs213950-rs1042077) identified as related genotype in exon region. Conclusions Chinese population showed significantly different genetic spectrum pattern in CFTR gene compared with Caucasian population, and thus a Chinese-specific CF screening panel is needed. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02279-9.
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Affiliation(s)
- Qi Ni
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Xiang Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China.,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, Shanghai, People's Republic of China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China
| | - Wenhao Zhou
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China. .,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China. .,Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China.
| | - Xinran Dong
- Children's Hospital and Institutes of Biomedical Sciences, Fudan University, National Children's Medical Center, Shanghai, 201102, People's Republic of China. .,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, People's Republic of China.
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Wang H, Yang L, Wang J. Etiology of neonatal cholestasis after emerging molecular diagnostics. Transl Pediatr 2022; 11:359-367. [PMID: 35378957 PMCID: PMC8976681 DOI: 10.21037/tp-21-503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/30/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In the pediatric group, most cholestatic patients had disease onset at 0-3 months of age, and more and more are found to have specific genetic defects after failing to obtain a definite diagnosis by routine evaluation. To investigate the etiological diagnosis for the newborns with cholestasis during the neonatal period after emerging molecular tests comprehensively. METHODS We conducted a retrospective study to evaluate clinical characteristics, etiologies and outcomes in infants with neonatal cholestasis after emerging molecular diagnostics from January 1st to December 31st, 2019 in Children's Hospital of Fudan University. RESULTS There were 160 cases of neonatal cholestasis with mean gestational age (GA) 32.6±4.8 weeks and birth weight (BW) 1,880±991 g, composing 3.4% of total neonatal admissions in 2019. Overall 97.5% (n=156) patients had a definite diagnosis, including 9 obtaining a genetic diagnosis after adding molecular test in routine evaluation, which made the diagnosis rate for cholestasis increased by 5.6%. The most common etiology of cholestasis in the neonatal period was parenteral nutrition-associated cholestasis (PNAC) 48.8% (n=78), followed by cardiovascular and circulatory disorders 18.1%, biliary anatomic obstruction 12.5%, infection 8.7% and genetic disorders 5.6%. PNAC and biliary anatomic obstruction were the most common etiology of cholestasis for preterm and term infants respectively. The mortality rate is 2.5% (n=4) and 91.9% (n=147) patients totally recovery or improve in follow-up. CONCLUSIONS The causes of cholestasis in neonates are complicated, molecular diagnostics can improve the etiological diagnosis for newborns with cholestasis. But still, quite amount of causes are remediable and transient during the neonatal period, gene test may help to rule out genetic causes and enhance confidence in judging prognosis.
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Affiliation(s)
- Huanhuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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Zhang P, Wu B, Wang Y, Ren Y, Li G, Qan Y, Lei C, Wang H. Identification of Pathogenic Variants in RPGRIP1L with Meckel Syndrome and Preimplantation Genetic Testing in a Chinese Family. Reprod Sci 2022; 29:2200-2207. [PMID: 35233738 DOI: 10.1007/s43032-022-00898-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/19/2022] [Indexed: 10/19/2022]
Abstract
Meckel syndrome (MKS, OMIM:249000) is a severe multiorgan dysplastic lethal ciliopathy with extreme genetic heterogeneity. Defects in RPGRIP1L are the cause of MKS type 5 (MKS5, OMIM:611561). However, only six different variants have been reported in eight MKS5 cases with biallelic variants. Here, we describe the case of a Chinese family with recurrent fetal malformations. The proband was a 14-week gestation fetus with occipital encephalocele, polycystic kidneys, polydactyly, and single ventricular heart. Trio whole-exome sequencing was performed, and two novel compound heterozygous variants of RPGRIP1L (c.427C > T, p.Gln143Ter and c.1351-11A > G) were identified. cDNA studies of the splicing variant demonstrated a reading-frame shift with a subsequent premature stop codon (p.Glu451Serfs*6). After the proband was diagnosed with MKS5, the couple chose preimplantation genetic testing for monogenic disorders (PGT-M) and prenatal genetic diagnosis (PND) to prevent the transmission of pathogenic variants, which led to a successful pregnancy recently. In summary, we have identified two novel variants of RPGRIP1L in a Chinese family, which expand the variant spectrum of MKS5. Furthermore, we have described the successful application of PGT-M and PND in this family. These techniques could assist couples with a genetic predisposition in avoiding the transmission of genetic diseases to their offspring.
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Affiliation(s)
- Ping Zhang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yunyun Ren
- Department of Ultrasound, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Qan
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Caixia Lei
- Prenatal Diagnosis Center, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China. .,Department of Genetics, Shanghai JiAi Genetics & IVF Institute, Shanghai, China.
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.
