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Wu R, Li X, Meng Z, Li P, He Z, Liang L. Phenotypic and genetic analysis of children with unexplained neurodevelopmental delay and neurodevelopmental comorbidities in a Chinese cohort using trio-based whole-exome sequencing. Orphanet J Rare Dis 2024; 19:205. [PMID: 38764027 PMCID: PMC11103872 DOI: 10.1186/s13023-024-03214-w] [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: 02/20/2023] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Trio-based whole-exome sequencing (trio-WES) enables identification of pathogenic variants, including copy-number variants (CNVs), in children with unexplained neurodevelopmental delay (NDD) and neurodevelopmental comorbidities (NDCs), including autism spectrum disorder (ASD), epilepsy, and attention deficit hyperactivity disorder. Further phenotypic and genetic analysis on trio-WES-tested NDD-NDCs cases may help to identify key phenotypic factors related to higher diagnostic yield of using trio-WES and novel risk genes associated with NDCs in clinical settings. METHODS In this study, we retrospectively performed phenotypic analysis on 163 trio-WES-tested NDD-NDCs children to determine the phenotypic differences between genetically diagnosed and non-genetically diagnosed groups. Additionally, we conducted genetic analysis of ASD genes with the help of Simons Foundation for Autism Research Institute (SFARI) Gene database to identify novel possible ASD-risk genes underlying genetic NDD conditions. RESULTS Among these 163 patients, pathogenic variants were identified in 82 cases (82/163, 50.3%), including 20 cases with CNVs. By comparing phenotypic variables between genetically diagnosed group (82 cases) and non-genetically diagnosed group (81 cases) with multivariate binary logistic regression analysis, we revealed that NDD-NDCs cases presenting with severe-profound NDD [53/82 vs 17/81, adjusted-OR (95%CI): 4.865 (2.213 - 10.694), adjusted-P < 0.001] or having multiple NDCs [26/82 vs 8/81, adjusted-OR (95%CI): 3.731 (1.399 - 9.950), adjusted-P = 0.009] or accompanying ASD [64/82 vs 35/81, adjusted-OR (95%CI): 3.256 (1.479 - 7.168), adjusted-P = 0.003] and head circumference abnormality [33/82 vs 11/81, adjusted-OR (95%CI): 2.788 (1.148 - 6.774), adjusted-P = 0.024] were more likely to have a genetic diagnosis using trio-WES. Moreover, 37 genes with monogenetic variants were identified in 48 patients genetically diagnosed with NDD-ASD, and 15 dosage-sensitive genes were identified in 16 individuals with NDD-ASD carrying CNVs. Most of those genes had been proven to be ASD-related genes. However, some of them (9 genes) were not proven sufficiently to correlate with ASD. By literature review and constructing protein-protein interaction networks among these 9 candidate ASD-risk genes and 102 established ASD genes obtained from the SFARI Gene database, we identified CUL4B, KCNH1, and PLA2G6 as novel possible ASD-risk genes underlying genetic NDD conditions. CONCLUSIONS Trio-WES testing is recommended for patients with unexplained NDD-NDCs that have severe-profound NDD or multiple NDCs, particularly those with accompanying ASD and head circumference abnormality, as these independent factors may increase the likelihood of genetic diagnosis using trio-WES. Moreover, NDD patients with pathogenic variants in CUL4B, KCNH1 and PLA2G6 should be aware of potential risks of developing ASD during their disease courses.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Xiaojuan Li
- Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Pinggan Li
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China
| | - Zhanwen He
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
| | - Liyang Liang
- Department of Children's Neuro-endocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, Guangdong, China.
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou Guangdong, 510120, China.
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van Slobbe M, van Haeringen A, Vissers LELM, Bijlsma EK, Rutten JW, Suerink M, Nibbeling EAR, Ruivenkamp CAL, Koene S. Reanalysis of whole-exome sequencing (WES) data of children with neurodevelopmental disorders in a standard patient care context. Eur J Pediatr 2024; 183:345-355. [PMID: 37889289 PMCID: PMC10858114 DOI: 10.1007/s00431-023-05279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
This study aims to inform future genetic reanalysis management by evaluating the yield of whole-exome sequencing (WES) reanalysis in standard patient care in the Netherlands. Single-center data of 159 patients with a neurodevelopmental disorder (NDD), in which WES analysis and reanalysis were performed between January 1, 2014, and December 31, 2021, was retrospectively collected. Patients were included if they were under the age of 18 years at initial analysis and if this initial analysis did not result in a diagnosis. Demographic, phenotypic, and genotypic characteristics of patients were collected and analyzed. The primary outcomes of our study were (i) diagnostic yield at reanalysis, (ii) reasons for detecting a new possibly causal variant at reanalysis, (iii) unsolicited findings, and (iv) factors associated with positive result of reanalysis. In addition, we conducted a questionnaire study amongst the 7 genetic department in the Netherlands creating an overview of used techniques, yield, and organization of WES reanalysis. The single-center data show that in most cases, WES reanalysis was initiated by the clinical geneticist (65%) or treating physician (30%). The mean time between initial WES analysis and reanalysis was 3.7 years. A new (likely) pathogenic variant or VUS with a clear link to the phenotype was found in 20 initially negative cases, resulting in a diagnostic yield of 12.6%. In 75% of these patients, the diagnosis had clinical consequences, as for example, a screening plan for associated signs and symptoms could be devised. Most (32%) of the (likely) causal variants identified at WES reanalysis were discovered due to a newly described gene-disease association. In addition to the 12.6% diagnostic yield based on new diagnoses, reclassification of a variant of uncertain significance found at initial analysis led to a definite diagnosis in three patients. Diagnostic yield was higher in patients with dysmorphic features compared to patients without clear dysmorphic features (yield 27% vs. 6%; p = 0.001). CONCLUSIONS Our results show that WES reanalysis in patients with NDD in standard patient care leads to a substantial increase in genetic diagnoses. In the majority of newly diagnosed patients, the diagnosis had clinical consequences. Knowledge about the clinical impact of WES reanalysis, clinical characteristics associated with higher yield, and the yield per year after a negative WES in larger clinical cohorts is warranted to inform guidelines for genetic reanalysis. These guidelines will be of great value for pediatricians, pediatric rehabilitation specialists, and pediatric neurologists in daily care of patients with NDD. WHAT IS KNOWN • Whole exome sequencing can cost-effectively identify a genetic cause of intellectual disability in about 30-40% of patients. • WES reanalysis in a research setting can lead to a definitive diagnosis in 10-20% of previously exome negative cases. WHAT IS NEW • WES reanalysis in standard patient care resulted in a diagnostic yield of 13% in previously exome negative children with NDD. • The presence of dysmorphic features is associated with an increased diagnostic yield of WES reanalysis.
