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Slavotinek AM, Thompson ML, Martin LJ, Gelb BD. Diagnostic yield after next-generation sequencing in pediatric cardiovascular disease. HGG ADVANCES 2024; 5:100286. [PMID: 38521975 PMCID: PMC11024993 DOI: 10.1016/j.xhgg.2024.100286] [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: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024] Open
Abstract
Genetic testing with exome sequencing and genome sequencing is increasingly offered to infants and children with cardiovascular diseases. However, the rates of positive diagnoses after genetic testing within the different categories of cardiac disease and phenotypic subtypes of congenital heart disease (CHD) have been little studied. We report the diagnostic yield after next-generation sequencing in 500 patients with CHD from diverse population subgroups that were enrolled at three different sites in the Clinical Sequencing Evidence-Generating Research consortium. Patients were ascertained due to a primary cardiovascular issue comprising arrhythmia, cardiomyopathy, and/or CHD, and corresponding human phenotype ontology terms were selected to describe the cardiac and extracardiac findings. We examined the diagnostic yield for patients with arrhythmia, cardiomyopathy, and/or CHD and phenotypic subtypes of CHD comprising conotruncal defects, heterotaxy, left ventricular outflow tract obstruction, septal defects, and "other" heart defects. We found a significant increase in the frequency of positive findings for patients who underwent genome sequencing compared to exome sequencing and for syndromic cardiac defects compared to isolated cardiac defects. We also found significantly higher diagnostic rates for patients who presented with isolated cardiomyopathy compared to isolated CHD. For patients with syndromic presentations who underwent genome sequencing, there were significant differences in the numbers of positive diagnoses for phenotypic subcategories of CHD, ranging from 31.7% for septal defects to 60% for "other". Despite variation in the diagnostic yield at each site, our results support genetic testing in pediatric patients with syndromic and isolated cardiovascular issues and in all subtypes of CHD.
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Affiliation(s)
- Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA; Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Michelle L Thompson
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH, USA; Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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2
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Weymann D, Buckell J, Fahr P, Loewen R, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, Elliott AM, Wordsworth S, Buchanan J, Regier DA. Health Care Costs After Genome-Wide Sequencing for Children With Rare Diseases in England and Canada. JAMA Netw Open 2024; 7:e2420842. [PMID: 38985473 PMCID: PMC11238031 DOI: 10.1001/jamanetworkopen.2024.20842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/07/2024] [Indexed: 07/11/2024] Open
Abstract
Importance Etiologic diagnoses for rare diseases can involve a diagnostic odyssey, with repeated health care interactions and inconclusive diagnostics. Prior studies reported cost savings associated with genome-wide sequencing (GWS) compared with cytogenetic or molecular testing through rapid genetic diagnosis, but there is limited evidence on whether diagnosis from GWS is associated with reduced health care costs. Objective To measure changes in health care costs after diagnosis from GWS for Canadian and English children with suspected rare diseases. Design, Setting, and Participants This cohort study was a quasiexperimental retrospective analysis across 3 distinct English and Canadian cohorts, completed in 2023. Mixed-effects generalized linear regression was used to estimate associations between GWS and costs in the 2 years before and after GWS. Difference-in-differences regression was used to estimate associations of genetic diagnosis and costs. Costs are in 2019 US dollars. GWS was conducted in a research setting (Genomics England 100 000 Genomes Project [100KGP] and Clinical Assessment of the Utility of Sequencing and Evaluation as a Service [CAUSES] Research Clinic) or clinical outpatient setting (publicly reimbursed GWS in British Columbia [BC], Canada). Participants were children with developmental disorders, seizure disorders, or both undergoing GWS between 2014 and 2019. Data were analyzed from April 2021 to September 2023. Exposures GWS and genetic diagnosis. Main Outcomes and Measures Annual health care costs and diagnostic costs per child. Results Study cohorts included 7775 patients in 100KGP, among whom 788 children had epilepsy (mean [SD] age at GWS, 11.6 [11.1] years; 400 female [50.8%]) and 6987 children had an intellectual disability (mean [SD] age at GWS, 8.2 [8.4] years; 2750 female [39.4%]); 77 patients in CAUSES (mean [SD] age at GWS, 8.5 [4.4] years; 33 female [42.9%]); and 118 publicly reimbursed GWS recipients from BC (mean [SD] age at GWS, 5.5 [5.2] years; 58 female [49.2%]). GWS diagnostic yield was 143 children (18.1%) for those with epilepsy and 1323 children (18.9%) for those with an intellectual disability in 100KGP, 47 children (39.8%) in the BC publicly reimbursed setting, and 42 children (54.5%) in CAUSES. Mean annual per-patient spending over the study period was $5283 (95% CI, $5121-$5427) for epilepsy and $3373 (95% CI, $3322-$3424) for intellectual disability in the 100KGP, $724 (95% CI, $563-$886) in CAUSES, and $1573 (95% CI, $1372-$1773) in the BC reimbursed setting. Receiving a genetic diagnosis from GWS was not associated with changed costs in any cohort. Conclusions and Relevance In this study, receiving a genetic diagnosis was not associated with cost savings. This finding suggests that patient benefit and cost-effectiveness should instead drive GWS implementation.
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Affiliation(s)
- Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - John Buckell
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Primary Health Care Sciences, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Biochemical Genetics, BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Alison M. Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Biomedical Research Centre, Oxford, United Kingdom
| | - Dean A. Regier
- Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Sandal S, Verma IC, Mahay SB, Dubey S, Sabharwal RK, Kulshrestha S, Saxena R, Suman P, Kumar P, Puri RD. Next-Generation Sequencing in Unexplained Intellectual Disability. Indian J Pediatr 2024; 91:682-695. [PMID: 37804371 DOI: 10.1007/s12098-023-04820-5] [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: 12/11/2022] [Accepted: 06/23/2023] [Indexed: 10/09/2023]
Abstract
OBJECTIVES To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. METHODS This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. RESULTS The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. CONCLUSIONS There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.
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Affiliation(s)
- Sapna Sandal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Ishwar Chander Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - R K Sabharwal
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Samarth Kulshrestha
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Suman
- Department of Developmental Pediatrics, Sir Ganga Ram Hospital, New Delhi, India
| | - Praveen Kumar
- Department of Pediatric Neurology, Sir Ganga Ram Hospital, New Delhi, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India.
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Cortés BI, Meza RC, Ancatén-González C, Ardiles NM, Aránguiz MI, Tomita H, Kaplan DR, Cornejo F, Nunez-Parra A, Moya PR, Chávez AE, Cancino GI. Loss of protein tyrosine phosphatase receptor delta PTPRD increases the number of cortical neurons, impairs synaptic function and induces autistic-like behaviors in adult mice. Biol Res 2024; 57:40. [PMID: 38890753 PMCID: PMC11186208 DOI: 10.1186/s40659-024-00522-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The brain cortex is responsible for many higher-level cognitive functions. Disruptions during cortical development have long-lasting consequences on brain function and are associated with the etiology of brain disorders. We previously found that the protein tyrosine phosphatase receptor delta Ptprd, which is genetically associated with several human neurodevelopmental disorders, is essential to cortical brain development. Loss of Ptprd expression induced an aberrant increase of excitatory neurons in embryonic and neonatal mice by hyper-activating the pro-neurogenic receptors TrkB and PDGFRβ in neural precursor cells. However, whether these alterations have long-lasting consequences in adulthood remains unknown. RESULTS Here, we found that in Ptprd+/- or Ptprd-/- mice, the developmental increase of excitatory neurons persists through adulthood, affecting excitatory synaptic function in the medial prefrontal cortex. Likewise, heterozygosity or homozygosity for Ptprd also induced an increase of inhibitory cortical GABAergic neurons and impaired inhibitory synaptic transmission. Lastly, Ptprd+/- or Ptprd-/- mice displayed autistic-like behaviors and no learning and memory impairments or anxiety. CONCLUSIONS These results indicate that loss of Ptprd has long-lasting effects on cortical neuron number and synaptic function that may aberrantly impact ASD-like behaviors.
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Affiliation(s)
- Bastián I Cortés
- Laboratorio de Neurobiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Rodrigo C Meza
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
| | - Carlos Ancatén-González
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
- Programa de Doctorado en Ciencias mención Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
| | - Nicolás M Ardiles
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
| | - María-Ignacia Aránguiz
- Laboratorio de Neurobiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile
| | - Hideaki Tomita
- Program in Neuroscience and Mental Health, The Hospital for Sick Children, Toronto, M5G 1X8, Canada
- Ludna Biotech Co., Ltd, Suita, Osaka, 565-0871, Japan
| | - David R Kaplan
- Program in Neuroscience and Mental Health, The Hospital for Sick Children, Toronto, M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1X8, Canada
| | - Francisca Cornejo
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - Alexia Nunez-Parra
- Cell Physiology Laboratory, Biology Department, Faculty of Science, Universidad de Chile, Santiago, 7800003, Chile
| | - Pablo R Moya
- Centro de Estudios Traslacionales en Estrés y Salud Mental (C-ESTRES), Universidad de Valparaíso, Valparaíso, 2340000, Chile
- Instituto de Fisiología, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
| | - Andrés E Chávez
- Centro Interdisciplinario de Neurociencia de Valparaíso (CINV), Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
- Instituto de Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, 2340000, Chile
| | - Gonzalo I Cancino
- Laboratorio de Neurobiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile.
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Zhang J, Xu Y, Liu Y, Yue L, Jin H, Chen Y, Wang D, Wang M, Chen G, Yang L, Zhang G, Zhang X, Li S, Zhao H, Zhao Y, Niu G, Gao Y, Cai Z, Yang F, Zhu C, Zhu D. Genetic Testing for Global Developmental Delay in Early Childhood. JAMA Netw Open 2024; 7:e2415084. [PMID: 38837156 PMCID: PMC11154162 DOI: 10.1001/jamanetworkopen.2024.15084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/03/2024] [Indexed: 06/06/2024] Open
Abstract
Importance Global developmental delay (GDD) is characterized by a complex etiology, diverse phenotypes, and high individual heterogeneity, presenting challenges for early clinical etiologic diagnosis. Cognitive impairment is the core symptom, and despite the pivotal role of genetic factors in GDD development, the understanding of them remains limited. Objectives To assess the utility of genetic detection in patients with GDD and to examine the potential molecular pathogenesis of GDD to identify targets for early intervention. Design, Setting, and Participants This multicenter, prospective cohort study enrolled patients aged 12 to 60 months with GDD from 6 centers in China from July 4, 2020, to August 31, 2023. Participants underwent trio whole exome sequencing (trio-WES) coupled with copy number variation sequencing (CNV-seq). Bioinformatics analysis was used to unravel pathogenesis and identify therapeutic targets. Main Outcomes and Measures The main outcomes of this study involved enhancing the rate of positive genetic diagnosis for GDD, broadening the scope of genetic testing indications, and investigating the underlying pathogenesis. The classification of children into levels of cognitive impairment was based on the developmental quotient assessed using the Gesell scale. Results The study encompassed 434 patients with GDD (262 [60%] male; mean [SD] age, 25.75 [13.24] months) with diverse degrees of cognitive impairment: mild (98 [23%]), moderate (141 [32%]), severe (122 [28%]), and profound (73 [17%]). The combined use of trio-WES and CNV-seq resulted in a 61% positive detection rate. Craniofacial abnormalities (odds ratio [OR], 2.27; 95% CI, 1.45-3.56), moderate or severe cognitive impairment (OR, 1.69; 95% CI, 1.05-2.70), and age between 12 and 24 months (OR, 1.57; 95% CI, 1.05-2.35) were associated with a higher risk of carrying genetic variants. Additionally, bioinformatics analysis suggested that genetic variants may induce alterations in brain development and function, which may give rise to cognitive impairment. Moreover, an association was found between the dopaminergic pathway and cognitive impairment. Conclusions and Relevance In this cohort study of patients with GDD, combining trio-WES with CNV-seq was a demonstrable, instrumental strategy for advancing the diagnosis of GDD. The close association among genetic variations, brain development, and clinical phenotypes contributed valuable insights into the pathogenesis of GDD. Notably, the dopaminergic pathway emerged as a promising focal point for potential targets in future precision medical interventions for GDD.