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Mei H, Yang L, Xiao T, Wang S, Wu B, Wang H, Lu Y, Dong X, Yang H, Zhou W. Genetic Spectrum Identified by Exome Sequencing in a Chinese Pediatric Cerebral Palsy Cohort. J Pediatr 2022; 242:206-212.e6. [PMID: 34788679 DOI: 10.1016/j.jpeds.2021.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To explore the genetic spectrum of cerebral palsy (CP) in a Chinese pediatric cohort. STUDY DESIGN This was a retrospective observational study of patients with CP from the Children's Hospital of Fudan University between June 2015 and December 2019. Their clinical data and exome sequencing data were collected and analyzed. RESULTS A total of 217 patients with CP were enrolled, and genetic variants were identified in 78 subjects (35.9%): 65 patients with single-nucleotide variants (SNVs), 12 patients with copy number variants, and 1 patient with both an SNV and a copy number variant. The genetic diagnosis rates were significantly greater in patients without clinical risk factors than in patients with clinical risk factors (χ2 = 21.705, P = .000) and were significantly greater in patients with a family history than in those without a family history (χ2 = 4.493, P = .034). Variants in genes related to neurologic disorders were the most commonly detected variants, affecting 41 patients (62.1%, 41/66). Among the patients with SNVs detected, the top 12 genes were found to cover 62.1% (41/66) of cases, and 39.4% (26/66) of patients with SNVs had medically actionable genetic findings. CONCLUSIONS The overall genetic diagnostic rate in this study was 35.9%, and patients without any clinical risk factors or with a family history were more likely to have genetic risk factors. The top 12 genes detected in this study as well as genes related to neurologic disorders or other medically actionable disorders should be noted in the analysis of genetic testing results in patients with CP.
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Affiliation(s)
- Hongfang Mei
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Pediatric Endocrinology and Inherited Metabolic Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Tiantian Xiao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Hong Yang
- Department of Rehabilitation, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China; Key Laboratory of Birth Defects, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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34
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Dai D, Mei M, Hu L, Cao Y, Wang X, Wang L, Lu Y, Yang L, Dong X, Wang H, Wu B, Qian L. Prevalence of monogenic disease in paediatric patients with a predominant respiratory phenotype. Arch Dis Child 2022; 107:141-147. [PMID: 34134972 PMCID: PMC8785068 DOI: 10.1136/archdischild-2021-322058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/03/2021] [Indexed: 11/11/2022]
Abstract
OBJECTIVE This study aimed to investigate the prevalence and clinical characteristics of monogenic disease in paediatric patients with a predominant respiratory phenotype. METHODS Exome sequencing was performed in a cohort of 971 children with a predominant respiratory phenotype and suspected genetic aetiology. A total of 140 positive cases were divided into subgroups based on recruitment age and the primary biological system(s) involved. RESULTS There were 140 (14.4%) patients with a positive molecular diagnosis, and their primary clinical manifestations were respiratory distress (12.9%, 18 of 140), respiratory failure (12.9%, 18 of 140) and recurrent/persistent lower respiratory infections (66.4%, 93 of 140). Primary immunodeficiency (49.3%), multisystem malformations/syndromes (17.9%), and genetic lung disease (16.4%) were the three most common genetic causes in the cohort, and they varied among the age subgroups. A total of 72 (51.4%) patients had changes in medical management strategies after genetic diagnosis, and the rate in those with genetic lung disease (82.6%, 19 of 23) was far higher than that in patients with genetic disease with lung involvement (45.3%, 53 of 117) (p=0.001). CONCLUSION Our findings demonstrate that exome sequencing is a valuable diagnostic tool for monogenic diseases in children with a predominant respiratory phenotype, and the genetic spectrum varies with age. Taken together, genetic diagnoses provide invaluable clinical and prognostic information that may also facilitate the development of precision medicine for paediatric patients.
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Affiliation(s)
- Dan Dai
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Mei Mei
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaochuan Wang
- Department of Clinical Immunology, Children's Hospital of Fudan University, Shanghai, China
| | - Libo Wang
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China,Shanghai Key Laboratory of Birth Defects, Shanghai, China
| | - Xinran Dong
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Molecular Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Division of Pulmonary Medicine, Children's Hospital of Fudan University, Shanghai, China .,Shanghai Key Laboratory of Birth Defects, Shanghai, China
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Yao R, Zhou Y, Tang J, Li N, Yu T, He Y, Wang C, Wang J, Wang J. Genetic Diagnosis Spectrum and Multigenic Burden of Exome-Level Rare Variants in a Childhood Epilepsy Cohort. Front Genet 2022; 12:782419. [PMID: 34992632 PMCID: PMC8725238 DOI: 10.3389/fgene.2021.782419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
Childhood epilepsy is a considerably heterogeneous neurological condition with a high worldwide incidence. Genetic diagnosis of childhood epilepsy provides the most accurate pathogenetic evidence; however, a large proportion of highly suspected cases remain undiagnosed. Accumulation of rare variants at the exome level as a multigenic burden contributing to childhood epilepsy should be further evaluated. In this retrospective analysis, exome-level sequencing was used to depict the mutation spectra of 294 childhood epilepsy patients from Shanghai Children’s Medical Center, Department of Neurology. Furthermore, variant information from exome sequencing data was analyzed apart from monogenic diagnostic purposes to elucidate the possible multigenic burden of rare variants related to epilepsy pathogenesis. Exome sequencing reached a diagnostic rate of 30.61% and identified six genes not currently listed in the epilepsy-associated gene list. A multigenic burden study revealed a three-fold possibility that deleterious missense mutations in ion channel and synaptic genes in the undiagnosed cohort may contribute to the genetic risk of childhood epilepsy, whereas variants in the gene categories of cell growth, metabolic, and regulatory function showed no significant difference. Our study provides a comprehensive overview of the genetic diagnosis of a Chinese childhood epilepsy cohort and provides novel insights into the genetic background of these patients. Harmful missense mutations in genes related to ion channels and synapses are most likely to produce a multigenic burden in childhood epilepsy.