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Affiliation(s)
- Michelle van Slobbe
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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4
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Zhu T, Bei F, He R, Gong X, Chen Y, Yin Z, Wang J, Sun Y, Zhang Y. Genetic Diseases and Invasive Infections in Infants 100 Days or Younger. Pediatr Infect Dis J 2023:00006454-990000000-00432. [PMID: 37171972 DOI: 10.1097/inf.0000000000003939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Understanding the association of genetic diseases with invasive infections in neonates or infants is important, given the clinical and public health implications of genetic diseases. METHODS We conducted a retrospective case-control study over a 5-year period to investigate the association between genetic diseases and invasive infections in neonates or infants. The case group included 56 patients with laboratory-confirmed invasive infections and a genetic etiology identified by exome sequencing. Another 155 patients without a genetic etiology were selected as controls from the same pool of patients. RESULTS An overview of genetic diseases that predispose patients to develop invasive infections were outlined. We identified 7 independent predictors for genetic conditions, including prenatal findings [adjusted odds ratio (aOR), 38.44; 95% confidence interval (CI): 3.94-374.92], neonatal intensive care unit admission (aOR, 46.87; 95% CI: 6.30-348.93), invasive ventilation (aOR, 6.66; 95% CI: 3.07-14.46), bacterial infections (aOR, 0.21; 95% CI: 0.06-0.69), fever (aOR, 0.15; 95% CI: 0.08-0.30), anemia (aOR, 6.64; 95% CI: 3.02-14.59) and neutrophilia (aOR, 0.98; 95% CI: 0.96-0.99). The area under the curve for the predictive model was 0.921 (95% CI: 0.876-0.954). We also found that a genetic etiology [hazard ratio (HR), 7.25; 95% CI: 1.71-30.81], neurological manifestations (HR, 3.56; 95% CI: 1.29-9.88) and septic shock (HR, 13.83; 95% CI: 3.18-60.10) were associated with severe outcomes. CONCLUSIONS Our study established predictive variables and risk factors for an underlying genetic etiology and its mortality in neonates or infants with invasive infections. These findings could lead to risk-directed screening and treatment strategies, which may improve patient outcomes.
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Affiliation(s)
- Tianwen Zhu
- From the Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Bei
- Department of Neonatology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruoqi He
- From the Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohui Gong
- Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- From the Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhanghua Yin
- From the Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China; and
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongjun Zhang
- From the Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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5
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Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities—A Narrative Review. CHILDREN 2023; 10:children10030501. [PMID: 36980059 PMCID: PMC10047410 DOI: 10.3390/children10030501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Unexplained global developmental delay (GDD) and intellectual disabilities (ID) together affect nearly 2% of the pediatric population. Establishing an etiologic diagnosis is crucial for disease management, prognostic evaluation, and provision of physical and psychological support for both the patient and the family. Advancements in genome sequencing have allowed rapid accumulation of gene–disorder associations and have accelerated the search for an etiologic diagnosis for unexplained GDD/ID. We reviewed recent studies that utilized genome-wide analysis technologies, and we discussed their diagnostic yield, strengths, and limitations. Overall, exome sequencing (ES) and genome sequencing (GS) outperformed chromosomal microarrays and targeted panel sequencing. GS provides coverage for both ES and chromosomal microarray regions, providing the maximal diagnostic potential, and the cost of ES and reanalysis of ES-negative results is currently still lower than that of GS alone. Therefore, singleton or trio ES is the more cost-effective option for the initial investigation of individuals with GDD/ID in clinical practice compared to a staged approach or GS alone. Based on these updated evidence, we proposed an evaluation algorithm with ES as the first-tier evaluation for unexplained GDD/ID.