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Affiliation(s)
- Jiamei Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yun Liu
- Kunming Children’s Hospital, Kunming, China
| | - Ling Yue
- Department of Neurological Rehabilitation, Children’s Hospital of Hebei Province, Shijiazhuang, China
| | - Hongfang Jin
- Qinghai Provincial Women and Children’s Hospital, Xining, China
| | | | - Dong Wang
- Department of Pediatric Neurology, Xi’an Children’s Hospital, Xi’an, China
| | - Mingmei Wang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gongxun Chen
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Yang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangyu Zhang
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoli Zhang
- Department of Pediatric Neurology, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sansong Li
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunxia Zhao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guohui Niu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongqiang Gao
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhijun Cai
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Changlian Zhu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Dengna Zhu
- Department of Rehabilitation Medicine, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Chi CS, Tsai CR, Lee HF. Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study. Arch Dis Child 2024:archdischild-2024-326985. [PMID: 38789118 DOI: 10.1136/archdischild-2024-326985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
OBJECTIVE To resolve unsolved whole-genome sequencing (WGS) data in individuals with paediatric neurological disorders. DESIGN A cohort study method using updated bioinformatic tools, new analysis targets, clinical information and literature databases was employed to reanalyse existing unsolved genome data. PARTICIPANTS From January 2016 to September 2023, a total of 615 individuals who aged under 18 years old, exhibited neurological disorders and received singleton WGS were recruited. 364 cases were unsolved during initial WGS analysis, in which 102 consented to reanalyse existing singleton WGS data. RESULTS Median duration for reanalysis after initial negative WGS results was 2 years and 4 months. The diagnostic yield was 29 of 102 individuals (28.4%) through reanalysis. New disease gene discovery and new target acquisitions contributed to 13 of 29 solved cases (44.8%). The reasons of non-detected causative variants during initial WGS analysis were variant reclassification in 9 individuals (31%), analytical issue in 9 (31%), new emerging disease-gene association in 8 (27.6%) and clinical update in 3 (10.3%). The 29 new diagnoses increased the cumulative diagnostic yield of clinical WGS in the entire study cohort to 45.5% after reanalysis. CONCLUSIONS Unsolved paediatric WGS individuals with neurological disorders could obtain molecular diagnoses through reanalysis within a timeframe of 2-2.5 years. New disease gene, structural variations and deep intronic splice variants make a significant contribution to diagnostic yield. This approach can provide precise genetic counselling to positive reanalysis results and end a diagnostic odyssey.
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Affiliation(s)
- Ching-Shiang Chi
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Ren Tsai
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Hsiu-Fen Lee
- Division of Pediatric Neurology, Children's Medical Center, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, Taiwan
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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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Lai W, Zhao Y, Chen Y, Dai Z, Chen R, Niu Y, Chen X, Chen S, Huang G, Shan Z, Zheng J, Hu Y, Chen Q, Gong S, Kang S, Guo H, Ma X, Song Y, Xia K, Wang J, Zhou L, So KF, Wang K, Qiu S, Zhang L, Chen J, Shi L. Autism patient-derived SHANK2B Y29X mutation affects the development of ALDH1A1 negative dopamine neuron. Mol Psychiatry 2024:10.1038/s41380-024-02578-6. [PMID: 38704506 DOI: 10.1038/s41380-024-02578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Autism spectrum disorder (ASD) encompasses a range of neurodevelopmental conditions. Different mutations on a single ASD gene contribute to heterogeneity of disease phenotypes, possibly due to functional diversity of generated isoforms. SHANK2, a causative gene in ASD, demonstrates this phenomenon, but there is a scarcity of tools for studying endogenous SHANK2 proteins in an isoform-specific manner. Here, we report a point mutation on SHANK2, which is found in a patient with autism, located on exon of the SHANK2B transcript variant (NM_133266.5), hereby SHANK2BY29X. This mutation results in an early stop codon and an aberrant splicing event that impacts SHANK2 transcript variants distinctly. Induced pluripotent stem cells (iPSCs) carrying this mutation, from the patient or isogenic editing, fail to differentiate into functional dopamine (DA) neurons, which can be rescued by genetic correction. Available SMART-Seq single-cell data from human midbrain reveals the abundance of SHANK2B transcript in the ALDH1A1 negative DA neurons. We then show that SHANK2BY29X mutation primarily affects SHANK2B expression and ALDH1A1 negative DA neurons in vitro during early neuronal developmental stage. Mice knocked in with the identical mutation exhibit autistic-like behavior, decreased occupancy of ALDH1A1 negative DA neurons and decreased dopamine release in ventral tegmental area (VTA). Our study provides novel insights on a SHANK2 mutation derived from autism patient and highlights SHANK2B significance in ALDH1A1 negative DA neuron.
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Affiliation(s)
- Wanjing Lai
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Yingying Zhao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, 999077, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yalan Chen
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Zhenzhu Dai
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Ruhai Chen
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Yimei Niu
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Xiaoxia Chen
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Shuting Chen
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Guanqun Huang
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Ziyun Shan
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiajun Zheng
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Yu Hu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qingpei Chen
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Siyi Gong
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Sai Kang
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Hui Guo
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Xiaokuang Ma
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 850004, USA
| | - Youqiang Song
- School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China
| | - Jie Wang
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Libing Zhou
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Kwok-Fai So
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Shenfeng Qiu
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 850004, USA
| | - Li Zhang
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China.
| | - Jiekai Chen
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, 999077, China.
| | - Lingling Shi
- Guangdong-Hongkong-Macau CNS Regeneration Institute of Jinan University, Key Laboratory of CNS Regeneration (Jinan University)-Ministry of Education, Guangdong Key Laboratory of Non-human Primate Research, Guangzhou, 510632, China.
- Department of Psychiatry, the First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, 510632, China.
- Co-innovation Center of Neuro-regeneration, Nantong University, Nantong, Jiangsu, 226019, China.
- Department of Neurology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China.
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9
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Ma H, Zhu L, Yang X, Ao M, Zhang S, Guo M, Dai X, Ma X, Zhang X. Genetic and phenotypic analysis of 225 Chinese children with developmental delay and/or intellectual disability using whole-exome sequencing. BMC Genomics 2024; 25:391. [PMID: 38649797 PMCID: PMC11034079 DOI: 10.1186/s12864-024-10279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
Developmental delay (DD), or intellectual disability (ID) is a very large group of early onset disorders that affects 1-2% of children worldwide, which have diverse genetic causes that should be identified. Genetic studies can elucidate the pathogenesis underlying DD/ID. In this study, whole-exome sequencing (WES) was performed on 225 Chinese DD/ID children (208 cases were sequenced as proband-parent trio) who were classified into seven phenotype subgroups. The phenotype and genomic data of patients with DD/ID were further retrospectively analyzed. There were 96/225 (42.67%; 95% confidence interval [CI] 36.15-49.18%) patients were found to have causative single nucleotide variants (SNVs) and small insertions/deletions (Indels) associated with DD/ID based on WES data. The diagnostic yields among the seven subgroups ranged from 31.25 to 71.43%. Three specific clinical features, hearing loss, visual loss, and facial dysmorphism, can significantly increase the diagnostic yield of WES in patients with DD/ID (P = 0.005, P = 0.005, and P = 0.039, respectively). Of note, hearing loss (odds ratio [OR] = 1.86%; 95% CI = 1.00-3.46, P = 0.046) or abnormal brainstem auditory evoked potential (BAEP) (OR = 1.91, 95% CI = 1.02-3.50, P = 0.042) was independently associated with causative genetic variants in DD/ID children. Our findings enrich the variation spectrums of SNVs/Indels associated with DD/ID, highlight the value genetic testing for DD/ID children, stress the importance of BAEP screen in DD/ID children, and help to facilitate early diagnose, clinical management and reproductive decisions, improve therapeutic response to medical treatment.
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Affiliation(s)
- Heqian Ma
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Lina Zhu
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Xiao Yang
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China
| | - Meng Ao
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Shunxiang Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Meizhen Guo
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xuelin Dai
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China
| | - Xiuwei Ma
- Faculty of Pediatrics, The Chinese PLA General Hospital, 100700, Beijing, China.
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, 100700, Beijing, China.
- Beijing Key Laboratory of Pediatric Organ Failure, 100700, Beijing, China.
| | - Xiaoying Zhang
- The School of Public Health, Guilin Medical University, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- The Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Heath, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
- Guangxi Health Commission Key Laboratory of Entire Lifecycle Health and Care, 1 Zhiyuan Road, Lingui District, 541199, Guilin, PR China.
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10
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Regier DA, Loewen R, Chan B, Ehman M, Pollard S, Friedman JM, Stockler-Ipsiroglu S, van Karnebeek C, Race S, Elliott AM, Dragojlovic N, Lynd LD, Weymann D. Real-world diagnostic outcomes and cost-effectiveness of genome-wide sequencing for developmental and seizure disorders: Evidence from Canada. Genet Med 2024; 26:101069. [PMID: 38205742 DOI: 10.1016/j.gim.2024.101069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
PURPOSE To determine real-world diagnostic rates, cost trajectories, and cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children with developmental and/or seizure disorders in British Columbia, Canada. METHODS Based on medical records review, we estimated real-world costs and outcomes for 491 patients who underwent standard of care (SOC) diagnostic testing at British Columbia Children's Hospital. Results informed a state-transition Markov model examining cost-effectiveness of 3 competing diagnostic strategies: (1) SOC with last-tier access to ES, (2) streamlined ES access, and (3) first-tier GS. RESULTS Through SOC, 49.4% (95% CI: 40.6, 58.2) of patients were diagnosed at an average cost of C$11,683 per patient (95% CI: 9200, 14,166). Compared with SOC, earlier ES or GS access yielded similar or improved diagnostic rates and shorter times to genetic diagnosis, with 94% of simulations demonstrating cost savings for streamlined ES and 60% for first-tier GS. Net benefit from the perspective of the health care system was C$2956 (95% CI: -608, 6519) for streamlined ES compared with SOC. CONCLUSION Using real-world data, we found earlier access to ES may yield more rapid genetic diagnosis of childhood developmental and seizure disorders and cost savings compared with current practice in a Canadian health care system.
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Affiliation(s)
- Dean A Regier
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Rosalie Loewen
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Brandon Chan
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Morgan Ehman
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Samantha Pollard
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Sylvia Stockler-Ipsiroglu
- BC Children's Hospital Research Institute, Vancouver, Canada; Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Clara van Karnebeek
- Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, Canada; Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Simone Race
- Division of Biochemical Genetics, BC Children's Hospital, Vancouver, Canada
| | - Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, Vancouver, Canada
| | - Nick Dragojlovic
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada; Centre for Health Evaluation and Outcomes Sciences, Providence Health Research Institute, Vancouver, Canada
| | - Deirdre Weymann
- Cancer Control Research, BC Cancer Research Institute, Vancouver, Canada.
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11
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Hiatt SM, Lawlor JM, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Nunez IR, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst ACE, Korf BR, Schmutz J, Grimwood J, Cooper GM. Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304633. [PMID: 38585854 PMCID: PMC10996728 DOI: 10.1101/2024.03.22.24304633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Variant detection from long-read genome sequencing (lrGS) has proven to be considerably more accurate and comprehensive than variant detection from short-read genome sequencing (srGS). However, the rate at which lrGS can increase molecular diagnostic yield for rare disease is not yet precisely characterized. We performed lrGS using Pacific Biosciences "HiFi" technology on 96 short-read-negative probands with rare disease that were suspected to be genetic. We generated hg38-aligned variants and de novo phased genome assemblies, and subsequently annotated, filtered, and curated variants using clinical standards. New disease-relevant or potentially relevant genetic findings were identified in 16/96 (16.7%) probands, eight of which (8/96, 8.33%) harbored pathogenic or likely pathogenic variants. Newly identified variants were visible in both srGS and lrGS in nine probands (~9.4%) and resulted from changes to interpretation mostly from recent gene-disease association discoveries. Seven cases included variants that were only interpretable in lrGS, including copy-number variants, an inversion, a mobile element insertion, two low-complexity repeat expansions, and a 1 bp deletion. While evidence for each of these variants is, in retrospect, visible in srGS, they were either: not called within srGS data, were represented by calls with incorrect sizes or structures, or failed quality-control and filtration. Thus, while reanalysis of older data clearly increases diagnostic yield, we find that lrGS allows for substantial additional yield (7/96, 7.3%) beyond srGS. We anticipate that as lrGS analysis improves, and as lrGS datasets grow allowing for better variant frequency annotation, the additional lrGS-only rare disease yield will grow over time.
