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Goh ESY, Chad L, Richer J, Bombard Y, Mighton C, Agatep R, Lacaria M, Penny B, Thomas MA, Zawati MH, MacFarlane J, Laberge AM, Nelson TN. Canadian College of Medical Geneticists: clinical practice advisory document - responsibility to recontact for reinterpretation of clinical genetic testing. J Med Genet 2024:jmg-2024-110330. [PMID: 39362754 DOI: 10.1136/jmg-2024-110330] [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: 08/18/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024]
Abstract
BACKGROUND Advances in technology and knowledge have facilitated both an increase in the number of patient variants reported and variants reclassified. While there is currently no duty to recontact for reclassified genetic variants, there may be a responsibility. The purpose of this clinical practice advisory document is to provide healthcare practitioners guidance for recontact of previously identified and classified variants, suggest methods for recontact, and principles to consider, taking account patient safety, feasibility, ethical considerations, health service capacity and resource constraints. The target audience are practitioners who order genetic testing, follow patients who have undergone genetic testing and those analysing and reporting genetic testing. METHODS A multidisciplinary group of laboratory and ordering clinicians, patient representatives, ethics and legal researchers and a genetic counsellor from the Canadian Association of Genetic Counsellors reviewed the existing literature and guidelines on responsibility to recontact in a clinical context to make recommendations. Comments were collected from the Canadian College of Medical Geneticists (CCMG) Education, Ethics, and Public Policy, Clinical Practice and Laboratory Practice committees, and the membership at large. RESULTS Following incorporation of feedback, and external review by the Canadian Association of Genetic Counsellors and patient groups, the document was approved by the CCMG Board of Directors. The CCMG is the Canadian organisation responsible for certifying laboratory and medical geneticists who provide medical genetics services, and for establishing professional and ethical standards for clinical genetics services in Canada. CONCLUSION The document describes the ethical and practical factors and suggests a shared responsibility between patients, ordering clinician and laboratory practitioners.
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Affiliation(s)
- Elaine Suk-Ying Goh
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lauren Chad
- The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Julie Richer
- Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Yvonne Bombard
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Chloe Mighton
- Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario, Canada
| | - Ron Agatep
- Genomics, Shared Health Diagnostic Services, Winnipeg, Manitoba, Canada
| | - Melanie Lacaria
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Mary Ann Thomas
- Departments of Medical Genetics and Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Ma'n H Zawati
- Human Genetics, Centre of Genomics and Policy - McGill University, Montreal, Quebec, Canada
| | - Julie MacFarlane
- Screening Programs, Perinatal Services BC, Vancouver, British Columbia, Canada
| | - Anne-Marie Laberge
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
- Medical Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Tanya N Nelson
- Genome Diagnostics, Pathology and Laboratory Medicine, BC Children's Hospital, Vancouver, British Columbia, Canada
- Genome Diagnostics, Pathology and Laboratory Medicine, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
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Chourasia N, Vaidya R, Sengupta S, Mefford HC, Wheless J. A Retrospective Review of Reclassification of Variants of Uncertain Significance in a Pediatric Epilepsy Cohort Undergoing Genetic Panel Testing. Pediatr Neurol 2024; 161:101-107. [PMID: 39357456 DOI: 10.1016/j.pediatrneurol.2024.09.009] [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: 01/02/2024] [Revised: 08/08/2024] [Accepted: 09/09/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND The interpretation and communication of variant of uncertain significance (VUS) genetic results often present a challenge in clinical practice. VUSs can be reclassified over time into benign/likely benign (B/LB) or pathogenic/likely pathogenic (P/LP) based on the availability of updated data. We evaluate the frequency of VUS reclassification in our tertiary care epilepsy cohort undergoing epilepsy genetic panel (EGP) testing. METHODS Patients with established diagnoses of epilepsy (neonates to 18 years of age) who underwent EGP testing between 2017 and 2022 from a single commercial laboratory were evaluated. Patients who had any variant reclassified from their initial EGP report were included. Duration between reclassification of VUSs and types of reclassifications were compared between developmental and epileptic encephalopathy (DEE) versus non-DEE phenotypes. RESULTS Over the five years, 1025 probands were tested using EGP. Eighty-five probands (8%) had at least one genetic variant reclassified. A total of 252 initial VUSs were reported in the 85 probands, of which 113 (45%) VUSs were reclassified. Of 113 reclassification events, 21 (19%) were upgraded to P/LP and 92 (81%) were reclassified to B/LB. The median (interquartile range) duration between variant reinterpretations in the cohort was 12 (14.5) months. There were no significant differences in the duration between reclassification and the likelihood of reclassification of VUSs to B/LB or P/LP between the two groups (DEE versus non-DEE). CONCLUSIONS VUS reclassification over time can lead to clinically significant variant reinterpretation in patients with unknown genetic diagnoses. Periodic genomic test reinterpretation, preferably yearly, is recommended in routine clinical practice.