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6
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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8
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Sun Y, Peng J, Liang D, Ye X, Xu N, Chen L, Yan D, Zhang H, Xiao B, Qiu W, Shen Y, Pang N, Liu Y, Liang C, Qin Z, Luo J, Chen F, Wang J, Zhang Z, Wei H, Du J, Yan H, Duan R, Wang J, Zhang Y, Liao S, Sun K, Wu L, Yu Y. Genome sequencing demonstrates high diagnostic yield in children with undiagnosed global developmental delay/intellectual disability: a prospective study. Hum Mutat 2022; 43:568-581. [PMID: 35143101 DOI: 10.1002/humu.24347] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
Genome sequencing(GS) has been used in the diagnosis of global developmental delay(GDD)/intellectual disability(ID). However, the performance of GS in patients with inconclusive results from chromosomal microarray analysis(CMA) and exome sequencing(ES) is unknown. We recruited 100 pediatric GDD/ID patients from multiple sites in China from February 2018 to August 2020 for GS. Patients have received at least one genomic diagnostic test prior to enrollment. Reanalysis of their CMA/ES data was performed. The yield of GS was calculated and explanations for missed diagnoses by CMA/ES were investigated. Clinical utility was assessed by interviewing the parents by phone. The overall diagnostic yield of GS was 21%. Seven cases could have been solved with reanalysis of ES data. Thirteen families were missed by previous CMA/ES due to improper methodology. Two remained unsolved after ES reanalysis due to complex variants missed by ES, and a CNV in untranslated regions. Follow-up of the diagnosed families revealed that nine families experienced changes in clinical management, including identification of targeted treatments, cessation of unnecessary treatment, and considerations for family planning. GS demonstrated high diagnostic yield and clinical utility in this undiagnosed GDD/ID cohort, detecting a wide range of variant types of different sizes in a single workflow. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, 410008, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, 410008, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Xiantao Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Na Xu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Linlin Chen
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Dan Yan
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, 410008, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, 410008, Changsha, China
| | - Yingdi Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Chen Liang
- Medical Genetics Center, Jiangmen Maternity and Child Health Care Hospital, 529000, Jiangmen, China
| | - Zailong Qin
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Fei Chen
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, 530003, Nanning, China
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Zhixin Zhang
- International Medical Services, China-Japan Friendship Hospital, 100029, Beijing, China
| | - Haiyan Wei
- Department of Endocrinologic and Inherited Metabolic, Childen's Hospital affiliated to Zhengzhou University, 450018, Zhengzhou, China
| | - Juan Du
- Reproductive and Genetic Hospital of CITIC-Xiangya, 410078, Changsha, China
| | - Huifang Yan
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Ruoyu Duan
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Junyu Wang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Yu Zhang
- Department of Pediatrics, Peking University First Hospital, 10034, Beijing, China
| | - Shixiu Liao
- Provincial People's Hospital, Medical Genetics Institute of Henan Province, 450003, Zhengzhou, Henan Province, China
| | - Kun Sun
- Center for Clinical Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, 410078, Changsha, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, 200092, Shanghai, China.,Shanghai Institute for Pediatric Research, 200092, Shanghai, China
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Luo X, Duan Y, Fang D, Sun Y, Xiao B, Zhang H, Han L, Liang L, Gong Z, Gu X, Yu Y, Qiu W. Diagnosis and follow-up of Glycogen Storage Disease (GSD) Type VI from the largest GSD center in China. Hum Mutat 2022; 43:557-567. [PMID: 35143115 DOI: 10.1002/humu.24345] [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: 07/25/2021] [Revised: 02/03/2022] [Accepted: 02/08/2022] [Indexed: 11/10/2022]
Abstract
Glycogen storage disease (GSD) type VI is a glycogenolysis disorder caused by variants of PYGL. Knowledge about this disease is limited because only approximately 50 cases have been reported. we investigated the clinical profiles, molecular diagnosis, and treatment outcomes in patients with gsd VI from 2000 to 2021. The main initial clinical features of this cohort include hepatomegaly, short stature, elevated liver transaminases, hypertriglyceridemia, fasting hypoglycemia, and hyperuricemia. After uncooked cornstarch treatment, the stature and biochemical parameters improved significantly (P < 0.05). However, hyperuricemia recurred in most patients during adolescence. Among the 56 GSD VI patients, 54 biallelic variants and two single allelic variants of PYGL were identified, of which 43 were novel. There were two hotspot variants, c.1621-258_2178-23del and c.2467C>T p.(Gln823*), mainly in patients from Southwest and South China. c.1621-258_2178-23del is a 3.6 kb deletion that results in an out-of-frame deletion r.1621_2177del and an in-frame deletion r.1621_2265del. Our data show for the first time that long-term monitoring of uric acid is recommended for older GSD VI patients. This study also broadens the variant spectrum of PYGL and indicates that there are two hot-spot variants in China. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiaomei Luo
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ying Duan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai
| | - Di Fang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai
| | - Yu Sun
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai.,Shanghai Institute for Pediatric Research, Shanghai, China
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10
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Parenti I, Kaiser FJ. Cornelia de Lange Syndrome as Paradigm of Chromatinopathies. Front Neurosci 2021; 15:774950. [PMID: 34803598 PMCID: PMC8603810 DOI: 10.3389/fnins.2021.774950] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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11
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Intellectual disability-associated mutations in the ceramide transport protein gene CERT1 lead to aberrant function and subcellular distribution. J Biol Chem 2021; 297:101338. [PMID: 34688657 PMCID: PMC8605338 DOI: 10.1016/j.jbc.2021.101338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022] Open
Abstract
The lipid molecule ceramide is transported from the endoplasmic reticulum to the Golgi apparatus for sphingomyelin production via the ceramide transport protein (CERT), encoded by CERT1. Hyperphosphorylation of CERT’s serine-repeat motif (SRM) decreases its functionality. Some forms of inherited intellectual disability (ID) have been associated with a serine-to-leucine substitution in the SRM (S132L mutation) and a glycine-to-arginine substitution outside the SRM (G243R mutation) in CERT; however, it is unclear if mutations outside the SRM disrupt the control of CERT functionality. In the current investigation, we identified a new CERT1 variant (dupAA) in a patient with mild ID that resulted from a frameshift at the C-terminus of CERT1. However, familial analysis revealed that the dupAA variant was not associated with ID, allowing us to utilize it as a disease-matched negative control for CERT1 variants that are associated with ID. Biochemical analysis showed that G243R and S132L, but not dupAA, impair SRM hyperphosphorylation and render the CERT variants excessively active. Additionally, both S132L and G243R mutations but not dupAA caused the proteins to be distributed in a punctate subcellular manner. On the basis of these findings, we infer that the majority of ID-associated CERT variants may impair SRM phosphorylation-dependent repression, resulting in an increase in sphingomyelin production concurrent with CERT subcellular redistribution.