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Affiliation(s)
- Ruen Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yunqing Zhou
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Tang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Niu Li
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tingting Yu
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingzhong He
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cuijin Wang
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiwen Wang
- Department of Neurology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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36
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Zhao X, Wu B, Chen H, Zhang P, Qian Y, Peng X, Dong X, Wang Y, Li G, Dong C, Wang H. Case report: A novel truncating variant of BCL11B associated with rare feature of craniosynostosis and global developmental delay. Front Pediatr 2022; 10:982361. [PMID: 36275064 PMCID: PMC9582536 DOI: 10.3389/fped.2022.982361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Craniosynostosis is a premature fusion of cranial sutures, resulting in abnormally shaped skull and brain development disorder. The description of craniosynostosis in patients with BCL11B mutations is rare. Here, we firstly report a 25-month-old Chinese boy with a novel frameshift variant in BCL11B gene. The patient was identified c.2346_2361del by whole-exome sequencing and was confirmed to be de novo by parental Sanger sequencing. This patient presented clinical phenotype of craniosynostosis as well as global developmental delay. He had a small mouth, thin upper lip, arched eyebrows, a long philtrum, midfacial hypoplasia and craniosynostosis. Brain MRI showed brain extracerebral interval and myelination changes, and brain CT with 3D reconstruction showed multi-craniosynostosis. Our study expands the clinical phenotypes of patients with BCL11B gene mutation, and our findings may help guide clinical treatment and family genetic counseling.
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Affiliation(s)
- Xuemei Zhao
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yaqiong Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Chenbin Dong
- Department of Plastic Surgery, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, Shanghai, China
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Hu L, Yang L, Yan K, Wu B, Wang H, Zhang R, Wang J, Cao Y, Cheng G, Zhou W. Importance of Early Genetic Sequencing in Neonates Admitted to NICU with Recurrent Hypernatremia: Results of a Prospective Cohort Study. Neonatology 2022; 119:103-110. [PMID: 34802008 DOI: 10.1159/000519634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/10/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The genetic characteristics in neonates admitted to the NICU with recurrent hypernatremia remained unknown. We aimed to implement early genetic sequencing to identify possible genetic etiologies, optimize the treatment, and improve the outcome. METHODS We prospectively performed exome sequencing or targeted panel sequencing on neonates diagnosed with recurrent hypernatremia (plasma sodium ≥150 mEq/L, ≥2 episodes) from January 1, 2016, to June 30, 2020. RESULTS Among 22,375 neonates admitted to the NICU, approximately 0.33% (73/22,375) developed hypernatremia. The incidence of hypernatremia >14 days and ≤14 days was 0.03% and 0.3%, respectively. Among 38 neonates who had ≥2 hypernatremia episodes, parents of 28 patients consented for sequencing. Genetic diagnosis was achieved in 25% neonates (7/28). Precision medicine treatment was performed in 85.7% (6/7) of the patients, including hydrochlorothiazide and indomethacin for 57.1% (4/7) with arginine vasopressin receptor 2 (AVPR2) deficiency-associated congenital nephrogenic diabetes insipidus; a special diet of fructose formula for 1 patient with solute carrier family 5 member 1 deficiency-associated congenital glucose-galactose malabsorption (1/7, 14.3%); and kallikrein-inhibiting ointment for 1 patient with serine protease inhibitor of Kazal-type 5 deficiency-associated Netherton syndrome (1/7, 14.3%). Only hypernatremia onset age (adjusted odds ratio 1.32 [1.01-1.72], p = 0.040) independently predicted the underlying genetic etiology. The risk of a genetic etiology of hypernatremia was 9.0 times higher for neonates with a hypernatremia onset age ≥17.5 days (95% confidence interval, 1.1-73.2; p = 0.038). CONCLUSIONS Single-gene disorders are common in neonates with recurrent hypernatremia, and >50% of cases are caused by AVPR2 deficiency-associated congenital nephrogenic diabetes insipidus. Early genetic testing can aid the diagnosis of unexplained recurrent neonatal hypernatremia and improve therapy and outcome.
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Affiliation(s)
- Liyuan Hu
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Yan
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, National Children's Medical Center, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects, National Children's Medical Center, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,China Neonatal Genomes Project (CNGP), Shanghai, China
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Xu S, Hu L, Yang L, Wu B, Cao Y, Zhang R, Xu X, Ma H, Zhou W, Cheng G, Zhang P, Hu L. Galloway-Mowat Syndrome Type 3 Caused by OSGEP Gene Variants: A Case Report and Literature Review. Front Pediatr 2022; 10:899991. [PMID: 35783322 PMCID: PMC9249162 DOI: 10.3389/fped.2022.899991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Galloway-Mowat syndrome type 3 (GAMOS3) is an extremely rare and severe autosomal-recessive disease characterized by early-onset nephrotic syndrome (NS), microcephaly and neurological impairment. Reported GAMOS cases have gradually increased since pathogenic OSGEP variants were identified as the aetiology in 2017. METHODS Using whole-exome sequencing and a data analysis process established by Children's Hospital of Fudan University, the clinical and molecular features of 3 infants with OSGEP mutations were summarized. Literature regarding the clinical features of GAMOS3 caused by OSGEP variants was reviewed. RESULTS Thirty-seven individuals (3 from this study) from 34 families were included. Twenty-two different OSGEP variants were identified. The c.740G>A (p.Arg247Gln) variant in OSGEP was detected in 15 families (44%), all from Asia. Most affected individuals (including patients I and II in this study) showed a typical phenotype, including microcephaly (92%) with brain anomalies (97%), developmental delay (81%), congenital NS (54%), and craniofacial (94%) and skeletal dysmorphism (84%). Renal manifestations varied from proteinuria (94%, median onset = 1.5 months) to NS (83%) and end-stage renal disease (48%, 11 months) during follow-up. Patients with congenital NS had a lower survival probability (median survival time = 3 months) than those without congenital NS (78 months) (P < 0.01, log-rank test). CONCLUSION GAMOS3 is a progressive renal-neurological syndrome with a poor prognosis, especially with congenital NS. Microcephaly with dysmorphic features are vital clues to further evaluate renal impairment and brain anomalies. Timely molecular diagnosis is crucial for clinical decision-making, appropriate treatment and genetic counselling.