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Affiliation(s)
- Susan M. Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Lori H. Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Donald R. Latner
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | | | | | - Lori Beth Boston
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Melissa Williams
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | | | - E. Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Michael A. Lopez
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Anna C. E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Bruce R. Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35924, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
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12
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Donnellan EP, Gorman KM, Shahwan A, Allen NM. Epileptic dyskinetic encephalopathy in KBG syndrome: Expansion of the phenotype. Epilepsy Behav Rep 2024; 25:100647. [PMID: 38317675 PMCID: PMC10839861 DOI: 10.1016/j.ebr.2024.100647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/07/2024] Open
Abstract
KBG syndrome is characterised by developmental delay, dental (macrodontia of upper central incisors), craniofacial and skeletal anomalies. Since the identification of variants in the gene (ANKRD11) responsible for KBG syndrome, wider phenotypes are emerging. While there is phenotypic variability within many features of KBG syndrome, epilepsy is not usually markedly severe and movement disorders largely undocumented. Here we describe a novel early onset phenotype of dyskinetic epileptic encephalopathy in a male, who presented during infancy with a florid hyperkinetic movement disorder and developmental regression. Initially he had epileptic spasms and tonic seizures, and EEGs revealed a modified hypsarrhythmia. The epilepsy phenotype evolved to Lennox-Gastaut syndrome with seizures resistant to multiple anti-seizure therapies and the movement disorder evolved to choreoathetosis of limbs and head with oro-lingual dyskinesias. Previous extensive neurometabolic and imaging investigations, including panel-based exome sequencing were unremarkable. Later trio exome sequencing identified a de novo pathogenic heterozygous frameshift deletion of ANKRD11 (c.6792delC; p.Ala2265Profs*72). Review of the literature did not identify any individuals with such a hyperkinetic movement disorder presentation in combination with early-onset epileptic encephalopathy. This report expands the phenotype of ANKRD11-related KBG syndrome to include epileptic dyskinetic encephalopathy.
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Affiliation(s)
- Eoin P. Donnellan
- Dept. of Paediatrics, Galway University Hospital, Ireland
- Dept. of Paediatrics, School of Medicine, University of Galway, Ireland
| | - Kathleen M. Gorman
- Dept of Paediatric Neurology and Neurophysiology, Children’s Health Ireland at Temple St., Dublin 1, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Amre Shahwan
- Dept of Paediatric Neurology and Neurophysiology, Children’s Health Ireland at Temple St., Dublin 1, Ireland
- School of Medicine, Royal College of Surgeons in Ireland, Ireland
| | - Nicholas M. Allen
- Dept. of Paediatrics, Galway University Hospital, Ireland
- Dept. of Paediatrics, School of Medicine, University of Galway, Ireland
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13
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Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F. Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:15-23. [PMID: 37725747 DOI: 10.1002/uog.27491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- N Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, Cambridge, UK
| | - C Sproule
- Department of Obstetrics & Gynaecology, South Eastern Health and Social Care Trust, Belfast, UK
| | - K W Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Z Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - K Gajewska-Knapik
- Department of Obstetrics & Gynaecology, Cambridge University Hospitals, Cambridge, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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14
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Shin S, Lee J, Kim YG, Ha C, Park JH, Kim JW, Lee J, Jang JH. Genetic Diagnosis of Children With Neurodevelopmental Disorders Using Whole Genome Sequencing. Pediatr Neurol 2023; 149:44-52. [PMID: 37776660 DOI: 10.1016/j.pediatrneurol.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/05/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) have diverse phenotypes. Their genetic diagnoses are often challenged by difficulties of targeting causative genes due to heterogeneous genetic etiologies. The objective of this study was to perform genetic diagnosis of children with NDDs using whole genome sequencing. METHODS This study included 78 pediatric patients with NDDs and their 152 family members for whole genome sequencing (WGS). All cases except one were families with at least two members. Seventy-five patients had previously undergone other genetic tests besides WGS. Detected variants were classified according to the guidelines of the American College of Medical Genetics and Genomics. RESULTS Among 78 probands, 26 patients were genetically diagnosed with NDDs through WGS, showing a diagnostic rate of 33.3%. Of them, 22 cases had de novo variants (DNVs) identified through trio analysis. Of these DNVs, half were novel variants. Three structural variants, including a multiexon deletion, a contiguous gene deletion involving 13 Mb, and a retrotransposon insertion, were revealed by WGS. All cases except one had defects in different genes, consistent with the phenotypically diverse nature of NDDs. In addition, three patients were inconclusive, two of them had one likely pathogenic variant in a gene associated with autosomal recessive disease and the other one had no clinical phenotypes associated with the detected DNV. CONCLUSIONS Our experience demonstrates the advantage of WGS in the diagnosis of NDDs, including detection of copy number variations and also the advantage of trio sequencing for interpretation of DNVs.
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Affiliation(s)
- Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Laboratory Medicine, Inje University Ilsan Paik Hospital, Goyang, Korea
| | - Jiwon Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeehun Lee
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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15
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Yesmin MF, Chowdhury MRK, Bornee FA, Kader M, Mondal MNI, Hossain M, Rashid M. Urban-rural difference in factors associated with childhood functional difficulty in Bangladesh: a cross-sectional study. Front Public Health 2023; 11:1270853. [PMID: 38026377 PMCID: PMC10652778 DOI: 10.3389/fpubh.2023.1270853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Objective Early childhood functional difficulty poses a substantial worldwide public health challenge, leading to adverse effects on children's quality of life and overall productivity. Moreover, it represents a significant social and economic problem in Bangladesh. Therefore, the current study aimed to identify factors contributing to childhood functional difficulty in Bangladesh within the context of urban-rural areas. Methods A nationally representative cross-sectional survey data from Multiple Indicator Cluster Survey (MICS), 2019 in Bangladesh was used in this study. Chi-square test and multivariable logistic regression analyses were carried out to identify factors associated with childhood functional difficulty. Results Functional difficulties were found in approximately 3.3% of children 2-4 years of age in urban areas and 2.5% in rural areas. Having a mother with functional difficulties and undernutrition were identified as significant factors common in both urban and rural areas. Further, mothers who had no formal education (AOR = 2.76, 95%CI = 1.18-6.45) and experienced infant death (AOR = 1.94, 95%CI = 1.01-3.70) were identified as significant factors of functional difficulty in urban areas. On the other hand, in rural areas, no access to mass media, children with acute respiratory infection (ARI) (AOR = 2.13, 95%CI = 1.39-3.28), female sex (AOR = 0.69, 95%CI = 0.53-0.91), child undernutrition (AOR = 1.73, 95%CI = 1.32-2.27) and poorer socio-economic status (AOR = 1.95, 95%CI = 1.08-3.55) were found significant factors. Conclusion Functional difficulty was found to be present in one out of every 35 children age 2 to 4 years in Bangladesh. Childhood functional difficulties were reported slightly higher in urban areas as compared to rural areas. Reducing childhood difficulties in urban areas demands comprehensive strategies: quality healthcare, inclusive education, community support, better information systems, and collaboration. To achieve urban-rural parity in child health, address disparities in economic development, healthcare, and education, especially for girls.
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Affiliation(s)
- Mst Farjana Yesmin
- Department of Population Science and Human Resource Development, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Rocky Khan Chowdhury
- Department of Population Science and Human Resource Development, University of Rajshahi, Rajshahi, Bangladesh
- Department of Public Health, First Capital University of Bangladesh, Chuadanga, Bangladesh
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Farzana Akhter Bornee
- Department of Pediatrics, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Manzur Kader
- Department of Medicine, Solna, Clinical Epidemiology Division, Karolinska Institutet, Stockholm, Sweden
| | - Md Nazrul Islam Mondal
- Department of Population Science and Human Resource Development, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Hossain
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Mamunur Rashid
- Department of Public Health and Sports Science, Faculty of Health and Occupational Studies, University of Gävle, Gävle, Sweden
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16
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Sloboda N, Renard E, Lambert L, Bonnet C, Leheup B, Todosi C, Schmitt E, Feillet F, Feigerlova E, Piton A, Journeau P, Klein M, Maillard L, Chelly J, Renaud M. MAST1-related mega-corpus-callosum syndrome with central hypogonadism. Eur J Med Genet 2023; 66:104853. [PMID: 37758169 DOI: 10.1016/j.ejmg.2023.104853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 07/20/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE Heterozygous variations in microtubule-associated serine/threonine kinase 1 gene (MAST1) were recently described in the mega-corpus-callosum syndrome with cerebellar hypoplasia and cortical malformations (MCCCHCM, MIM 618273), revealing the importance of the MAST genes family in global brain development. To date, patients with MAST1 gene mutations were mostly young children with central nervous system involvement, impaired motor function, speech delay, and brain magnetic resonance imaging (MRI) abnormalities. Here, we report the clinical presentation of an adult patient with a rare and de novo MAST1 mutation with central hypogonadism that could extend this phenotype. METHODS A panel of 333 genes involved in epilepsy or cortical development was sequenced in the described patient. Routine biochemical analyses were performed, and hormonal status was investigated. RESULT We report a 22-year-old man with a de novo, heterozygous missense variant in MAST1 (Chr19(GRCh37):g.12975903G > A, NP_055790.1:p.Gly517Ser). He presented with an epileptic encephalopathy associated with cerebral malformations, short stature, hypogonadotropic hypogonadism, and secondary osteopenia. CONCLUSION This is the first patient with MAST1 gene mutation described with central hypogonadism, which may be associated with the phenotype of MCCCHCM syndrome.
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Affiliation(s)
- Natacha Sloboda
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; Centre de Référence des Epilepsies Rares (CRéER) Centre Hospitalier Régional Universitaire, Nancy, F-54000, France
| | - Emeline Renard
- INSERM UMRS 1256 NGERE, Nutrition, Genetics, and Environmental Risk Exposure, National Center of Hospitalier Régional Universitaire, Nancy, France; Service de MédecineInfantile, Centre Hospitalier Régional Universitaire, Nancy, France.
| | - Laetitia Lambert
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; Centre de Référence des Epilepsies Rares (CRéER) Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; INSERM UMRS 1256 NGERE, Nutrition, Genetics, and Environmental Risk Exposure, National Center of Hospitalier Régional Universitaire, Nancy, France
| | - Céline Bonnet
- Laboratoire de Génétique, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Bruno Leheup
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; INSERM UMRS 1256 NGERE, Nutrition, Genetics, and Environmental Risk Exposure, National Center of Hospitalier Régional Universitaire, Nancy, France
| | - Calina Todosi
- Centre de Référence des Epilepsies Rares (CRéER) Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; Laboratoire de Génétique, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Emmanuelle Schmitt
- Service de Neuroradiologie, Centre Hospitalier Régional Universitaire, Nancy, France
| | - François Feillet
- INSERM UMRS 1256 NGERE, Nutrition, Genetics, and Environmental Risk Exposure, National Center of Hospitalier Régional Universitaire, Nancy, France; Service de MédecineInfantile, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Eva Feigerlova
- Service d'Endocrinologie, Centre Hospitalier Régional Universitaire, Nancy, France; INSERM UMR_S 1116 - DCAC, Medical Faculty, Université de Lorraine, Nancy, France
| | - Amélie Piton
- Service de Diagnostic Génétique, Hôpital Civil de Strasbourg, Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France
| | - Pierre Journeau
- Service de Chirurgie Orthopédique Infantile, Hôpital d'Enfants, Vandoeuvre les Nancy, France
| | - Marc Klein
- Service d'Endocrinologie, Centre Hospitalier Régional Universitaire, Nancy, France
| | - Louis Maillard
- Centre de Référence des Epilepsies Rares (CRéER) Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; Service de Neurologie, Centre Hospitalier Régional Universitaire, Nancy, France; CNRS UMR7039,CRAN, Université de Lorraine, Nancy, France
| | - Jamel Chelly
- Service de Diagnostic Génétique, Hôpital Civil de Strasbourg, Hôpitaux Universitaires de Strasbourg, 67091, Strasbourg, France
| | - Mathilde Renaud
- Service de Génétique Clinique, Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; Centre de Référence des Epilepsies Rares (CRéER) Centre Hospitalier Régional Universitaire, Nancy, F-54000, France; INSERM UMRS 1256 NGERE, Nutrition, Genetics, and Environmental Risk Exposure, National Center of Hospitalier Régional Universitaire, Nancy, France
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17
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Mir A, Song Y, Lee H, Khanahmad H, Khorram E, Nasiri J, Tabatabaiefar MA. Whole exome sequencing revealed variants in four genes underlying X-linked intellectual disability in four Iranian families: novel deleterious variants and clinical features with the review of literature. BMC Med Genomics 2023; 16:239. [PMID: 37821930 PMCID: PMC10566173 DOI: 10.1186/s12920-023-01680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
AIM AND OBJECTIVE Intellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims. METHODS Nine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge. RESULTS In three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings. CONCLUSION The current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling.