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12
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Su M, Page S, Haag M, Swisshelm K, Hennerich D, Graw S, LeRoux J, Brzeskiewicz P, Svihovec S, Bao L. Clinical utility and cost-effectiveness analysis of chromosome testing concomitant with chromosomal microarray of patients with constitutional disorders in a U.S. academic medical center. J Genet Couns 2021; 31:364-374. [PMID: 34397147 DOI: 10.1002/jgc4.1496] [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: 01/28/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022]
Abstract
Chromosomal microarray (CMA) is now widely used as first-tier testing for the detection of copy number variants (CNVs) and absence of heterozygosity (AOH) in patients with multiple congenital anomalies (MCA), autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Chromosome analysis is commonly used to complement CMA in the detection of balanced genomic aberrations. However, the cost-effectiveness and the impact on clinical management of chromosome analysis concomitant with CMA were not well studied, and there is no consensus on how to best utilize these two tests. To assess the clinical utility and cost-effectiveness of chromosome analysis concomitant with CMA in patients with MCA, ASD, DD, and/or ID, we retrospectively analyzed 3,360 postnatal cases for which CMA and concomitant chromosome analysis were performed in the Colorado Genetic Laboratory (CGL) at the University Of Colorado School Of Medicine. Chromosome analysis alone yielded a genetic diagnosis in two patients (0.06%) and contributed additional information to CMA results in 199 (5.92%) cases. The impact of abnormal chromosome results on patient management was primarily related to counseling for reproductive and recurrence risks assessment (101 cases, 3.01%) while a few (5 cases, 0.15%) led to changes in laboratory testing and specialist referral (25 cases, 0.74%). The incremental cost-effectiveness ratio (ICER) of combined testing demonstrated the cost of each informative chromosome finding was significantly higher for patients with clinically insignificant (CI) CMA findings versus clinically significant (CS) CMA results. Our results suggest that a stepwise approach with CMA testing with reflex to chromosome analysis on cases with CS CMA findings is a more cost-effective testing algorithm for patients with MCA, ASD, and/or DD/ID.
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Affiliation(s)
- Meng Su
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Stephanie Page
- Genetics Counseling Program, Department of Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Karen Swisshelm
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Deborrah Hennerich
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sharon Graw
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jamie LeRoux
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Peter Brzeskiewicz
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Shayna Svihovec
- Clinical Genetics and Metabolism, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Liming Bao
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
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13
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Hiraide T, Yamoto K, Masunaga Y, Asahina M, Endoh Y, Ohkubo Y, Matsubayashi T, Tsurui S, Yamada H, Yanagi K, Nakashima M, Hirano K, Sugimura H, Fukuda T, Ogata T, Saitsu H. Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing. Clin Genet 2021; 100:40-50. [PMID: 33644862 DOI: 10.1111/cge.13951] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 12/20/2022]
Abstract
Whole-exome sequencing (WES) enables identification of pathogenic variants, including copy number variants (CNVs). In this study, we performed WES in 101 Japanese patients with unexplained developmental delay (DD) or intellectual disability (ID) (63 males and 38 females), 98 of them with trio-WES. Pathogenic variants were identified in 54 cases (53.5%), including four cases with pathogenic CNVs. In one case, a pathogenic variant was identified by reanalysis of exome data; and in two cases, two molecular diagnoses were identified. Among 58 pathogenic variants, 49 variants occurred de novo in 48 patients, including two somatic variants. The accompanying autism spectrum disorder and external ear anomalies were associated with detection of pathogenic variants with odds ratios of 11.88 (95% confidence interval [CI] 2.52-56.00) and 3.46 (95% CI 1.23-9.73), respectively. These findings revealed the importance of reanalysis of WES data and detection of CNVs and somatic variants in increasing the diagnostic yield for unexplained DD/ID. In addition, genetic testing is recommended when patients suffer from the autism spectrum disorder or external ear anomalies, which potentially suggests the involvement of genetic factors associated with gene expression regulation.
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Affiliation(s)
- Takuya Hiraide
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Miki Asahina
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Yusaku Endoh
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Yumiko Ohkubo
- Department of Pediatrics, Shizuoka Saiseikai Hospital, Shizuoka, Japan
| | - Tomoko Matsubayashi
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Pediatric Neurology, Shizuoka Children's Hospital, Shizuoka, Japan
| | - Satoshi Tsurui
- Department of Pediatrics, Seirei-Numazu Hospital, Numazu, Japan
| | - Hidetaka Yamada
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kouichi Hirano
- Department of Pediatrics, Hamamatsu City Welfare and Medical Center for Development, Hamamatsu, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tokiko Fukuda
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
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14
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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15
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Arslan Satılmış SB, Kurt EE, Akçay EP, Sazci A, Ceylan AC. A novel missense mutation in the UBE2A gene causes intellectual disability in the large X-linked family. J Gene Med 2020; 23:e3307. [PMID: 33368912 DOI: 10.1002/jgm.3307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/16/2020] [Accepted: 12/16/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND X-linked intellectual disability type Nascimento (XIDTN) is a disorder of the ubiquitin-proteasome pathway of protein degradation controlled by the UBE2A gene. The disease is characterized by intellectual disability, speech impairment, dysmorphic facial features, skin and nail anomalies, and, frequently, seizures. Eight affected males from a four-generation family who have intellectual disability and speech disorders were examined within an extended family of 57 individuals. Methods A number of methods were used for the molecular diagnosis. Conventional karyotype analyses, array-based comparative genomic hybridization (aCGH), whole exome swquencing (WES), sanger sequencing were performed. Results First, the conventional karyotype analyses were normal, and the results of the aCGH analyses were normal. Then, WES revealed a novel missense mutation of the UBE2A gene at exon 4 NM_003336.3: c.182A>G (p.Glu61Gly). Seven affected individuals and nine carriers in the multigenerational, large family were diagnosed through Sanger sequencing. CONCLUSIONS We identified the mutation causing intellectual disability in the large family and demonstrated its phenotypic effects. Our cases showed that dysmorphic features could be considered mild, whereas intellectual disability and speech disorders are common features in XIDTN. The structure and function of the gene will be better understood in the novel UBE2A mutation. The genotype-phenotype correlation and phenotypic variations in XIDTN were identified through a literature review. Accordingly, XIDTN should be considered in individuals who exhibit an X-linked pedigree pattern and have intellectual disability and speech disorders.