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Affiliation(s)
- Suhua Xu
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lan Hu
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Xin Xu
- Department of Neonatology, Xiamen Children's Hospital, Xiamen, China
| | - Haiyan Ma
- Department of Neonatology, Zhuhai Women and Children's Hospital, Zhuhai, China
| | - Wenhao Zhou
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Clinical Genetic Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Peng Zhang
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
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Zou D, Wang L, Liao J, Xiao H, Duan J, Zhang T, Li J, Yin Z, Zhou J, Yan H, Huang Y, Zhan N, Yang Y, Ye J, Chen F, Zhu S, Wen F, Guo J. Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study. Brain 2021; 144:3623-3634. [PMID: 34145886 PMCID: PMC8719847 DOI: 10.1093/brain/awab233] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 05/25/2021] [Accepted: 06/05/2021] [Indexed: 02/05/2023] Open
Abstract
The aim of this study is to evaluate the diagnostic value of genome sequencing in children with epilepsy, and to provide genome sequencing-based insights into the molecular genetic mechanisms of epilepsy to help establish accurate diagnoses, design appropriate treatments and assist in genetic counselling. We performed genome sequencing on 320 Chinese children with epilepsy, and interpreted single-nucleotide variants and copy number variants of all samples. The complete pedigree and clinical data of the probands were established and followed up. The clinical phenotypes, treatments, prognoses and genotypes of the patients were analysed. Age at seizure onset ranged from 1 day to 17 years, with a median of 4.3 years. Pathogenic/likely pathogenic variants were found in 117 of the 320 children (36.6%), of whom 93 (29.1%) had single-nucleotide variants, 22 (6.9%) had copy number variants and two had both single-nucleotide variants and copy number variants. Single-nucleotide variants were most frequently found in SCN1A (10/95, 10.5%), which is associated with Dravet syndrome, followed by PRRT2 (8/95, 8.4%), which is associated with benign familial infantile epilepsy, and TSC2 (7/95, 7.4%), which is associated with tuberous sclerosis. Among the copy number variants, there were three with a length <25 kilobases. The most common recurrent copy number variants were 17p13.3 deletions (5/24, 20.8%), 16p11.2 deletions (4/24, 16.7%), and 7q11.23 duplications (2/24, 8.3%), which are associated with epilepsy, developmental retardation and congenital abnormalities. Four particular 16p11.2 deletions and two 15q11.2 deletions were considered to be susceptibility factors contributing to neurodevelopmental disorders associated with epilepsy. The diagnostic yield was 75.0% in patients with seizure onset during the first postnatal month, and gradually decreased in patients with seizure onset at a later age. Forty-two patients (13.1%) were found to be specifically treatable for the underlying genetic cause identified by genome sequencing. Three of them received corresponding targeted therapies and demonstrated favourable prognoses. Genome sequencing provides complete genetic diagnosis, thus enabling individualized treatment and genetic counselling for the parents of the patients. Genome sequencing is expected to become the first choice of methods for genetic testing of patients with epilepsy.
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Affiliation(s)
- Dongfang Zou
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Lin Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | | | - Jing Duan
- Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | | | | | | | - Jing Zhou
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | | | - Ying Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jingyu Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen 518083, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Feiqiu Wen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, China
- Correspondence may also be addressed to: Feiqiu Wen Shenzhen Children’s Hospital No. 7019 Yitian Road, Shenzhen 518038 Guangdong, China E-mail:
| | - Jian Guo
- BGI-Shenzhen, Shenzhen 518083, China
- Correspondence to: Jian Guo BGI-Shenzhen, Beishan Industry Zone Shenzhen 518083, Guangdong, China E-mail:
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Qian Y, Zhou Y, Wu B, Chen H, Xu S, Wang Y, Zhang P, Li G, Xu Q, Zhou W, Xu X, Wang H. Novel Variants of the SMARCA4 Gene Associated with Autistic Features Rather Than Typical Coffin-Siris Syndrome in Eight Chinese Pediatric Patients. J Autism Dev Disord 2021; 52:5033-5041. [PMID: 34813034 DOI: 10.1007/s10803-021-05365-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2021] [Indexed: 11/29/2022]
Abstract
Autism spectrum disorders (ASDs) are a group of neurodevelopmental-related disorders with a high genetic risk. Recently, chromatin remodeling factors have been found to be related to ASDs. SMARCA4 is such a catalytic subunit of the chromatin-remodeling complex. In this report, we identified seven novel missense variants in the SMARCA4 gene from eight pediatric patients. All eight patients had moderate to severe intellectual disability, and seven showed autistic/likely autistic features. Compared with the patients reported in the literature, our patients were less likely to show craniofacial or finger/toe anomalies. Our findings further supported that SMARCA4 is associated with ASDs. We suggest that individuals with the abovementioned phenotypes should consider genetic testing.