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Affiliation(s)
- Atefeh Mir
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Yongjun Song
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Khorram
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran.
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
- Deputy of Research and Technology, GenTArget Corp (GTAC), Isfahan University of Medical Sciences, Isfahan, Iran.
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18
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Halley MC, Young JL, Tang C, Mintz KT, Lucas-Griffin S, Maghiro A, Ashley EA, Tabor HK. Genomics Research with Undiagnosed Children: Ethical Challenges at the Boundaries of Research and Clinical Care. J Pediatr 2023; 261:113537. [PMID: 37271495 PMCID: PMC10527480 DOI: 10.1016/j.jpeds.2023.113537] [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: 01/17/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To explore the perspectives of parents of undiagnosed children enrolled in genomic diagnosis research regarding their motivations for enrolling their children, their understanding of the potential burdens and benefits, and the extent to which their experiences ultimately aligned with or diverged from their original expectations. STUDY DESIGN In-depth interviews were conducted with parents, audio-recorded and transcribed. A structured codebook was applied to each transcript, after which iterative memoing was used to identify themes. RESULTS Fifty-four parents participated, including 17 (31.5%) whose child received a diagnosis through research. Themes describing parents' expectations and experiences of genomic diagnosis research included (1) the extent to which parents' motivations for participation focused on their hope that it would directly benefit their child, (2) the ways in which parents' frustrations regarding the research process confused the dual clinical and research goals of their participation, and (3) the limited clinical benefits parents ultimately experienced for their children. CONCLUSIONS Our results suggest that parents of undiagnosed children seeking enrollment in genomic diagnosis research are at risk of a form of therapeutic misconception-in this case, diagnostic misconception. These findings indicate the need to examine the processes and procedures associated with this research to communicate appropriately and balance the potential burdens and benefits of study participation.
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Affiliation(s)
- Meghan C Halley
- Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA.
| | - Jennifer L Young
- Center for Genetic Medicine, Northwestern Feinberg School of Medicine, Chicago, IL
| | - Charis Tang
- Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
| | - Kevin T Mintz
- Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
| | - Sawyer Lucas-Griffin
- Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
| | | | - Euan A Ashley
- Department of Genetics, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Holly K Tabor
- Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA; Department of Medicine, Stanford University School of Medicine; Stanford, CA
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19
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Li N, Kang H, Zou Y, Liu Z, Deng Y, Wang M, Li L, Qin H, Qiu X, Wang Y, Zhu J, Agostino M, Heng JIT, Yu P. A novel heterozygous ZBTB18 missense mutation in a family with non-syndromic intellectual disability. Neurogenetics 2023; 24:251-262. [PMID: 37525067 DOI: 10.1007/s10048-023-00727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Intellectual disability (ID) is a common neurodevelopmental disorder characterized by significantly impaired adaptive behavior and cognitive capacity. High throughput sequencing approaches have revealed the genetic etiologies for 25-50% of ID patients, while inherited genetic mutations were detected in <5% cases. Here, we investigated the genetic cause for non-syndromic ID in a Han Chinese family. Whole genome sequencing was performed on identical twin sisters diagnosed with ID, their respective children, and their asymptomatic parents. Data was filtered for rare variants, and in silico prediction tools were used to establish pathogenic alleles. Candidate mutations were validated by Sanger sequencing. In silico modeling was used to evaluate the mutation's effects on the protein encoded by a candidate coding gene. A novel heterozygous variant in the ZBTB18 gene c.1323C>G (p.His441Gln) was identified. This variant co-segregated with affected individuals in an autosomal dominant pattern and was not detected in asymptomatic family members. Molecular studies reveal that a p.His441Gln substitution disrupts zinc binding within the second zinc finger and disrupts the capacity for ZBTB18 to bind DNA. This is the first report of an inherited ZBTB18 mutation for ID. This study further validates WGS for the accurate molecular diagnosis of ID.
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Affiliation(s)
- Nana Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Hong Kang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Yanna Zou
- Department of Gynaecology and Obstetrics, Changyi Maternal and Child Care Hospital, Weifang, Shandong, China
| | - Zhen Liu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Ying Deng
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Meixian Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Lu Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Hong Qin
- Department of Gynaecology and Obstetrics, Wuhou District People's Hospital, Chengdu, Sichuan, China
| | - Xiaoqiong Qiu
- Department of Obstetrics and Gynecology, Pidu District People's Hospital, Chengdu, China
| | - Yanping Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China
| | - Mark Agostino
- Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Australia
- Curtin Medical School, Curtin University, Bentley, Australia
| | - Julian I-T Heng
- Faculty of Health Sciences, Curtin University, Bentley, Australia.
| | - Ping Yu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, China.
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20
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. Genet Med 2023; 25:100880. [PMID: 37158195 PMCID: PMC10789486 DOI: 10.1016/j.gim.2023.100880] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. METHODS Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. RESULTS A total of 645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses (P < .001). Yield was greater for GS vs TGPs in Hispanic/Latino(a) (17.2% vs 9.5%, P < .001) and White/European American (19.8% vs 7.9%, P < .001) but not in Black/African American (11.5% vs 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. CONCLUSION GS may yield up to twice as many diagnoses in pediatric patients compared with TGP testing but not yet across all population groups.
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Affiliation(s)
- Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe, Inc., Sunnyvale, CA
| | - Priya N Marathe
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Nicole R Kelly
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katherine E Bonini
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Monisha Sebastin
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Jacqueline A Odgis
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Kaitlyn Brown
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Illumina Incorporated, San Diego, CA
| | - Miranda Di Biase
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Katie M Gallagher
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Invitae Corporation, San Francisco, CA
| | - Saurav Guha
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Nicolette Ioele
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; Memorial Sloan Kettering Cancer Center, New York, NY
| | - Volkan Okur
- Molecular Diagnostics, New York Genome Center, New York, NY
| | - Michelle A Ramos
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jessica E Rodriguez
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | | | - Randi E Zinberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - George A Diaz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY; iECURE Incorporated, Philadelphia, PA
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Vaidehi Jobanputra
- Molecular Diagnostics, New York Genome Center, New York, NY; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Sabrina A Suckiel
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Carol R Horowitz
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY; Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Melissa P Wasserstein
- Department of Pediatrics, Division of Pediatric Genetic Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY.
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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21
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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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22
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Chepkirui D, Kipkemoi P, Bitta M, Harris E, Musesengwa R, Kamuya D. Ethical issues of involving people with intellectual disabilities in genomic research: a scoping review protocol. Wellcome Open Res 2023; 8:340. [PMID: 37928211 PMCID: PMC10624948 DOI: 10.12688/wellcomeopenres.19403.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 11/07/2023] Open
Abstract
Background: Psychiatric genomic research is a growing field of research in Africa that is looking at epigenetics of psychiatric disorders; within which a specific focus is neurodevelopmental disorders including intellectual disability (ID). Conducting this type of research is important to identify etiologies and possible interventions or areas for further research. However, genomic research generally, and psychiatric genomic research, faces many social, ethical, cultural, and legal issues; research involving people with ID is particularly challenging. All research stakeholders - researchers, research review bodies, regulators, patient groups - generally agree that involving people with ID require several considerations, including extra protection. It is also recognized that not involving people with ID in research that is relevant to them means that opportunities to learn on specific issues including lived experiences are missed. In this scoping review, we aim to describe the range of ethical and social-cultural issues concerning involvement of people with intellectual disability in genomic research from existing literature. Methods: This scoping review will be conducted based on the Joanna Briggs Institute guidance for scoping review and reported using the PRISMA-ScR guidelines. Iterative review stages will include systematic search of six databases (Embase, Ovid Global Health, PubMed, Scopus, PsycInfo and Web of Science core collection), screening, charting and synthesis of the data. Forward and backward citation screening will also be done for the articles included in the final review. We will include peer reviewed journal articles, guidance documents and reports. Screening and selection of studies based on the eligibility criteria will be done independently by three reviewers; conflicts will be resolved through discussion with a third reviewer and other experts. Results: The results will be included in the scoping review publication. Conclusions: This scoping review will identify key areas of ethical tensions and possible solutions and inform opportunities for empirical ethics studies.
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Affiliation(s)
- Dorothy Chepkirui
- Health Systems and Research Ethics, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Patricia Kipkemoi
- Health Systems and Research Ethics, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Mary Bitta
- Health Systems and Research Ethics, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
| | - Eli Harris
- Bodleian Health Care Libraries, University of Oxford, Oxford, England, UK
| | | | - Dorcas Kamuya
- Health Systems and Research Ethics, KEMRI Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK
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23
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Valencia AM, Sankar A, van der Sluijs PJ, Satterstrom FK, Fu J, Talkowski ME, Vergano SAS, Santen GWE, Kadoch C. Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders. Nat Genet 2023; 55:1400-1412. [PMID: 37500730 PMCID: PMC10412456 DOI: 10.1038/s41588-023-01451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
DNA sequencing-based studies of neurodevelopmental disorders (NDDs) have identified a wide range of genetic determinants. However, a comprehensive analysis of these data, in aggregate, has not to date been performed. Here, we find that genes encoding the mammalian SWI/SNF (mSWI/SNF or BAF) family of ATP-dependent chromatin remodeling protein complexes harbor the greatest number of de novo missense and protein-truncating variants among nuclear protein complexes. Non-truncating NDD-associated protein variants predominantly disrupt the cBAF subcomplex and cluster in four key structural regions associated with high disease severity, including mSWI/SNF-nucleosome interfaces, the ATPase-core ARID-armadillo repeat (ARM) module insertion site, the Arp module and DNA-binding domains. Although over 70% of the residues perturbed in NDDs overlap with those mutated in cancer, ~60% of amino acid changes are NDD-specific. These findings provide a foundation to functionally group variants and link complex aberrancies to phenotypic severity, serving as a resource for the chromatin, clinical genetics and neurodevelopment communities.
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Affiliation(s)
- Alfredo M Valencia
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Chemical Biology Program, Harvard University, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Akshay Sankar
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - F Kyle Satterstrom
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Jack Fu
- Massachusetts General Hospital, Boston, MA, USA
| | - Michael E Talkowski
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Samantha A Schrier Vergano
- Children's Hospital of the King's Daughters, Norfolk, Virginia, USA
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Cigall Kadoch
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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24
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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25
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Ballesta-Martínez MJ, Pérez-Fernández V, López-González V, Sánchez-Soler MJ, Serrano-Antón AT, Rodríguez-Peña LI, Barreda-Sánchez M, Armengol-Dulcet L, Guillén-Navarro E. Validation of clinical exome sequencing in the diagnostic procedure of patients with intellectual disability in clinical practice. Orphanet J Rare Dis 2023; 18:201. [PMID: 37480025 PMCID: PMC10362575 DOI: 10.1186/s13023-023-02809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/05/2023] [Indexed: 07/23/2023] Open
Abstract
Intellectual disability (ID) has a prevalence of 1-3% and aproximately 30-50% of ID cases have a genetic cause. Development of next-generation sequencing has shown a high diagnostic potential. The aim of this work was to evaluate the diagnostic yield of clinical exome sequencing in 188 ID patients and the economic impact of its introduction in clinical practice. An analysis of diagnostic yield according to the different clinical variables was performed in order to establish an efficient diagnostic protocol for ID patients. Diagnostic yield of clinical exome sequencing was significant (34%) supporting its utility in diagnosis of ID patients. Wide genetic heterogeneity and predominance of autosomal dominant de novo variants in ID patients were observed. Time to diagnosis was shortened and diagnostic study costs decreased by 62% after implementation of clinical exome sequencing. No association was found between any of the variables analyzed and a higher diagnostic yield; added to the fact that many of the diagnoses weren't clinically detectable, the reduction of time to diagnosis and the economic savings with respect to classical diagnostic studies, strengthen the clinical and economical convenience of early implementation of clinical exome sequencing in the diagnostic workup of ID patients in clinical practice.