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Affiliation(s)
| | - Emin Emre Kurt
- Department of Medical Genetics, Ankara City Hospital, Ankara, Turkey.,Department of Medical Genetics, Ankara Yıldırım Beyazit University, Ankara, Turkey
| | - Ebru Perim Akçay
- Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Ali Sazci
- Department of Medical Biology, Kocaeli University, Kocaeli, Turkey
| | - Ahmet Cevdet Ceylan
- Department of Medical Genetics, Ankara City Hospital, Ankara, Turkey.,Department of Medical Genetics, Ankara Yıldırım Beyazit University, Ankara, Turkey
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16
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Stefanski A, Calle-López Y, Leu C, Pérez-Palma E, Pestana-Knight E, Lal D. Clinical sequencing yield in epilepsy, autism spectrum disorder, and intellectual disability: A systematic review and meta-analysis. Epilepsia 2020; 62:143-151. [PMID: 33200402 PMCID: PMC7839709 DOI: 10.1111/epi.16755] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022]
Abstract
Objective Clinical genetic sequencing is frequently utilized to diagnose individuals with neurodevelopmental disorders (NDDs). Here we perform a meta‐analysis and systematic review of the success rate (diagnostic yield) of clinical sequencing through next‐generation sequencing (NGS) across NDDs. We compare the genetic testing yield across NDD subtypes and sequencing technology. Methods We performed a systematic review of the PubMed literature until May 2020. We included clinical sequencing studies that utilized NGS in individuals with epilepsy, autism spectrum disorder (ASD), or intellectual disability (ID). Data were extracted, reviewed, and categorized according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines. Two investigators performed clinical evaluation and grouping following the International League Against Epilepsy (ILAE) guidelines. Pooled rates of the diagnostic yield and 95% confidence intervals were estimated with a random‐effects model. Results We identified 103 studies (epilepsy, N = 72; ASD, N = 14; ID, N = 21) across 32,331 individuals. Targeted gene panel sequencing was used in 73, and exome sequencing in 36 cohorts. Given highly selected patient cohorts, the diagnostic yield was 17.1% for ASD, 24% for epilepsy, and 28.2% for ID (23.7% overall). The highest diagnostic yield for epilepsy subtypes was observed in individuals with ID (27.9%) and early onset seizures (36.8%). The diagnostic yield for exome sequencing was higher than for panel sequencing, even though not statistically significant (27.2% vs 22.6%, P = .071). We observed that clinical sequencing studies are performed predominantly in countries with a high Inequality‐adjusted Human Development Index (IHDI) (countries with sequencing studies: IHDI median = 0.84, interquartile range [IQR] = 0.09 vs countries without sequencing studies: IHDI median = 0.56, IQR = 0.3). No studies from Africa, India, or Latin America were identified, indicating potential barriers to genetic testing. Significance This meta‐analysis and systematic review provides a comprehensive overview of clinical sequencing studies of NDDs and will help guide policymaking and steer decision‐making in patient management.
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yamile Calle-López
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Program, Neuroclinica, University of Antioquia, Medellín, CO, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA.,Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK
| | - Eduardo Pérez-Palma
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elia Pestana-Knight
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
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17
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Liu YD, Lin HJ, Li CY, Sun GF, Hu XB, Ma MY, Sun Y, Feng BZ, Li QB, Kong QX. Compound heterozygous mutations in the ALDH3A2 gene cause Sjögren-Larsson syndrome: a case report. Int J Neurosci 2020; 130:1156-1160. [PMID: 31944864 DOI: 10.1080/00207454.2020.1716750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: Sjögren-Larsson syndrome is a rare, autosomal, recessive neurocutaneous disorder caused by mutations in the ALDH3A2 gene, which encodes the fatty aldehyde dehydrogenase enzyme. Deficiency in fatty aldehyde dehydrogenase results in an abnormal accumulation of toxic fatty aldehydes in the brain and skin, which cause spasticity, intellectual disability, ichthyosis, and other clinical manifestations. We present the clinical features and mutation analyses of a case of SLS.Materials and Methods: The family history and clinical data of the patient were collected. Genomic DNA was extracted from peripheral blood samples of the patient and her parents, and next-generation sequencing was performed. The candidate mutation sites that required further validation were then sequenced by Sanger sequencing. Bioinformatics software PSIPRED and RaptorX were used to predict the secondary and tertiary structures of proteins.Results: The patient, a five-year-old girl with complaints of cough for three days and intermittent convulsions for seven hours, was admitted to the hospital. Other clinical manifestations included spastic paraplegia, mental retardation, tooth defects, and ichthyosis. Brain magnetic resonance imaging showed periventricular leukomalacia. Genetic screening revealed compound heterozygous mutations in the ALDH3A2 gene: a frameshift mutation c.779delA (p.K260Rfs*6) and a missense mutation c.1157A > G (p.N386S). Neither of the ALDH3A2 alleles in the compound heterozygote patient were able to generate normal fatty aldehyde dehydrogenase, which were likely responsible for her phenotype of Sjögren-Larsson syndrome.Conclusion: The compound heterozygous mutations found in the ALDH3A2 gene support the diagnosis of Sjögren-Larsson syndrome in the patient and expand the genotype spectrum of the gene.
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Affiliation(s)
- Yi-Dan Liu
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China.,Institute of Epilepsy, Jining Medical University, Jining, Shandong, 272000, China
| | - Hong-Juan Lin
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China
| | - Chun-Yan Li
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China.,Institute of Epilepsy, Jining Medical University, Jining, Shandong, 272000, China
| | - Guang-Fei Sun
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China
| | - Xi-Bin Hu
- Department of Imaging, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China
| | - Meng-Yu Ma
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.,Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China.,Institute of Epilepsy, Jining Medical University, Jining, Shandong, 272000, China
| | - Ying Sun
- North China Medical Feng Feng General Hospital, Handan, Hebei, 056200, China
| | - Bang-Zhe Feng
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Qiu-Bo Li
- Department of Pediatrics, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China
| | - Qing-Xia Kong
- Department of Neurology, Affiliated Hospital of Jining Medical University, Jining, Shandong, 272000, China.,Institute of Epilepsy, Jining Medical University, Jining, Shandong, 272000, China
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18
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Sun Y, Ye X, Fan Y, Wang L, Luo X, Liu H, Gao X, Gong Z, Wang Y, Qiu W, Zhang H, Han L, Liang L, Ye H, Xiao B, Gu X, Yu Y. High Detection Rate of Copy Number Variations Using Capture Sequencing Data: A Retrospective Study. Clin Chem 2020; 66:455-462. [PMID: 32031585 DOI: 10.1093/clinchem/hvz033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Capture sequencing (CS) is widely applied to detect small genetic variations such as single nucleotide variants or indels. Algorithms based on depth comparison are becoming available for detecting copy number variation (CNV) from CS data. However, a systematic evaluation with a large sample size has not been conducted to evaluate the efficacy of CS-based CNV detection in clinical diagnosis. METHODS We retrospectively studied 3010 samples referred to our diagnostic laboratory for CS testing. We used 68 chromosomal microarray analysis-positive samples (true set [TS]) and 1520 reference samples to build a robust CS-CNV pipeline. The pipeline was used to detect candidate clinically relevant CNVs in 1422 undiagnosed samples (undiagnosed set [UDS]). The candidate CNVs were confirmed by an alternative method. RESULTS The CS-CNV pipeline detected 78 of 79 clinically relevant CNVs in TS samples, with analytical sensitivity of 98.7% and positive predictive value of 49.4%. Candidate clinically relevant CNVs were identified in 106 UDS samples. CNVs were confirmed in 96 patients (90.6%). The diagnostic yield was 6.8%. The molecular etiology includes aneuploid (n = 7), microdeletion/microduplication syndrome (n = 40), and Mendelian disorders (n = 49). CONCLUSIONS These findings demonstrate the high yield of CS-based CNV. With further improvement of our CS-CNV pipeline, the method may have clinical utility for simultaneous evaluation of CNVs and small variations in samples referred for pre- or postnatal analysis.