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Affiliation(s)
- Yanyan Qian
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yuanfeng Zhou
- Neurology Department, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, 201102, China
| | - Bingbing Wu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Huiyao Chen
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Suzhen Xu
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yao Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Ping Zhang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Gang Li
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Qiong Xu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Wenhao Zhou
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China
| | - Xiu Xu
- Department of Child Health Care, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
| | - Huijun Wang
- Center of Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, 399 Wanyuan Road, Shanghai, 201102, China.
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41
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Five novel copy number variations detected in patients with familial exudative vitreoretinopathy. Mol Vis 2021; 27:632-642. [PMID: 34924743 PMCID: PMC8645187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/18/2021] [Indexed: 11/05/2022] Open
Abstract
Purpose Familial exudative vitreoretinopathy (FEVR) is an inherited retinal vascular disease genetically heterogeneous with multiple causative genes. The aim of this study is to report five novel copy number variation (CNV) regions in FEVR patients and to investigate the possible contributions of novel CNVs to FEVR. Methods In this study, 824 FEVR families were collected. All cases were performed using the targeted next generation sequencing (NGS) assay, and families with no definite pathogenic mutations in FEVR genes were screened for CNVs according to the NGS results. Droplet digital polymerase chain reaction (ddPCR) testing was introduced to validate the screened CNV regions. We also reviewed the clinical presentations of the probands and affected family members associated with the novel CNVs and conducted segregation analysis. Results Five CNVs in five patients were detected in this study: heterozygous deletions of kinesin family member 11 (KIF11) exons 2-4, KIF11 exon 11, KIF11 exons 1-10, tetraspanin-12 (TSPAN12) exons 1-3, and low-density lipoprotein receptor-related protein 5 (LRP5) exons 19-21. Among the five affected families, TSPAN12 exons 1-3 heterozygous deletion and LRP5 exons 19-21 heterozygous deletion originate from the mother and the father of the proband, respectively. No other family members manifested as FEVR except for the probands. The correlation between disease severity and CNV loci seems uncertain. Conclusions Five novel CNV loci in FEVR patients were uncovered in this study, including one maternally-inherited and one paternally-inherited CNV region. Though there is no evidence of co-segregation between these CNVs and FEVR, our findings suggest novel genetic risk factors for FEVR.
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Yang L, Wei Z, Chen X, Hu L, Peng X, Wang J, Lu C, Kong Y, Dong X, Ni Q, Lu Y, Wu B, Wang H, Meirelles K, Tian X, Zhang J, Chang F, Liu L, Li C, You W, Cheng G, Wang L, Cao Y, Chen C, Fang P, Tang S, Zhou W. Use of medical exome sequencing for identification of underlying genetic defects in NICU: Experience in a cohort of 2303 neonates in China. Clin Genet 2021; 101:101-109. [PMID: 34671977 DOI: 10.1111/cge.14075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/27/2021] [Accepted: 10/15/2021] [Indexed: 12/17/2022]
Abstract
Emerging evidence demonstrates the clinical utility of genomic applications in newborn intensive care unit (NICU) patients with strong indications of Mendelian etiology. However, such applications' diagnostic yield and utility remain unclear for NICU cohorts with minimal phenotype selection. In this study, focused medical exome sequencing was used as a first-tier, singleton-focused diagnostic tool for 2303 unrelated sick neonates. Integrated analysis of single nucleotide variants (SNVs), small insertions and deletions (Indels), and large copy number variants (CNVs) was performed. The diagnostic rate in this NICU cohort is 12.3% (284/2303), with 190 probands with molecular diagnoses made from SNV/Indel analyses (66.9%), 93 patients with diagnostic aneuploidy/CNVs findings (32.8%), and 1 patient with both SNV and CNV (0.4%). In addition, 54 (2.3%) of patients had a reportable incidental finding. Multiple organ involvements, craniofacial abnormalities, and dermatologic abnormalities were the strongest positive predictors for a molecular diagnosis. Among the 190 cases with SNV/Indel defects, direct impacts on medical management were observed in 46.8% of patients after the results were reported. In this study, we demonstrate that focused medical exome sequencing is a powerful first-line diagnostic tool for NICU patients. Significant number of diagnosed NICU patients can benefit from more focused medical management and long-term care.