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Affiliation(s)
- María Juliana Ballesta-Martínez
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
| | - Virginia Pérez-Fernández
- Departamento de Ciencias Sociosanitarias-Área de Bioestadística, Facultad de Medicina, Universidad de Murcia, Murcia, Spain
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain
| | - María José Sánchez-Soler
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Ana Teresa Serrano-Antón
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain
| | - Lidia Isolina Rodríguez-Peña
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | - Lluís Armengol-Dulcet
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, Catalonia, Spain
| | - Encarna Guillén-Navarro
- Sección de Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain.
- Instituto Murciano de Investigación Biomédica (IMIB), Murcia, Spain.
- Centro de Investigación Biomédica en Red-Enfermedades Raras (CIBERER-Instituto de Salud Carlos III), Madrid, Spain.
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26
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Harms FL, Weiss D, Lisfeld J, Alawi M, Kutsche K. A deep intronic variant in DNM1 in a patient with developmental and epileptic encephalopathy creates a splice acceptor site and affects only transcript variants including exon 10a. Neurogenetics 2023; 24:171-180. [PMID: 37039969 DOI: 10.1007/s10048-023-00716-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
DNM1 developmental and epileptic encephalopathy (DEE) is characterized by severe to profound intellectual disability, hypotonia, movement disorder, and refractory epilepsy, typically presenting with infantile spasms. Most of the affected individuals had de novo missense variants in DNM1. DNM1 undergoes alternative splicing that results in expression of six different transcript variants. One alternatively spliced region affects the tandemly arranged exons 10a and 10b, producing isoforms DNM1A and DNM1B, respectively. Pathogenic variants in the DNM1 coding region affect all transcript variants. Recently, a de novo DNM1 NM_001288739.1:c.1197-8G > A variant located in intron 9 has been reported in several unrelated individuals with DEE that causes in-frame insertion of two amino acids and leads to disease through a dominant-negative mechanism. We report on a patient with DEE and a de novo DNM1 variant NM_001288739.2:c.1197-46C > G in intron 9, upstream of exon 10a. By RT-PCR and Sanger sequencing using fibroblast-derived cDNA of the patient, we identified aberrantly spliced DNM1 mRNAs with exon 9 spliced to the last 45 nucleotides of intron 9 followed by exon 10a (NM_001288739.2:r.1196_1197ins[1197-1_1197-45]). The encoded DNM1A mutant is predicted to contain 15 novel amino acids between Ile398 and Arg399 [NP_001275668.1:p.(Ile398_Arg399ins15)] and likely functions in a dominant-negative manner, similar to other DNM1 mutants. Our data confirm the importance of the DNM1 isoform A for normal human brain function that is underscored by previously reported predominant expression of DMN1A transcripts in pediatric brain, functional differences of the mouse Dnm1a and Dnm1b isoforms, and the Dnm1 fitful mouse, an epilepsy mouse model.
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Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Deike Weiss
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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27
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Thompson JLP, Karaa A, Pham H, Yeske P, Krischer J, Xiao Y, Long Y, Kramer A, Dimmock D, Holbert A, Gorski C, Engelstad KM, Buchsbaum R, Rosales XQ, Hirano M. The evolution of the mitochondrial disease diagnostic odyssey. Orphanet J Rare Dis 2023; 18:157. [PMID: 37349818 PMCID: PMC10288668 DOI: 10.1186/s13023-023-02754-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/04/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Mitochondrial diseases often require multiple years and clinicians to diagnose. We lack knowledge of the stages of this diagnostic odyssey, and factors that affect it. Our goals are to report the results of the 2018 Odyssey2 (OD2) survey of patients with a medical diagnosis of mitochondrial disease; and to propose steps to reduce the odyssey going forward, and procedures to evaluate them. METHODS Data are from the NIH-funded NAMDC-RDCRN-UMDF OD2 survey (N = 215). The main outcomes are Time from symptom Onset to mitochondrial disease Diagnosis (TOD) and Number of Doctors Seen during this diagnostic process (NDOCS). RESULTS Expert recoding increased analyzable responses by 34% for final mitochondrial diagnosis and 39% for prior non-mitochondrial diagnosis. Only one of 122 patients who initially saw a primary care physician (PCP) received a mitochondrial diagnosis, compared to 26 of 86 (30%) who initially saw a specialist (p < 0.001). Mean TOD overall was 9.9 ± 13.0 years, and mean NDOCS 6.7 ± 5.2. Mitochondrial diagnosis brings extensive benefits through treatment changes and increased membership in and support of advocacy groups. CONCLUSIONS Because TOD is long and NDOCS high, there is great potential for shortening the mitochondrial odyssey. Although prompt patient contact with primary mitochondrial disease specialists, or early implementation of appropriate tests, may shorten the diagnostic odyssey, specific proposals for improvement require testing and confirmation with adequately complete, unbiased data across all its stages, and appropriate methods. Electronic Health Record (EHRs) may help by accessing diagnostic codes early, but their reliability and diagnostic utility have not been established for this group of diseases.
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Affiliation(s)
- John L P Thompson
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, USA.
| | - Amel Karaa
- Division of Genetics, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Hung Pham
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, USA
| | | | - Jeffrey Krischer
- University of South Florida Health Informatics Institute, Tampa, FL, USA
| | - Yi Xiao
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, USA
| | - Yuelin Long
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, USA
| | - Amanda Kramer
- Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, USA
| | | | | | | | - Kristin M Engelstad
- Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Richard Buchsbaum
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, USA
| | - Xiomara Q Rosales
- Department of Neurology, Columbia University Irving Medical Center, New York, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, USA
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28
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Zhang L, Tie X, Che F, Wang G, Ge Y, Li B, Yang Y. Novel maternal duplication of 6p22.3-p25.3 with subtelomeric 6p25.3 deletion: new clinical findings and genotype-phenotype correlations. Mol Cytogenet 2023; 16:11. [PMID: 37303060 DOI: 10.1186/s13039-023-00640-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Copy-number variants (CNVs) drive many neurodevelopmental-related disorders. Although many neurodevelopmental-related CNVs can give rise to widespread phenotypes, it is necessary to identify the major genes contributing to phenotypic presentation. Copy-number variations in chromosome 6, such as independent 6p deletion and 6p duplication, have been reported in several live-born infants and present widespread abnormalities such as intellectual disability, growth deficiency, developmental delay, and multiple dysmorphic facial features. However, a contiguous deletion and duplication in chromosome 6p regions have been reported in only a few cases. CASE PRESENTATION In this study, we reported the first duplication of chromosome band 6p25.3-p22.3 with deletion of 6p25.3 in a pedigree. This is the first case reported involving CNVs in these chromosomal regions. In this pedigree, we reported a 1-year-old boy with maternal 6p25-pter duplication characterized by chromosome karyotype. Further analysis using CNV-seq revealed a 20.88-Mb duplication at 6p25.3-p22.3 associated with a contiguous 0.66-Mb 6p25.3 deletion. Whole exome sequencing confirmed the deletion/duplication and identified no pathogenic or likely pathogenic variants related with the patient´s phenotype. The proband presented abnormal growth, developmental delay, skeletal dysplasia, hearing loss, and dysmorphic facial features. Additionally, he presented recurrent infection after birth. CNV-seq using the proband´s parental samples showed that the deletion/duplication was inherited from the proband´s mother, who exhibited a similar phenotype to the proband. When compared with other cases, this proband and his mother presented a new clinical finding: forearm bone dysplasia. The major candidate genes contributing to recurrent infection, eye development, hearing loss features, neurodevelopmental development, and congenital bone dysplasia were further discussed. CONCLUSIONS Our results showed a new clinical finding of a contiguous deletion and duplication in chromosome 6p regions and suggested candidate genes associated with phenotypic features, such as FOXC1, SERPINB6, NRN1, TUBB2A, IRF4, and RIPK1.
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Affiliation(s)
- Liyu Zhang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Xiaoling Tie
- Department of Rehabilitation, Xi'an Children's Hospital, Xi'an, China
| | - Fengyu Che
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Guoxia Wang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Ge
- The Center Laboratory Medicine, Xi'an Children's Hospital, Xi'an, China
| | - Benchang Li
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Yang
- Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China.
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29
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Martin EA, Michel JC, Kissinger JS, Echeverry FA, Lin YP, O'Brien J, Pereda AE, Miller AC. Neurobeachin controls the asymmetric subcellular distribution of electrical synapse proteins. Curr Biol 2023; 33:2063-2074.e4. [PMID: 37172585 PMCID: PMC10266475 DOI: 10.1016/j.cub.2023.04.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/27/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
The subcellular positioning of synapses and their specialized molecular compositions form the fundamental basis of neural circuits. Like chemical synapses, electrical synapses are constructed from an assortment of adhesion, scaffolding, and regulatory molecules, yet little is known about how these molecules localize to specific neuronal compartments. Here, we investigate the relationship between the autism- and epilepsy-associated gene Neurobeachin, the neuronal gap junction channel-forming Connexins, and the electrical synapse scaffold ZO1. Using the zebrafish Mauthner circuit, we find Neurobeachin localizes to the electrical synapse independently of ZO1 and Connexins. By contrast, we show Neurobeachin is required postsynaptically for the robust localization of ZO1 and Connexins. We demonstrate that Neurobeachin binds ZO1 but not Connexins. Finally, we find Neurobeachin is required to restrict electrical postsynaptic proteins to dendrites, but not electrical presynaptic proteins to axons. Together, the results reveal an expanded understanding of electrical synapse molecular complexity and the hierarchical interactions required to build neuronal gap junctions. Further, these findings provide novel insight into the mechanisms by which neurons compartmentalize the localization of electrical synapse proteins and provide a cell biological mechanism for the subcellular specificity of electrical synapse formation and function.
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Affiliation(s)
- E Anne Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | | | - Jane S Kissinger
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Fabio A Echeverry
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ya-Ping Lin
- Department of Ophthalmology & Visual Science, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - John O'Brien
- Department of Ophthalmology & Visual Science, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alberto E Pereda
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
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30
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Abul-Husn NS, Marathe PN, Kelly NR, Bonini KE, Sebastin M, Odgis JA, Abhyankar A, Brown K, Di Biase M, Gallagher KM, Guha S, Ioele N, Okur V, Ramos MA, Rodriguez JE, Rehman AU, Thomas-Wilson A, Edelmann L, Zinberg RE, Diaz GA, Greally JM, Jobanputra V, Suckiel SA, Horowitz CR, Wasserstein MP, Kenny EE, Gelb BD. Molecular diagnostic yield of genome sequencing versus targeted gene panel testing in racially and ethnically diverse pediatric patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.18.23286992. [PMID: 36993157 PMCID: PMC10055570 DOI: 10.1101/2023.03.18.23286992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Purpose Adoption of genome sequencing (GS) as a first-line test requires evaluation of its diagnostic yield. We evaluated the GS and targeted gene panel (TGP) testing in diverse pediatric patients (probands) with suspected genetic conditions. Methods Probands with neurologic, cardiac, or immunologic conditions were offered GS and TGP testing. Diagnostic yield was compared using a fully paired study design. Results 645 probands (median age 9 years) underwent genetic testing, and 113 (17.5%) received a molecular diagnosis. Among 642 probands with both GS and TGP testing, GS yielded 106 (16.5%) and TGPs yielded 52 (8.1%) diagnoses ( P < .001). Yield was greater for GS vs . TGPs in Hispanic/Latino(a) (17.2% vs . 9.5%, P < .001) and White/European American (19.8% vs . 7.9%, P < .001), but not in Black/African American (11.5% vs . 7.7%, P = .22) population groups by self-report. A higher rate of inconclusive results was seen in the Black/African American (63.8%) vs . White/European American (47.6%; P = .01) population group. Most causal copy number variants (17 of 19) and mosaic variants (6 of 8) were detected only by GS. Conclusion GS may yield up to twice as many diagnoses in pediatric patients compared to TGP testing, but not yet across all population groups.