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Affiliation(s)
- Yu Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xiantao Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lili Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xiaomei Luo
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Huili Liu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xueren Gao
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yu Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Hui Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
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19
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Maya I, Smirin-Yosef P, Kahana S, Morag S, Yacobson S, Agmon-Fishman I, Matar R, Bitton E, Shohat M, Basel-Salmon L, Salmon-Divon M. A study of normal copy number variations in Israeli population. Hum Genet 2020; 140:553-563. [PMID: 32980975 DOI: 10.1007/s00439-020-02225-4] [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: 07/29/2020] [Accepted: 09/19/2020] [Indexed: 10/23/2022]
Abstract
The population of Israel is ethnically diverse, and individuals from different ethnic groups share specific genetic variations. These variations, which have been passed on from common ancestors, are usually reported in public databases as rare variants. Here, we aimed to identify ethnicity-based benign copy number variants (CNVs) and generate the first Israeli CNV database. We applied a data-mining approach to the results of 10,193 chromosomal microarray tests, of which 2150 tests were from individuals of 13 common ethnic backgrounds (n ≥ 10). We found 165 CNV regions (> 50 kbp) that are unique to specific ethnic groups (uCNVRs). The frequency of more than 19% of these uCNVRs is between 1 and 20% of the common ethnic origin, while their frequency in the overall cohort is between 0.5 and 1.6%. Of these 165 uCNVRs, 98 are reported as variants of unknown significance or as not available in dbVar; we postulate that these uCNVRs should be annotated as either "likely benign" or "benign". The ethnic-specific CNVs extracted in this study will allow geneticists to distinguish between relevant pathogenic genomic aberrations and benign ethnicity-related variations, thus preventing variant misinterpretation that may lead to unnecessary pregnancy terminations.
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Affiliation(s)
- Idit Maya
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Pola Smirin-Yosef
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Sarit Kahana
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Sne Morag
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Shiri Yacobson
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Ifaat Agmon-Fishman
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Reut Matar
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
| | - Elisheva Bitton
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Mordechai Shohat
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel-Hashomer, Israel.,Maccabi Health Services, Rehovot, Israel
| | - Lina Basel-Salmon
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel. .,The Adelson School of Medicine, Ariel University, Ariel, Israel.
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20
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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21
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Murakami H, Tsurusaki Y, Enomoto K, Kuroda Y, Yokoi T, Furuya N, Yoshihashi H, Minatogawa M, Abe-Hatano C, Ohashi I, Nishimura N, Kumaki T, Enomoto Y, Naruto T, Iwasaki F, Harada N, Ishikawa A, Kawame H, Sameshima K, Yamaguchi Y, Kobayashi M, Tominaga M, Ishikiriyama S, Tanaka T, Suzumura H, Ninomiya S, Kondo A, Kaname T, Kosaki K, Masuno M, Kuroki Y, Kurosawa K. Update of the genotype and phenotype of KMT2D and KDM6A by genetic screening of 100 patients with clinically suspected Kabuki syndrome. Am J Med Genet A 2020; 182:2333-2344. [PMID: 32803813 DOI: 10.1002/ajmg.a.61793] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/05/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
Kabuki syndrome is characterized by a variable degree of intellectual disability, characteristic facial features, and complications in various organs. Many variants have been identified in two causative genes, that is, lysine methyltransferase 2D (KMT2D) and lysine demethylase 6A (KDM6A). In this study, we present the results of genetic screening of 100 patients with a suspected diagnosis of Kabuki syndrome in our center from July 2010 to June 2018. We identified 76 variants (43 novel) in KMT2D and 4 variants (3 novel) in KDM6A as pathogenic or likely pathogenic. Rare variants included a deep splicing variant (c.14000-8C>G) confirmed by RNA sequencing and an 18% mosaicism level for a KMT2D mutation. We also characterized a case with a blended phenotype consisting of Kabuki syndrome, osteogenesis imperfecta, and 16p13.11 microdeletion. We summarized the clinical phenotypes of 44 patients including a patient who developed cervical cancer of unknown origin at 16 years of age. This study presents important details of patients with Kabuki syndrome including rare clinical cases and expands our genetic understanding of this syndrome, which will help clinicians and researchers better manage and understand patients with Kabuki syndrome they may encounter.