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Affiliation(s)
- Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Zejun Wei
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Jin Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chunmei Lu
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yanting Kong
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Qi Ni
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, Shanghai, China
| | | | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | | | - Liu Liu
- Sema4, Branford, Connecticut, USA
| | | | - Wesley You
- Google LLC, Mountain View, California, USA
| | - Guoqiang Cheng
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Chao Chen
- Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Fang
- KingMed Diagnostics, Guangzhou, China
| | - Sha Tang
- KingMed Diagnostics, Guangzhou, China
| | - Wenhao Zhou
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China.,Division of Neonatology, Children's Hospital of Fudan University, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai, China
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Yu S, Chen WX, Zhang YF, Ni Y, Lu P, Wang B, Wang Y, Wu B, Ni Q, Wang H, Xu ZM. Apparent homozygosity for a novel splicing variant in EPS8 causes congenital profound hearing loss. Eur J Med Genet 2021; 64:104362. [PMID: 34637946 DOI: 10.1016/j.ejmg.2021.104362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/17/2021] [Accepted: 10/08/2021] [Indexed: 12/27/2022]
Abstract
Autosomal recessive deafness-102 (DFNB102), a new profound prelingual non-syndromic hearing loss, is caused by mutations in the EPS8 gene. To date, only three such consanguineous families with three different homozygous variants in EPS8 have been reported. Here, we report the fourth case from a non-consanguineous Chinese family, an 11-month-old male infant presented with congenital profound non-syndromic hearing loss. Trio whole-exome sequencing initially identified the patient with a novel seemingly homozygous splicing variant NM_004447.5: c.1435-2A > T in intron 14 of the EPS8 gene and was inherited from his father; further CNVs analysis identified a novel 65.9 kb intragenic deletion and was inherited from his mother. The deletion is covering intron 14 that could account for the apparent homozygosity of the patient. In vitro splicing assay showed the variant c.1435-2A > T creates a new donor site at position c.1443, which is predicted to produce a stop codon after 14 additional amino acids (p.His479Cysfs*14). Furthermore, quantitative allele-specific expression assay showed that relative EPS8 gene expression in the patient significantly decreased (0-fold for the wild-type transcript and 0.25-0.27-fold for the mutant transcript) compared to the control (P < 0.05), indicating the pathogenicity of the identified variants. Overall, our study provides additional evidence that EPS8 is a causative gene for DFNB102 and highlights the clinical utility of simultaneous analysis of CNVs and SNVs to avoid potential errors in the diagnosis and interpretation of patients with apparent homozygosity.
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Affiliation(s)
- Sha Yu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wen-Xia Chen
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun-Fei Zhang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yihua Ni
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Lu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bin Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yan Wang
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Pediatrics Research Institute, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
| | - Zheng-Min Xu
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.
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Xiao F, Lu Y, Wu B, Liu B, Li G, Zhang P, Zhou Q, Sun J, Wang H, Zhou W. High-Frequency Exon Deletion of DNA Cross-Link Repair 1C Accounting for Severe Combined Immunodeficiency May Be Missed by Whole-Exome Sequencing. Front Genet 2021; 12:677748. [PMID: 34421990 PMCID: PMC8372405 DOI: 10.3389/fgene.2021.677748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/28/2021] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) has been used to detect severe combined immunodeficiency (SCID) in patients, and some patients with DNA cross-link repair 1C (DCLRE1C) variants have been identified. Moreover, some compound variants, such as copy number variants (CNV) and single nucleotide variants (SNV), have been reported. The purpose of this study was to expand the genetic data related to patients with SCID carrying the compound DCLRE1C variant. Whole-exome sequencing (WES) was performed for genetic analysis, and variants were verified by performing Sanger sequencing or quantitative PCR. Moreover, we searched PubMed and summarized the data of the reported variants. Four SCID patients with DCLRE1C variants were identified in this study. WES revealed a homozygous deletion in the DCLRE1C gene from exons 1–5 in patient 1, exons 1–3 deletion and a novel rare variant (c.92T>C, p.L31P) in patient 2, exons 1–3 deletion and a novel rare variant (c.328C>G, p.L110V) in patient 3, and exons 1–4 deletion and a novel frameshift variant (c.449dup, p.His151Alafs*20) in patient 4. Based on literature review, exons 1–3 was recognized as a hotspot region for deletion variation. Moreover, we found that compound variations (CNV + SNV) accounted for approximately 7% variations in all variants. When patients are screened for T-cell receptor excision circles (TRECs), NGS can be used to expand genetic testing. Deletion of the DCLRE1C gene should not be ignored when a variant has been found in patients with SCID.
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Affiliation(s)
- Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qinhua Zhou
- Department of Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jinqiao Sun
- Department of Immunology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Department of Neonates, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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45
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Guan J, Li J, Chen G, Shi T, Lan L, Wu X, Zhao C, Wang D, Wang H, Wang Q. Family trio-based sequencing in 404 sporadic bilateral hearing loss patients discovers recessive and De novo genetic variants in multiple ways. Eur J Med Genet 2021; 64:104311. [PMID: 34416374 DOI: 10.1016/j.ejmg.2021.104311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 08/07/2021] [Accepted: 08/15/2021] [Indexed: 11/29/2022]
Abstract
Hereditary hearing loss (HL) has high genetic and phenotypical heterogeneity including the overlapping and variable phenotypic features. For sporadic HL without a family history, it is more difficult to indicate the contribution of genetic factors to define a pattern of inheritance. We assessed the contribution of genetic variants and patterns of inheritance by a family trio-based sequencing and provided new insight into genetics. We conducted an analysis of data from unrelated sporadic patients with HL (n = 404) who underwent trio-based whole-exome sequencing (trio-WES) or proband-only WES (p-WES) or targeted exome sequencing (TES), and the samples of their unaffected-parents (n = 808)were validated. A molecular diagnosis was rendered for 191 of 404 sporadic HL patients (47.3%) in multiple modes of inheritance, including autosomal recessive (AR), autosomal dominant (AD) caused by de novo variants, copy-number variants (CNVs), X-linked recessive, and dual genetic diagnosis. Among these patients, 83 (43.5%) cases were diagnosed with variants in rare genes. Sporadic HL patients were identified by multiple modes of transmission. Observed variations in rare genes and multiple modes of inheritance can strikingly emphasize the important etiological contribution of recessive and de novo genetic variants to a large cohort of sporadic HL cases plus their parents.