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Hartley T, Soubry É, Acker M, Osmond M, Couse M, Gillespie MK, Ito Y, Marshall AE, Lemire G, Huang L, Chisholm C, Eaton AJ, Price EM, Dowling JJ, Ramani AK, Mendoza-Londono R, Costain G, Axford MM, Szuto A, McNiven V, Damseh N, Jobling R, de Kock L, Mojarad BA, Young T, Shao Z, Hayeems RZ, Graham ID, Tarnopolsky M, Brady L, Armour CM, Geraghty M, Richer J, Sawyer S, Lines M, Mercimek-Andrews S, Carter MT, Graham G, Kannu P, Lazier J, Li C, Aul RB, Balci TB, Dlamini N, Badalato L, Guerin A, Walia J, Chitayat D, Cohn R, Faghfoury H, Forster-Gibson C, Gonorazky H, Grunebaum E, Inbar-Feigenberg M, Karp N, Morel C, Rusnak A, Sondheimer N, Warman-Chardon J, Bhola PT, Bourque DK, Chacon IJ, Chad L, Chakraborty P, Chong K, Doja A, Goh ESY, Saleh M, Potter BK, Marshall CR, Dyment DA, Kernohan K, Boycott KM. Bridging clinical care and research in Ontario, Canada: Maximizing diagnoses from reanalysis of clinical exome sequencing data. Clin Genet 2023; 103:288-300. [PMID: 36353900 DOI: 10.1111/cge.14262] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/11/2022]
Abstract
We examined the utility of clinical and research processes in the reanalysis of publicly-funded clinical exome sequencing data in Ontario, Canada. In partnership with eight sites, we recruited 287 families with suspected rare genetic diseases tested between 2014 and 2020. Data from seven laboratories was reanalyzed with the referring clinicians. Reanalysis of clinically relevant genes identified diagnoses in 4% (13/287); four were missed by clinical testing. Translational research methods, including analysis of novel candidate genes, identified candidates in 21% (61/287). Of these, 24 families have additional evidence through data sharing to support likely diagnoses (8% of cohort). This study indicates few diagnoses are missed by clinical laboratories, the incremental gain from reanalysis of clinically-relevant genes is modest, and the highest yield comes from validation of novel disease-gene associations. Future implementation of translational research methods, including continued reporting of compelling genes of uncertain significance by clinical laboratories, should be considered to maximize diagnoses.
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Affiliation(s)
- Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Élisabeth Soubry
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - Meryl Acker
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | | | - Meredith K Gillespie
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Yoko Ito
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Aren E Marshall
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Gabrielle Lemire
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Lijia Huang
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Alison J Eaton
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- University of Alberta, Edmonton, Canada
| | - E Magda Price
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | - James J Dowling
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | | | | | - Gregory Costain
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Michelle M Axford
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Anna Szuto
- Hospital for Sick Children, Toronto, Canada
| | - Vanda McNiven
- Hospital for Sick Children, Toronto, Canada
- University Health Network, Toronto, Canada
| | | | | | - Leanne de Kock
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
| | | | - Ted Young
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Zhuo Shao
- University of Toronto, Toronto, Canada
- North York General Hospital, Toronto, Canada
| | | | - Ian D Graham
- University of Ottawa, Ottawa, Canada
- Ottawa Hospital Research Institute, Ottawa, Canada
| | | | | | - Christine M Armour
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Julie Richer
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Sarah Sawyer
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Matthew Lines
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Melissa T Carter
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Gail Graham
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Peter Kannu
- Hospital for Sick Children, Toronto, Canada
- University of Alberta, Edmonton, Canada
| | - Joanna Lazier
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Chumei Li
- McMaster Children's Hospital, Hamilton, Canada
| | - Ritu B Aul
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Tugce B Balci
- London Health Sciences Center, Western University, London, Canada
| | | | - Lauren Badalato
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Andrea Guerin
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - Jagdeep Walia
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | - David Chitayat
- Hospital for Sick Children, Toronto, Canada
- Mount Sinai Hospital, Toronto, Canada
| | | | | | | | | | | | | | - Natalya Karp
- London Health Sciences Center, Western University, London, Canada
| | | | - Alison Rusnak
- Children's Hospital of Eastern Ontario, Ottawa, Canada
- Kingston Health Sciences Center, Queen's University, Kingston, Canada
| | | | - Jodi Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
- The Ottawa Hospital, Ottawa, Canada
| | - Priya T Bhola
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Danielle K Bourque
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Lauren Chad
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - Pranesh Chakraborty
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Asif Doja
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Maha Saleh
- London Health Sciences Center, Western University, London, Canada
| | | | - Beth K Potter
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
| | - Christian R Marshall
- Hospital for Sick Children, Toronto, Canada
- University of Toronto, Toronto, Canada
| | - David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kristin Kernohan
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada
- University of Ottawa, Ottawa, Canada
- Children's Hospital of Eastern Ontario, Ottawa, Canada
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Zhuang J, Luo Q, Xie M, Chen Y, Jiang Y, Zeng S, Wang Y, Xie Y, Chen C. Etiological identification of recurrent male fatality due to a novel NSDHL gene mutation using trio whole-exome sequencing: A rare case report and literature review. Mol Genet Genomic Med 2023; 11:e2121. [PMID: 36504312 PMCID: PMC10009909 DOI: 10.1002/mgg3.2121] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Congenital hemidysplasia with ichthyosiform nevus and limb defects (CHILD) syndrome is a rare X-linked dominant, lethal male disorder caused by mutations to the NSDHL (NAD(P)H steroid dehydrogenase-like protein) gene. It primarily exhibits strictly unilateral congenital hemidysplasia with ichthyosiform erythroderma and ipsilateral limb defects in female individuals. METHODS A Chinese couple suffering from recurrent spontaneous abortion in male fetuses was enrolled in this study. Chromosomal microarray analysis and whole-exome sequencing were performed for genetic etiological diagnosis. RESULTS A 33-year-old pregnant woman with recurrent spontaneous abortion was experiencing her third pregnancy with a male embryo. In this pregnancy, a miscarriage occurred at a gestational age of 10+6 weeks with no copy number variants. However, a novel mutation c.790-6C>T in the NSDHL gene was observed in the fetus through whole-exome sequencing (WES). Parental verification indicated that the NSDHL gene variant was inherited from the mother. Additionally, the variant in the NSDHL gene was absent in her subsequent pregnancy with a female fetus. CONCLUSION In this study, we detected c.790-6C>T, a novel variant in the NSDHL gene that results in recurrent miscarriage in males. Our study may broaden the scope of research on the NSDHL gene in CHILD syndrome and strengthens the application value of WES for the genetic etiological identification of recurrent miscarriage.
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Affiliation(s)
- Jianlong Zhuang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Qi Luo
- Department of Public Health for Women and Children, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian, China
| | - Meihua Xie
- Prenatal Diagnosis Center, Yueyang Central Hospital, Yueyang, China
| | - Yu'e Chen
- Ultrasonography, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Yuying Jiang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Shuhong Zeng
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yuanbai Wang
- Center for Prenatal Diagnosis, Quanzhou Women's and Children's Hospital, Quanzhou, Fujian Province, China
| | - Yingjun Xie
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China.,Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Chunnuan Chen
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, PR China
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Hsu RH, Lee CH, Chien YH, Lin SP, Hung MZ, Chen NC, Lin YL, Hwu WL, Lee NC. Utility of whole-exome sequencing for patients with multiple congenital anomalies with or without intellectual disability/developmental delay in East Asia population. Mol Genet Genomic Med 2023:e2160. [PMID: 36849876 PMCID: PMC10364928 DOI: 10.1002/mgg3.2160] [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: 08/15/2022] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Congenital anomalies (CAs) with or without intellectual disability (ID)/developmental delay (DD) comprise a heterogeneous spectrum of diseases that affect approximately 3% of live births worldwide. Recently, whole-exome sequencing (WES) demonstrated the highly heterogeneous genetic causes of CAs. The purpose of this study was to evaluate a referral system to increase the yield of WES for CAs. METHODS From August 2018 to July 2019, patients with CAs, with or without ID/DD, after excluding gross chromosomal aberrations, were referred to geneticists in two medical centers. Variant prioritization was conducted with an AI-assisted tool for whole exomes or a CA-related gene panel. RESULTS Forty patients (27 males and 13 females) with CAs were enrolled in the study with a mean age of 4.71 years (range, 0.01-18.2). Pathogenic variants in 14 genes were discovered in 16 patients (three patients with CHD7 and 13 patients with one gene each of ATP6V1B2, TAF6, COL4A3BP, ANKH, BMP2, SMARCA4, CUL4B, PGAP3, SOX11, FBN2, PTPN11, SOS1, or PROKR2), with a positive diagnostic rate of 40%. Among the 16 positive cases, 13 (81%) also had ID/DD. The inheritance was autosomal dominant in 13 (81%), autosomal recessive in two (13%), and X-linked in one (6%). Only five patients received a correct clinical diagnosis before WES. The analyses of patients with a negative genetic diagnosis revealed a phenotype and gene mutation load similar to those of the positive-finding patients but with a lower percentage of ID/DD. CONCLUSIONS The careful selection of patients by experienced geneticists and the exclusion of chromosomal aberrations raises the positive rate of the molecular diagnosis for CAs to 40%. However, more than half of the patients with CAs still do not have a genetic diagnosis by current technologies.
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Affiliation(s)
- Rai-Hseng Hsu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, E-Da Hospital, Kaohsiung, Taiwan.,School of Medicine, I-Shou University, Kaohsiung, Taiwan.,Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Shuan-Pei Lin
- Rare Disease Center, MacKay Memorial Hospital, Taipei, Taiwan.,Department of Genetics and Metabolism, MacKay Children's Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taiwan
| | - Miao-Zi Hung
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Nai-Chi Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Lin Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan
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Carter MT, Srour M, Au PYB, Buhas D, Dyack S, Eaton A, Inbar-Feigenberg M, Howley H, Kawamura A, Lewis SME, McCready E, Nelson TN, Vallance H. Genetic and metabolic investigations for neurodevelopmental disorders: position statement of the Canadian College of Medical Geneticists (CCMG). J Med Genet 2023; 60:523-532. [PMID: 36822643 DOI: 10.1136/jmg-2022-108962] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023]
Abstract
PURPOSE AND SCOPE The aim of this position statement is to provide recommendations for clinicians regarding the use of genetic and metabolic investigations for patients with neurodevelopmental disorders (NDDs), specifically, patients with global developmental delay (GDD), intellectual disability (ID) and/or autism spectrum disorder (ASD). This document also provides guidance for primary care and non-genetics specialists caring for these patients while awaiting consultation with a clinical geneticist or metabolic specialist. METHODS OF STATEMENT DEVELOPMENT A multidisciplinary group reviewed existing literature and guidelines on the use of genetic and metabolic investigations for the diagnosis of NDDs and synthesised the evidence to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and to the Canadian Pediatric Society (Mental Health and Developmental Disabilities Committee); following incorporation of feedback, it was approved by the CCMG Board of Directors on 1 September 2022. RESULTS AND CONCLUSIONS Chromosomal microarray is recommended as a first-tier test for patients with GDD, ID or ASD. Fragile X testing should also be done as a first-tier test when there are suggestive clinical features or family history. Metabolic investigations should be done if there are clinical features suggestive of an inherited metabolic disease, while the patient awaits consultation with a metabolic physician. Exome sequencing or a comprehensive gene panel is recommended as a second-tier test for patients with GDD or ID. Genetic testing is not recommended for patients with NDDs in the absence of GDD, ID or ASD, unless accompanied by clinical features suggestive of a syndromic aetiology or inherited metabolic disease.