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Affiliation(s)
- Hiroaki Murakami
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keisuke Enomoto
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takayuki Yokoi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noritaka Furuya
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Yoshihashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mari Minatogawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Chihiro Abe-Hatano
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ikuko Ohashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Naoto Nishimura
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Tatsuro Kumaki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Fuminori Iwasaki
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriaki Harada
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Aki Ishikawa
- Department of Medical Genetics and Genomics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kawame
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kiyoko Sameshima
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Yu Yamaguchi
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Masahisa Kobayashi
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Makiko Tominaga
- Children's Medical Center, Northern Yokohama Hospital, Showa University, Yokohama, Japan
| | - Satoshi Ishikiriyama
- Division of Clinical Genetics and Cytogenetics, Shizuoka Children's Hospital, Shizuoka, Japan
| | | | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Kurashiki, Japan
| | - Akane Kondo
- Department of Gynecology, Shikoku Medical Center for Children and Adults, Kagawa, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuo Masuno
- Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Yoshikazu Kuroki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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22
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Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities. Pediatr Neurol 2019; 99:47-54. [PMID: 30952489 DOI: 10.1016/j.pediatrneurol.2019.02.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/16/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Whole exome sequencing on family trios gives the highest diagnostic yield, but high cost limits its application. Here, we performed proband-only clinical exome sequencing in a population of patients with neurodevelopmental disabilities and tested the diagnostic yield. METHODS This observational, retrospective study included 108 unrelated patients with neurodevelopmental disabilities who underwent clinical exome sequencing at the outpatient clinics of the Severance Children's Hospital, Seoul, South Korea, between March 2017 and May 2018. Clinical exome sequencing targeted 4503 disease-causing genes. RESULTS The overall diagnostic rate was 38.0% (41 of 108) when proband-only clinical exome sequencing was performed without additional parental testing. Four sequence variants were reclassified as likely pathogenic after parental testing, representing an additional 3.7% of the diagnostic yield. The final diagnostic rate was 41.7% (45 of 108). Of 45 patients with genetic abnormalities, a total of 38 sequence variations were detected in 33 (30.6%) patients with five homozygous cases, and 13 chromosomal copy number variants were detected in 12 (11.1%) patients. Novel variants of known causal genes for neurodevelopmental disabilities were detected in 18 (16.7%) patients. These were variants that could be reclassified as likely pathogenic if the de novo nature of the mutation was confirmed after testing of parental samples. CONCLUSIONS Proband-only clinical exome sequencing is a practical diagnostic tool that may be implemented in the clinical setting for patients with neurodevelopmental disabilities. A cost-effective approach to neurodevelopmental disabilities would be a proband-only clinical exome sequencing followed by parental testing of selective candidate variants.
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23
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Srivastava S, Love-Nichols JA, Dies KA, Ledbetter DH, Martin CL, Chung WK, Firth HV, Frazier T, Hansen RL, Prock L, Brunner H, Hoang N, Scherer SW, Sahin M, Miller DT. Meta-analysis and multidisciplinary consensus statement: exome sequencing is a first-tier clinical diagnostic test for individuals with neurodevelopmental disorders. Genet Med 2019; 21:2413-2421. [PMID: 31182824 PMCID: PMC6831729 DOI: 10.1038/s41436-019-0554-6] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Purpose For neurodevelopmental disorders (NDDs), etiological evaluation can
be a diagnostic odyssey involving numerous genetic tests, underscoring the need
to develop a streamlined algorithm maximizing molecular diagnostic yield for
this clinical indication. Our objective was to compare the yield of exome
sequencing (ES) with that of chromosomal microarray (CMA), the current
first-tier test for NDDs. Methods We performed a PubMed scoping review and meta-analysis investigating
the diagnostic yield of ES for NDDs as the basis of a consensus development
conference. We defined NDD as global developmental delay, intellectual
disability, and/or autism spectrum disorder. The consensus development
conference included input from genetics professionals, pediatric neurologists,
and developmental behavioral pediatricians. Results After applying strict inclusion/exclusion criteria, we identified 30
articles with data on molecular diagnostic yield in individuals with isolated
NDD, or NDD plus associated conditions (such as Rett-like features). Yield of ES
was 36% overall, 31% for isolated NDD, and 53% for the NDD plus associated
conditions. ES yield for NDDs is markedly greater than previous studies of CMA
(15–20%). Conclusion Our review demonstrates that ES consistently outperforms CMA for
evaluation of unexplained NDDs. We propose a diagnostic algorithm placing ES at
the beginning of the evaluation of unexplained NDDs.
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Affiliation(s)
- Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie A Love-Nichols
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kira A Dies
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Christa L Martin
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA.,SFARI, Simons Foundation, New York, NY, USA
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Robin L Hansen
- MIND Institute, Department of Pediatrics, University of California Davis, Sacramento, CA, USA
| | - Lisa Prock
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Developmental Medicine Center, Boston Children's Hospital, Boston, MA, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.,The Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ny Hoang
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON, Canada.,Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Mustafa Sahin
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
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24
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Dikow N, Moog U, Karch S, Sander A, Kilian S, Blank R, Reuner G. What do parents expect from a genetic diagnosis of their child with intellectual disability? JOURNAL OF APPLIED RESEARCH IN INTELLECTUAL DISABILITIES 2019; 32:1129-1137. [PMID: 30983121 DOI: 10.1111/jar.12602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 02/28/2019] [Accepted: 03/22/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Caring for a child with intellectual disability (ID) has been associated with increased social and psychological burdens. Diagnostic and prognostic uncertainty may enhance emotional stress in families. METHOD The present authors assessed the motivations, expectations, mental health, physical health and the quality of life of 194 parents whose children with intellectual disability were undergoing a genetic diagnostic workup. RESULTS Most parents considered a diagnosis highly relevant for their own emotional relief, their child's therapies and education, or family planning. Parental mental health was significantly lower compared with the normative sample, but physical health was not different. The severity of the child's intellectual disability correlated negatively with their parents' mental and physical health, quality of life, and positively with parental anxiety. CONCLUSION Healthcare providers should be aware of the disadvantages facing families with intellectually disabled children. Receiving practical, social and psychological support as well as genetic testing might be particularly relevant for families with severely disabled children.