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Affiliation(s)
- Jing Guan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Jin Li
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Guohui Chen
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Tao Shi
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Lan Lan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Xiaonan Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Cui Zhao
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Dayong Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Hongyang Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
| | - Qiuju Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853, China; National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, China & Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China.
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46
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Jiang T, Gao J, Jiang L, Xu L, Zhao C, Su X, Shen Y, Gu W, Kong X, Yang Y, Gao F. Application of Trio-Whole Exome Sequencing in Genetic Diagnosis and Therapy in Chinese Children With Epilepsy. Front Mol Neurosci 2021; 14:699574. [PMID: 34489640 PMCID: PMC8417468 DOI: 10.3389/fnmol.2021.699574] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Epilepsy is one of the most common neurological disorders in pediatric patients with other underlying neurological defects. Identifying the underlying etiology is crucial for better management of the disorder. We performed trio-whole exome sequencing in 221 pediatric patients with epilepsy. Probands were divided into seizures with developmental delay/intellectual disability (DD/ID) and seizures without DD/ID groups. Pathogenic (P) or likely pathogenic (LP) variants were identified in 71/110 (64.5%) patients in the seizures with DD/ID group and 21/111 (18.9%) patients in the seizures without DD/ID group (P < 0.001). Eighty-seven distinct P/LP single nucleotide variants (SNVs)/insertion deletions (Indels) were detected, with 55.2% (48/87) of them being novel. All aneuploidy and P/LP copy number variants (CNVs) larger than 100 Kb were identifiable by both whole-exome sequencing and copy number variation sequencing (CNVseq) in 123 of individuals (41 pedigrees). Ten of P/LP CNVs in nine patients and one aneuploidy variant in one patient (Patient #56, #47, XXY) were identified by CNVseq. Herein, we identified seven genes (NCL, SEPHS2, PA2G4, SLC35G2, MYO1C, GPR158, and POU3F1) with de novo variants but unknown pathogenicity that were not previously associated with epilepsy. Potential effective treatment options were available for 32 patients with a P/LP variant, based on the molecular diagnosis. Genetic testing may help identify the molecular etiology of early onset epilepsy and DD/ID and further aid to choose the appropriate treatment strategy for patients.
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Affiliation(s)
- Tiejia Jiang
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Jia Gao
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lihua Jiang
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lu Xu
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Congying Zhao
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiaojun Su
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yaping Shen
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Weiyue Gu
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | - Xiaohong Kong
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | - Ying Yang
- Beijing Chigene Translational Medical Research Center Co., Ltd., Beijing, China
| | - Feng Gao
- Department of Neurology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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47
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Ge M, Gan M, Yan K, Xiao F, Yang L, Wu B, Xiao M, Ba Y, Zhang R, Wang J, Cheng G, Wang L, Cao Y, Zhou W, Hu L. Combining Metagenomic Sequencing With Whole Exome Sequencing to Optimize Clinical Strategies in Neonates With a Suspected Central Nervous System Infection. Front Cell Infect Microbiol 2021; 11:671109. [PMID: 34222042 PMCID: PMC8253254 DOI: 10.3389/fcimb.2021.671109] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
Objectives Central nervous system (CNS) infection has a high incidence and mortality in neonates, but conventional tests are time-consuming and have a low sensitivity. Some rare genetic diseases may have some similar clinical manifestations as CNS infection. Therefore, we aimed to evaluate the performance of metagenomic next-generation sequencing (mNGS) in diagnosing neonatal CNS infection and to explore the etiology of neonatal suspected CNS infection by combining mNGS with whole exome sequencing (WES). Methods We prospectively enrolled neonates with a suspected CNS infection who were admitted to the neonatal intensive care unit(NICU) from September 1, 2019, to May 31, 2020. Cerebrospinal fluid (CSF) samples collected from all patients were tested by using conventional methods and mNGS. For patients with a confirmed CNS infection and patients with an unclear clinical diagnosis, WES was performed on blood samples. Results Eighty-eight neonatal patients were enrolled, and 101 CSF samples were collected. Fourty-three blood samples were collected for WES. mNGS showed a sample diagnostic yield of 19.8% (20/101) compared to 4.95% (5/101) for the conventional methods. In the empirical treatment group, the detection rate of mNGS was significantly higher than that of conventional methods [27% vs. 6.3%, p=0.002]. Among the 88 patients, 15 patients were etiologically diagnosed by mNGS alone, five patients were etiologically identified by WES alone, and one patient was diagnosed by both mNGS and WES. Twelve of 13 diagnoses based solely on mNGS had a likely clinical effect. Six patients diagnosed by WES also experienced clinical effect. Conclusions For patients with a suspected CNS infections, mNGS combined with WES might significantly improve the diagnostic rate of the etiology and effectively guide clinical strategies.
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Affiliation(s)
- Mengmeng Ge
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Mingyu Gan
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Kai Yan
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Feifan Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Lin Yang
- Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Children's Hospital of Fudan University, Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Shanghai, China
| | - Mili Xiao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yin Ba
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Jin Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Laishuan Wang
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital, Fudan University, Shanghai, China
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48
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Wen C, Zhou C, Jin Y, Hu Y, Wang H, Wang X, Yang X. Metabolic Changes in Rat Plasma After Epilepsy by UPLC-MS/MS. CURR PHARM ANAL 2021. [DOI: 10.2174/1573412916666200206145207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Introduction:
Epilepsy is one of the most common neurological diseases in clinical practice.