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Affiliation(s)
| | - Myriam Srour
- Division of Neurology, McGill University Health Centre, Montreal, Québec, Canada
- Department of Pediatrics, McGill University, Montréal, QC, Canada
| | - Ping-Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, McGill University, Montreal, Québec, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Sarah Dyack
- Division of Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Alison Eaton
- Department of Medical Genetics, Stollery Children's Hospital, Edmonton, Alberta, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michal Inbar-Feigenberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Heather Howley
- Office of Research Services, CHEO Research Institute, Ottawa, Ontario, Canada
| | - Anne Kawamura
- Division of Developmental Pediatrics, Holland Bloorview Kids Rehabilitation Hospital, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
- Mental Health and Developmental Disability Committee, Canadian Pediatric Society, Ottawa, ON, Canada
- Canadian Paediatric Society, Toronto, Ontario, Canada
| | - Suzanne M E Lewis
- Department of Medical Genetics, BC Children's and Women's Hospital, Vancouver, British Columbia, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, McMaster University, Hamilton, ON, Canada, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences Centre, Hamilton, ON, Canada
| | - Tanya N Nelson
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hilary Vallance
- Department of Pathology and Laboratory Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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Evaluation of Individuals with Non-Syndromic Global Developmental Delay and Intellectual Disability. CHILDREN 2023; 10:children10030414. [PMID: 36979972 PMCID: PMC10047567 DOI: 10.3390/children10030414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/11/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Global Developmental Delay (GDD) and Intellectual Disability (ID) are two of the most common presentations encountered by physicians taking care of children. GDD/ID is classified into non-syndromic GDD/ID, where GDD/ID is the sole evident clinical feature, or syndromic GDD/ID, where there are additional clinical features or co-morbidities present. Careful evaluation of children with GDD and ID, starting with detailed history followed by a thorough examination, remain the cornerstone for etiologic diagnosis. However, when initial history and examination fail to identify a probable underlying etiology, further genetic testing is warranted. In recent years, genetic testing has been shown to be the single most important diagnostic modality for clinicians evaluating children with non-syndromic GDD/ID. In this review, we discuss different genetic testing currently available, review common underlying copy-number variants and molecular pathways, explore the recent evidence and recommendations for genetic evaluation and discuss an approach to the diagnosis and management of children with non-syndromic GDD and ID.
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36
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FitzHugh ZT, Schiller MR. Systematic Assessment of Protein C-Termini Mutated in Human Disorders. Biomolecules 2023; 13:biom13020355. [PMID: 36830724 PMCID: PMC9953674 DOI: 10.3390/biom13020355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
All proteins have a carboxyl terminus, and we previously summarized eight mutations in binding and trafficking sequence determinants in the C-terminus that, when disrupted, cause human diseases. These sequence elements for binding and trafficking sites, as well as post-translational modifications (PTMs), are called minimotifs or short linear motifs. We wanted to determine how frequently mutations in minimotifs in the C-terminus cause disease. We searched specifically for PTMs because mutation of a modified amino acid almost always changes the chemistry of the side chain and can be interpreted as loss-of-function. We analyzed data from ClinVar for disease variants, Minimotif Miner and the C-terminome for PTMs, and RefSeq for protein sequences, yielding 20 such potential disease-causing variants. After additional screening, they include six with a previously reported PTM disruption mechanism and nine with new hypotheses for mutated minimotifs in C-termini that may cause disease. These mutations were generally for different genes, with four different PTM types and several different diseases. Our study helps to identify new molecular mechanisms for nine separate variants that cause disease, and this type of analysis could be extended as databases grow and to binding and trafficking motifs. We conclude that mutated motifs in C-termini are an infrequent cause of disease.
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Affiliation(s)
- Zachary T. FitzHugh
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Pkwy, Las Vegas, NV 89154, USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Pkwy, Las Vegas, NV 89154, USA
- School of Life Sciences, University of Nevada, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
- Heligenics Inc., 833 Las Vegas Blvd. North, Suite B, Las Vegas, NV 89101, USA
- Correspondence: ; Tel.: +1-702-895-5546; Fax: +1-702-895-5728
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37
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Wright CA, Taylor JW, Cochran M, Lawlor JM, Moyers BA, Amaral MD, Bonnstetter ZT, Carter P, Solomon V, Myers RM, Love MN, Geldmacher DS, Cooper SJ, Roberson ED, Cochran JN. Contributions of rare and common variation to early-onset and atypical dementia risk. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.06.23285383. [PMID: 36798301 PMCID: PMC9934786 DOI: 10.1101/2023.02.06.23285383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We collected and analyzed genomic sequencing data from individuals with clinician- diagnosed early-onset or atypical dementia. Thirty-two patients were previously described, with sixty-eight newly described in this report. Of those sixty-eight, sixty-two patients reported Caucasian, non-Hispanic ethnicity and six reported as African American, non-Hispanic. Fifty-three percent of patients had a returnable variant. Five patients harbored a pathogenic variant as defined by the American College of Medical Genetics criteria for pathogenicity. A polygenic risk score was calculated for Alzheimer's patients in the total cohort and compared to the scores of a late-onset Alzheimer's cohort and a control set. Patients with early-onset Alzheimer's had higher non- APOE polygenic risk scores than patients with late onset Alzheimer's, supporting the conclusion that both rare and common genetic variation associate with early-onset neurodegenerative disease risk.
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Affiliation(s)
- Carter A. Wright
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA,University of Alabama in Huntsville, Huntsville, Alabama 35899, USA
| | - Jared W. Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Meagan Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - James M.J. Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Belle A. Moyers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | | | | | - Princess Carter
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Veronika Solomon
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Richard M. Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Marissa Natelson Love
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - David S. Geldmacher
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Sara J. Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Erik D. Roberson
- Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - J. Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA,Alzheimer’s Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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38
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Wang Y, Liu C, Deng J, Xu Q, Lin J, Li H, Hu M, Hu C, Li Q, Xu X. Behavioral and Sensory Deficits Associated with Dysfunction of GABAergic System in a Novel shank2-Deficient Zebrafish Model. Int J Mol Sci 2023; 24:2208. [PMID: 36768529 PMCID: PMC9916955 DOI: 10.3390/ijms24032208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Hyper-reactivity to sensory inputs is a common and debilitating symptom of autism spectrum disorder (ASD), but the underlying neural abnormalities remain unclear. Two of three patients in our clinical cohort screen harboring de novo SHANK2 mutations also exhibited high sensitivity to visual, auditory, and tactile stimuli, so we examined whether shank2 deficiencies contribute to sensory abnormalities and other ASD-like phenotypes by generating a stable shank2b-deficient zebrafish model (shank2b-/-). The adult shank2b-/- zebrafish demonstrated reduced social preference and kin preference as well as enhanced behavioral stereotypy, while larvae exhibited hyper-sensitivity to auditory noise and abnormal hyperactivity during dark-to-light transitions. This model thus recapitulated the core developmental and behavioral phenotypes of many previous genetic ASD models. Expression levels of γ-aminobutyric acid (GABA) receptor subunit mRNAs and proteins were also reduced in shank2b-/- zebrafish, and these animals exhibited greater sensitivity to drug-induced seizures. Our results suggest that GABAergic dysfunction is a major contributor to the sensory hyper-reactivity in ASD, and they underscore the need for interventions that target sensory-processing disruptions during early neural development to prevent disease progression.
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Affiliation(s)
- Yi Wang
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Chunxue Liu
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Jingxin Deng
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Qiong Xu
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Jia Lin
- Center for Translational Medicine, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children’s Hopstial of Fudan University, National Children’s Medical Center, 399 Wangyuan Road, Shanghai 201102, China
| | - Huiping Li
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Meixin Hu
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Chunchun Hu
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
| | - Qiang Li
- Center for Translational Medicine, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children’s Hopstial of Fudan University, National Children’s Medical Center, 399 Wangyuan Road, Shanghai 201102, China
| | - Xiu Xu
- Division of Child Health Care, Children’s Hospital of Fudan University, National Children’s Medical Center, 399 Wanyuan Road, Shanghai 201102, China
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The exploration of genetic aetiology and diagnostic strategy for 321 Chinese individuals with intellectual disability. Clin Chim Acta 2023; 538:94-103. [PMID: 36368352 DOI: 10.1016/j.cca.2022.10.023] [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: 08/31/2022] [Revised: 10/08/2022] [Accepted: 10/28/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Intellectual disability is a heterogeneous neurodevelopmental disorder with complex genetic architectures. Different sequential methodologies are usually applied to identify the genetic aetiologies of ID patients. METHODS We collected 321 consecutive ID patients. All patients underwent karyotyping, while 293 and 164 cases further received copy number variation sequencing (CNV-seq) and whole-exome sequencing (WES). The updated WES technology can detect CNVs simultaneously. The diagnostic data from 137 patients who received WES and CNV-seq were used to define the approach that could be recommended as the first-tier test. RESULTS WES obtains the highest diagnostic yield of 50% (82/164), compared with karyotyping (7.79%, 25/321) and CNV-seq (19.80%, 58/293). Among the variants detected by WES, 66.67% (44/66) de novo and 57.58% (38/66) novel pathogenic/likely pathogenic (P/LP) variants were identified in patients with ID. Besides, 24 out of 25P/LP CNVs discovered by CNV-seq can also be accurately identified using WES in 137 patients who received WES and CNV-seq. Thus, genetic abnormalities found through karyotyping, CNV-seq, and WES can be completely detected by combined karyotyping and WES. CONCLUSIONS This study illustrates the genetic aberrations of a Chinese ID cohort and expands the mutation spectrum of ID-related genes. Compared with the conventional diagnostic strategy, a combination of karyotype analysis and WES could be recommended as the first-tier diagnostic strategy for ID patients.
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Shimelis H, Oetjens MT, Walsh LK, Wain KE, Znidarsic M, Myers SM, Finucane BM, Ledbetter DH, Martin CL. Prevalence and Penetrance of Rare Pathogenic Variants in Neurodevelopmental Psychiatric Genes in a Health Care System Population. Am J Psychiatry 2023; 180:65-72. [PMID: 36475376 PMCID: PMC10017070 DOI: 10.1176/appi.ajp.22010062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Autism, schizophrenia, and other clinically distinct neurodevelopmental psychiatric disorders (NPDs) have shared genetic etiologies, including single-gene and multigenic copy number variants (CNVs). Because rare variants are primarily investigated in clinical cohorts, population-based estimates of their prevalence and penetrance are lacking. The authors determined the prevalence, penetrance, and NPD risk of pathogenic single-gene variants in a large health care system population. METHODS The authors analyzed linked genomic and electronic health record (EHR) data in a subset of 90,595 participants from Geisinger's MyCode Community Health Initiative, known as the DiscovEHR cohort. Loss-of-function pathogenic variants in 94 high-confidence NPD genes were identified through exome sequencing, and NPD penetrance was calculated using preselected EHR diagnosis codes. NPD risk was estimated using a case-control comparison of DiscovEHR participants with and without NPD diagnoses. Results from single-gene variant analyses were also compared with those from 31 previously reported pathogenic NPD CNVs. RESULTS Pathogenic variants were identified in 0.34% of the DiscovEHR cohort and demonstrated a 34.3% penetrance for NPDs. Similar to CNVs, sequence variants collectively conferred a substantial risk for several NPD diagnoses, including autism, schizophrenia, and bipolar disorder. Significant NPD risk remained after participants with intellectual disability were excluded from the analysis, confirming the association with major psychiatric disorders in individuals without severe cognitive deficits. CONCLUSIONS Collectively, rare single-gene variants and CNVs were found in >1% of individuals in a large health care system population and play an important contributory role in mental health disorders. Diagnostic genetic testing for pathogenic variants among symptomatic individuals with NPDs could improve clinical outcomes through early intervention and anticipatory therapeutic support.