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Affiliation(s)
- Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Stephanie Karch
- Section for Neuropediatrics and Inborn Errors of Metabolism, University Children's Hospital, Clinic I, Heidelberg, Germany
| | - Anja Sander
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Samuel Kilian
- Institute of Medical Biometry and Informatics, University of Heidelberg, Heidelberg, Germany
| | - Rainer Blank
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Gitta Reuner
- Section for Neuropediatrics and Inborn Errors of Metabolism, University Children's Hospital, Clinic I, Heidelberg, Germany
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25
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de Oliveira JF, do Prado PFV, da Costa SS, Sforça ML, Canateli C, Ranzani AT, Maschietto M, de Oliveira PSL, Otto PA, Klevit RE, Krepischi ACV, Rosenberg C, Franchini KG. Mechanistic insights revealed by a UBE2A mutation linked to intellectual disability. Nat Chem Biol 2018; 15:62-70. [PMID: 30531907 DOI: 10.1038/s41589-018-0177-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 10/26/2018] [Indexed: 12/30/2022]
Abstract
Ubiquitin-conjugating enzymes (E2) enable protein ubiquitination by conjugating ubiquitin to their catalytic cysteine for subsequent transfer to a target lysine side chain. Deprotonation of the incoming lysine enables its nucleophilicity, but determinants of lysine activation remain poorly understood. We report a novel pathogenic mutation in the E2 UBE2A, identified in two brothers with mild intellectual disability. The pathogenic Q93E mutation yields UBE2A with impaired aminolysis activity but no loss of the ability to be conjugated with ubiquitin. Importantly, the low intrinsic reactivity of UBE2A Q93E was not overcome by a cognate ubiquitin E3 ligase, RAD18, with the UBE2A target PCNA. However, UBE2A Q93E was reactive at high pH or with a low-pKa amine as the nucleophile, thus providing the first evidence of reversion of a defective UBE2A mutation. We propose that Q93E substitution perturbs the UBE2A catalytic microenvironment essential for lysine deprotonation during ubiquitin transfer, thus generating an enzyme that is disabled but not dead.
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Affiliation(s)
| | | | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mauricio Luis Sforça
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Camila Canateli
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Americo Tavares Ranzani
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | - Mariana Maschietto
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Paulo A Otto
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Kleber Gomes Franchini
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, Brazil. .,Department of Internal Medicine, School of Medicine, University of Campinas, Campinas, Brazil.
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26
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Cala-Pérez L, Losa-Iglesias ME, Rodríguez-Sanz D, Calvo-Lobo C, López-López D, Becerro-de-Bengoa-Vallejo R. Evaluation of podiatric disorders in a sample of children with intellectual disabilities: an analytical cross-sectional study. SAO PAULO MED J 2018; 136:505-510. [PMID: 30892480 PMCID: PMC9897143 DOI: 10.1590/1516-3180.2018.0202161118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/16/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Intellectual disabilities (IDs) usually derive from neurodevelopmental disabilities. They limit intellectual functioning and cause adaptive behaviors and orthopedic problems. These disabilities have harmful effects on health, everyday practical skills and social functioning, and they diminish quality of life. The goal of our research was to perform podiatric evaluations on schoolchildren with and without ID and ascertain their records of foot disorders. DESIGN AND SETTING Analytical cross-sectional study conducted at a podiatric clinic in the city of Piedras Blancas, province of Asturias, Spain. METHODS An analytical cross-sectional study on 82 schoolchildren affected by ID, compared with 117 healthy schoolchildren, was conducted at a podiatric clinic. Demographic data, clinical characteristics and measurements relating to podiatric examinations were recorded among the participants who completed all phases of the tool that was used in the study process. RESULTS Almost 90% of the schoolchildren with and without ID presented foot disorders relating to smaller toes, nail disorders, flat feet or lower-limb alterations. CONCLUSIONS The participants showed elevated prevalence of foot disorders. Podiatric evaluations are a significant means for preventing the appearance of medical conditions and/or foot problems, and they also improve general health.
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Affiliation(s)
- Laura Cala-Pérez
- DP, MSc, PhD. External Collaborator, Department of Nursing, Faculty of Health Sciences, Universidad Rey Juan Carlos, Madrid, Spain
| | - Marta Elena Losa-Iglesias
- RN, DP, BSc, MSc, PhD. Professor, Department of Nursing, Faculty of Health Sciences, Universidad Rey Juan Carlos, Madrid, Spain
| | - David Rodríguez-Sanz
- DP, PT, MSc, PhD. Assistant Professor, Faculty of Sport Sciences, Universidad Europea de Madrid, Madrid 28670, Spain
- PT, MSc, PhD. Assistant Professor, Department of Nursing and Physical Therapy, Faculty of Health Sciences, Universidad de León, Ponferrada, León, Spain
| | - César Calvo-Lobo
- PT, MSc, PhD. Assistant Professor, Department of Nursing and Physical Therapy, Faculty of Health Sciences, Universidad de León, Ponferrada, León, Spain
| | - Daniel López-López
- DP, BSc, MSc, PhD. Professor and Researcher, Health and Podiatry Research Unit, Department of Health Sciences, Faculty of Nursing and Podiatry, Universidade da Coruña, Spain
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27
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Improved diagnostics by exome sequencing following raw data
reevaluation by clinical geneticists involved in the medical care of the individuals
tested. Genet Med 2018; 21:1443-1451. [DOI: 10.1038/s41436-018-0343-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/09/2018] [Indexed: 11/09/2022] Open
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28
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Strande NT, Brnich SE, Roman TS, Berg JS. Navigating the nuances of clinical sequence variant interpretation in Mendelian disease. Genet Med 2018; 20:918-926. [PMID: 29988079 PMCID: PMC6679919 DOI: 10.1038/s41436-018-0100-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Understanding clinical genetic test results in the era of next-generation sequencing has become increasingly complex, necessitating clear and thorough guidelines for sequence variant interpretation. To meet this need the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published guidelines for a systematic approach for sequence variant interpretation in 2015. This framework is intended to be adaptable to any Mendelian condition, promoting transparency and consistency in variant interpretation, yet its comprehensive nature yields important challenges and caveats that end users must understand. In this review, we address some of these nuances and discuss the evolving efforts to refine and adapt this framework. We also consider the added complexity of distinguishing between variant-level interpretations and case-level conclusions, particularly in the context of the large gene panel approach to clinical diagnostics.
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Affiliation(s)
- Natasha T Strande
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah E Brnich
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tamara S Roman
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jonathan S Berg
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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