The combined application of metabolomics technology plays a great advantage in the screening of biomarkers.
Methods:
In this study, Wistar rats were used as experimental subjects to model intractable epilepsy
and to detect the metabolic changes of small molecules in plasma. UPLC-MS/MS was used to determine
the small molecules in rat plasma. UPLC HSS C18 (2.1mm×100mm, 1.7 μm) column was used
for separation, column temperature of 40°C. The initial mobile phase was acetonitrile -0.3% formic
acid with gradient elution, the flow rate was 0.3 mL/min, total running time 4.0 min. Quantitative analysis
was performed with multi-response monitoring (MRM).
Results:
Compared to the control group, the L-Alanine and L-Arginine decreased in the Epilepsy group
(p<0.05); while Cytosine, Adenosine, L-Tyrosine, Citric acid, Fructose increased (p<0.05).
Conclusion:
In the screening of epilepsy biomarkers using metabolomics, various amino acids that
lead to increased energy production and neurotransmitter imbalance play an important role in epileptic
seizures.
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Affiliation(s)
- Congcong Wen
- Laboratory Animal Centre, Wenzhou Medical University, Wenzhou 325035,China
| | - Caiping Zhou
- Laboratory Animal Centre, Wenzhou Medical University, Wenzhou 325035,China
| | - Yongxi Jin
- Department of Rehabilitation, Wenzhou Municipal Hospital of Traditional Chinese Medicine, Wenzhou 325005,China
| | - Yujie Hu
- Laboratory Animal Centre, Wenzhou Medical University, Wenzhou 325035,China
| | - Hongzhe Wang
- Laboratory Animal Centre, Wenzhou Medical University, Wenzhou 325035,China
| | - Xianqin Wang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou 325035,China
| | - Xuezhi Yang
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000,China
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49
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Xiao F, Liu X, Lu Y, Wu B, Liu R, Liu B, Yan K, Chen H, Cheng G, Wang L, Ni Q, Li G, Zhang P, Peng X, Cao Y, Shen C, Wang H, Zhou W. Overdosage of HNF1B Gene Associated With Annular Pancreas Detected in Neonate Patients With 17q12 Duplication. Front Genet 2021; 12:615072. [PMID: 34025713 PMCID: PMC8138176 DOI: 10.3389/fgene.2021.615072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
The annular pancreas (AP) is a congenital anomaly of the pancreas that can cause acute abdominal pain and vomiting after birth. However, the genetic cause of AP is still unknown, and no study has reported AP in patients with 17q12 duplication. This study retrospectively analyzed the next-generation sequencing (NGS) data of individuals from January 2016 to June 2020 for 17q12 duplication. To identify the function of the key gene of HNF1B in the 17q12 duplication region, human HNF1B mRNA was microinjected into LiPan zebrafish transgenic embryos. A total of 19 cases of 17q12 duplication were confirmed. AP was diagnosed during exploratory laparotomy in four patients (21.1%). The other common features of 17q12 duplication included intellectual disability (50%), gross motor delay (50%), and seizures/epilepsy (31.58%). The ratio of the abnormal pancreas in zebrafish was significantly higher in the HNF1B overexpression models. In conclusion, we first reported AP in patients with duplication of the 17q12 region, resulting in the phenotype of 17q12 duplication syndrome. Furthermore, our zebrafish studies verified the role of the HNF1B gene in pancreatic development.
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Affiliation(s)
- Feifan Xiao
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiuyun Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Kai Yan
- Division of Neonatology, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huiyao Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Qi Ni
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Chun Shen
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Division of Neonatology, Key Laboratory of Neonatal Diseases, Ministry of Health, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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Qian Y, Wu B, Liu R, Lu Y, Zhang P, Shao C, Huang Y, Wang H. Case Report: Complete Maternal Uniparental Isodisomy of Chromosome 5 (iUPD(5)mat) With PCSK1 Nonsense Variant in an Infant With Recurrent Diarrhea. Front Genet 2021; 12:668326. [PMID: 34025722 PMCID: PMC8134681 DOI: 10.3389/fgene.2021.668326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Congenital diarrhea diseases are a heterogeneous group of conditions and are the major cause of neonatal mortality worldwide. Proprotein convertase 1/3 (PC1/3) deficiency has been associated with severe malabsorptive diarrhea, obesity, and certain endocrine abnormalities. We report an infant born to non-consanguineous parents who is diagnosed with PC1/3 deficiency due to nonsense homozygous variant (c.238 C>T, p.Arg80Ter) in the PCSK1 gene, identified by Trio-exome sequencing (Trio-ES). The baby girl presented with recurrent diarrhea, transient liver dysfunction and hypoglycemia. Trio-ES showed complete maternal uniparental isodisomy (iUPD) of chromosome 5. Our finding provides accurate genetic counseling to this family and expands the clinical spectrum of iUPD with pathogenic variants causing recessive disease.
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Affiliation(s)
- Yanyan Qian
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Caihong Shao
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Ying Huang
- Department of Gastroenterology, Pediatric Inflammatory Bowel Disease Research Center, National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, National Children's Medical Center, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
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