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Affiliation(s)
- Hermela Shimelis
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Matthew T Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Lauren K Walsh
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Karen E Wain
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Masa Znidarsic
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Scott M Myers
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Brenda M Finucane
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
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Anjum A, Ahammed T, Hasan MM, Chowdhury MAB, Uddin MJ. Mother's functional difficulty is affecting the child functioning: Findings from a nationally representative MICS 2019 cross-sectional survey in Bangladesh. Health Sci Rep 2022; 6:e1023. [PMID: 36582634 PMCID: PMC9793826 DOI: 10.1002/hsr2.1023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Background Functional difficulties in children can be transmitted from mother to child, which is a major concern. We sought to determine whether there was a correlation between a mother's functional difficulty and functional difficulty in kids between the ages of 2-4 and 5-17. We also want to evaluate other fundamental aspects that influence on child's functionality. Methods We used Multiple Indicator Cluster Survey (MICS) data sets. For two different age groups, the children's difficulty status was evaluated. The sociodemographic factors served as explanatory variables in this study. We used χ 2 tests and survey logistic regression models to analyze the data. Results Functional difficulties were less common in children aged 2-4 years (2.78%) but 8.27% in those aged 5-17 years. The study specifies that the mother's functional difficulty (odds ratio [OR]: 2.66, confidence interval [CI]: 1.35-5.24 for children aged 2-4 years and OR: 3.36, CI: 2.80-4.03 for children aged 5-17 years) were significantly associated with the functional difficulty of both age groups' children. Not attending early childhood education programs (OR: 1.89, CI: 1.16-3.10 for children aged 2-4 years and OR: 2.66, CI: 2.19-3.22 for children aged 5-17 years) and divisions were also significantly affecting the functional difficulty of both age groups' children. Moreover, area of residence and gender were significant factors for the older age group. Conclusions The prevalence of difficulty among children in Bangladesh is high. Children's functional difficulty, regardless of age, is greatly influenced by the functional difficulty of their mothers, their absence from early childhood education programs, and divisions. Reducing the prevalence of child functioning difficulties will be more successful if the government and NGOs consider these factors while developing appropriate intervention programs.
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Affiliation(s)
- Aniqua Anjum
- Department of StatisticsShahjalal University of Science and TechnologySylhetBangladesh
| | - Tanvir Ahammed
- Department of StatisticsShahjalal University of Science and TechnologySylhetBangladesh
| | - Md Mahedi Hasan
- Faculty of Business StudiesBangladesh University of Professionals (BUP)DhakaBangladesh,Department of Mathematics and StatisticsWashington State UniversityPullmanWashingtonUSA
| | - Muhammad Abdul Baker Chowdhury
- Department of StatisticsShahjalal University of Science and TechnologySylhetBangladesh,Department of NeurosurgeryUniversity of Florida College of MedicineGainesvilleFloridaUSA
| | - Md. Jamal Uddin
- Department of StatisticsShahjalal University of Science and TechnologySylhetBangladesh,Department of General Educational Development (GED)Daffodil International UniversityDhakaBangladesh
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Pitfalls of whole exome sequencing in undefined clinical conditions with a suspected genetic etiology. Genes Genomics 2022; 45:637-655. [PMID: 36454368 DOI: 10.1007/s13258-022-01341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Whole-Exome Sequencing (WES) is a valuable tool for the molecular diagnosis of patients with a suspected genetic condition. In complex and heterogeneous diseases, the interpretation of WES variants is more challenging given the absence of diagnostic handles and other reported cases with overlapping clinical presentations. OBJECTIVE To describe candidate variants emerging from trio-WES and possibly associated with the clinical phenotype in clinically heterogeneous conditions. METHODS We performed WES in ten patients from eight families, selected because of the lack of a clear clinical diagnosis or suspicion, the presence of multiple clinical signs, and the negative results of traditional genetic tests. RESULTS Although we identified ten candidate variants, reaching the diagnosis of these cases is challenging, given the complexity and the rarity of these syndromes and because affected genes are already associated with known genetic diseases only partially recapitulating patients' phenotypes. However, the identification of these variants could shed light into the definition of new genotype-phenotype correlations. Here, we describe the clinical and molecular data of these cases with the aim of favoring the match with other similar cases and, hopefully, confirm our diagnostic hypotheses. CONCLUSION This study emphasizes the major limitations associated with WES data interpretation, but also highlights its clinical utility in unraveling novel genotype-phenotype correlations in complex and heterogeneous undefined clinical conditions with a suspected genetic etiology.
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Chander V, Mahmoud M, Hu J, Dardas Z, Grochowski CM, Dawood M, Khayat MM, Li H, Li S, Jhangiani S, Korchina V, Shen H, Weissenberger G, Meng Q, Gingras MC, Muzny DM, Doddapaneni H, Posey JE, Lupski JR, Sabo A, Murdock DR, Sedlazeck FJ, Gibbs RA. Long read sequencing and expression studies of AHDC1 deletions in Xia-Gibbs syndrome reveal a novel genetic regulatory mechanism. Hum Mutat 2022; 43:2033-2053. [PMID: 36054313 PMCID: PMC10167679 DOI: 10.1002/humu.24461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Xia-Gibbs syndrome (XGS; MIM# 615829) is a rare mendelian disorder characterized by Development Delay (DD), intellectual disability (ID), and hypotonia. Individuals with XGS typically harbor de novo protein-truncating mutations in the AT-Hook DNA binding motif containing 1 (AHDC1) gene, although some missense mutations can also cause XGS. Large de novo heterozygous deletions that encompass the AHDC1 gene have also been ascribed as diagnostic for the disorder, without substantial evidence to support their pathogenicity. We analyzed 19 individuals with large contiguous deletions involving AHDC1, along with other genes. One individual bore the smallest known contiguous AHDC1 deletion (∼350 Kb), encompassing eight other genes within chr1p36.11 (Feline Gardner-Rasheed, IFI6, FAM76A, STX12, PPP1R8, THEMIS2, RPA2, SMPDL3B) and terminating within the first intron of AHDC1. The breakpoint junctions and phase of the deletion were identified using both short and long read sequencing (Oxford Nanopore). Quantification of RNA expression patterns in whole blood revealed that AHDC1 exhibited a mono-allelic expression pattern with no deficiency in overall AHDC1 expression levels, in contrast to the other deleted genes, which exhibited a 50% reduction in mRNA expression. These results suggest that AHDC1 expression in this individual is compensated by a novel regulatory mechanism and advances understanding of mutational and regulatory mechanisms in neurodevelopmental disorders.
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Affiliation(s)
- Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Moez Dawood
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - David R. Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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Attard TJ, Welburn JPI, Marsh JA. Understanding molecular mechanisms and predicting phenotypic effects of pathogenic tubulin mutations. PLoS Comput Biol 2022; 18:e1010611. [PMID: 36206299 PMCID: PMC9581425 DOI: 10.1371/journal.pcbi.1010611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/19/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022] Open
Abstract
Cells rely heavily on microtubules for several processes, including cell division and molecular trafficking. Mutations in the different tubulin-α and -β proteins that comprise microtubules have been associated with various diseases and are often dominant, sporadic and congenital. While the earliest reported tubulin mutations affect neurodevelopment, mutations are also associated with other disorders such as bleeding disorders and infertility. We performed a systematic survey of tubulin mutations across all isotypes in order to improve our understanding of how they cause disease, and increase our ability to predict their phenotypic effects. Both protein structural analyses and computational variant effect predictors were very limited in their utility for differentiating between pathogenic and benign mutations. This was even worse for those genes associated with non-neurodevelopmental disorders. We selected tubulin-α and -β disease mutations that were most poorly predicted for experimental characterisation. These mutants co-localise to the mitotic spindle in HeLa cells, suggesting they may exert dominant-negative effects by altering microtubule properties. Our results show that tubulin mutations represent a blind spot for current computational approaches, being much more poorly predicted than mutations in most human disease genes. We suggest that this is likely due to their strong association with dominant-negative and gain-of-function mechanisms.
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Affiliation(s)
- Thomas J. Attard
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Julie P. I. Welburn
- Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Joseph A. Marsh
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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Banerjee S, Munshi A, Li C, Ayub M. Editorial: Developmental delay and intellectual disability. Front Genet 2022; 13:934815. [PMID: 36159972 PMCID: PMC9493353 DOI: 10.3389/fgene.2022.934815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/15/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, China
- *Correspondence: Santasree Banerjee,
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Chen Li
- School of Medicine, Graduate School, Zhejiang University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Zhejiang University School of Medicine, Hangzhou, China
| | - Muhammad Ayub
- Department of Psychiatry, Queens University, Kingston, Ontario, Canada
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York NS, Sanchez-Arias JC, McAdam ACH, Rivera JE, Arbour LT, Swayne LA. Mechanisms underlying the role of ankyrin-B in cardiac and neurological health and disease. Front Cardiovasc Med 2022; 9:964675. [PMID: 35990955 PMCID: PMC9386378 DOI: 10.3389/fcvm.2022.964675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The ANK2 gene encodes for ankyrin-B (ANKB), one of 3 members of the ankyrin family of proteins, whose name is derived from the Greek word for anchor. ANKB was originally identified in the brain (B denotes “brain”) but has become most widely known for its role in cardiomyocytes as a scaffolding protein for ion channels and transporters, as well as an interacting protein for structural and signaling proteins. Certain loss-of-function ANK2 variants are associated with a primarily cardiac-presenting autosomal-dominant condition with incomplete penetrance and variable expressivity characterized by a predisposition to supraventricular and ventricular arrhythmias, arrhythmogenic cardiomyopathy, congenital and adult-onset structural heart disease, and sudden death. Another independent group of ANK2 variants are associated with increased risk for distinct neurological phenotypes, including epilepsy and autism spectrum disorders. The mechanisms underlying ANKB's roles in cells in health and disease are not fully understood; however, several clues from a range of molecular and cell biological studies have emerged. Notably, ANKB exhibits several isoforms that have different cell-type–, tissue–, and developmental stage– expression profiles. Given the conservation within ankyrins across evolution, model organism studies have enabled the discovery of several ankyrin roles that could shed important light on ANKB protein-protein interactions in heart and brain cells related to the regulation of cellular polarity, organization, calcium homeostasis, and glucose and fat metabolism. Along with this accumulation of evidence suggesting a diversity of important ANKB cellular functions, there is an on-going debate on the role of ANKB in disease. We currently have limited understanding of how these cellular functions link to disease risk. To this end, this review will examine evidence for the cellular roles of ANKB and the potential contribution of ANKB functional variants to disease risk and presentation. This contribution will highlight the impact of ANKB dysfunction on cardiac and neuronal cells and the significance of understanding the role of ANKB variants in disease.
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Affiliation(s)
- Nicole S. York
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Alexa C. H. McAdam
- Department of Medical Genetics, University of British Columbia, Victoria, BC, Canada
| | - Joel E. Rivera
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Laura T. Arbour
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Medical Genetics, University of British Columbia, Victoria, BC, Canada
- *Correspondence: Laura T. Arbour
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Cellular and Physiological Sciences and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Leigh Anne Swayne
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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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Avaria MDLÁ. Aproximación clínica al retardo del desarrollo psicomotor y discapacidad intelectual. REVISTA MÉDICA CLÍNICA LAS CONDES 2022. [DOI: 10.1016/j.rmclc.2022.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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Aravamuthan BR, Shusterman M, Green Snyder L, Lemmon ME, Bain JM, Gross P. Diagnostic preferences include discussion of etiology for adults with cerebral palsy and their caregivers. Dev Med Child Neurol 2022; 64:723-733. [PMID: 35092695 PMCID: PMC10091392 DOI: 10.1111/dmcn.15164] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022]
Abstract
AIM To determine the views of individuals with cerebral palsy (CP) and their caregivers (CP community members) about carrying a CP diagnosis, an etiological diagnosis, or both diagnoses together. METHOD We surveyed CP community members across two registries querying their views on carrying a CP diagnosis, one type of etiological diagnosis (specifically, a genetic diagnosis), or both. Open-ended responses were analyzed using a conventional content analysis approach. RESULTS Of 197 respondents (108 adults with CP and 89 caregivers), most (75%) valued knowing the cause of their CP. Of those with a diagnostic preference, most preferred carrying both CP and etiological diagnoses together (68%). When compared with carrying an etiological diagnosis alone, significantly more respondents felt a CP diagnosis helped anticipate symptom evolution (84% vs 54%), explain symptoms to others (86% vs 48%), access services (86% vs 48%), and join support communities (78% vs 50%) (p < 0.01, χ2 test). INTERPRETATION Most CP community members surveyed want to know the cause of their CP and would prefer carrying both CP and etiological diagnoses together. Clinical practice should evolve to meet these community needs.
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Affiliation(s)
- Bhooma R Aravamuthan
- Department of Neurology, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO, USA
| | | | | | - Monica E Lemmon
- Department of Pediatrics, Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA
| | - Jennifer M Bain
- Department of Neurology, Division of Child Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Paul Gross
- The Cerebral Palsy Research Network, Salt Lake City, UT, USA.,University of Utah, Salt Lake City, UT, USA
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- Simons Foundation, New York, NY, USA
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- The Cerebral Palsy Research Network, Salt Lake City, UT, USA
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