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Affiliation(s)
- Nitish Chourasia
- Le Bonheur Children's Comprehensive Epilepsy Center, University of Tennessee Health Science Center, Memphis, Tennessee.
| | - Rohan Vaidya
- Le Bonheur Children's Comprehensive Epilepsy Center, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - James Wheless
- Le Bonheur Children's Comprehensive Epilepsy Center, University of Tennessee Health Science Center, Memphis, Tennessee
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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4
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Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [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: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
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Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
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Sparber P, Bychkov I, Pyankov D, Skoblov M. Functional investigation of SCN1A deep-intronic variants activating poison exons inclusion. Hum Genet 2023; 142:1043-1053. [PMID: 37186029 DOI: 10.1007/s00439-023-02564-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Dravet syndrome is a devastating epileptic syndrome characterized by intractable epilepsy with an early age of onset, regression of developmental milestones, ataxia, and motor deficits. Loss-of-function pathogenic variants in the SCN1A gene are found in the majority of patients with Dravet syndrome; however, a significant number of patients remain undiagnosed even after comprehensive genetic testing. Previously, it was shown that intronic elements in the SCN1A gene called poison exons can incorporate into SCN1A mRNA, leading to haploinsufficiency and potentially causing Dravet syndrome. Here, we developed a splicing reporter assay for all described poison exons of the SCN1A gene and validated it using previously reported and artificially introduced variants. Overall, we tested 18 deep-intronic single nucleotide variants and one complex allele in the SCN1A gene. Our approach is capable of evaluating the effect of both variants affecting cis-regulatory sequences and splice-site variants, with the potential to functionally annotate every possible variant within these elements. Moreover, using antisense-modified uridine-rich U7 small nuclear RNAs, we were able to block poison exon incorporation in mutant constructs, an approach that could be used as a promising therapeutic intervention in Dravet syndrome patients with deep-intronic variants.
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Affiliation(s)
- Peter Sparber
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow, Russia, 115478.
| | - Igor Bychkov
- Laboratory of Hereditary Metabolic Diseases, Research Centre for Medical Genetics, Moscow, Russia
| | | | - Mikhail Skoblov
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moskvorechie Street 1, Moscow, Russia, 115478
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Gordon LG, Elliott TM, Bennett C, Hollway G, Waddell N, Vadlamudi L. Early cost-utility analysis of genetically guided therapy for patients with drug-resistant epilepsy. Epilepsia 2022; 63:3111-3121. [PMID: 36082520 DOI: 10.1111/epi.17408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Existing gene panels were developed to understand the etiology of epilepsy, and further benefits will arise from an effective pharmacogenomics panel for personalizing therapy and achieving seizure control. Our study assessed the cost-effectiveness of a pharmacogenomics panel for patients with drug-resistant epilepsy, compared with usual care. METHODS A cost-utility analysis was employed using a discrete event simulation model. The microsimulation model aggregated the costs and benefits of genetically guided treatment versus usual care for 5000 simulated patients. The 10-year model combined data from various sources including genomic databases on prevalence of variants, population-level pharmaceutical claims on antiseizure medications, published long-term therapy retention rates, patient-level cost data, and systematic reviews. Incremental cost per quality-adjusted life-year (QALY) gained was computed. Deterministic and probabilistic sensitivity analyses were undertaken to address uncertainty in model parameters. RESULTS The mean cost of the genetically guided treatment option was AU$98 199 compared with AU$95 386 for usual care. Corresponding mean QALYs were 4.67 compared with 4.28 for genetically guided and usual care strategies, respectively. The incremental cost per QALY gained was AU$7381. In probabilistic sensitivity analyses, the incremental cost per QALY gained was AU$6321 (95% uncertainty interval = AU$3604-AU$9621), with a 100% likelihood of being cost-effective in the Australian health care system. The most influential drivers of the findings were the monthly health care costs associated with reduced seizures, costs when seizures continued, and the quality-of-life estimates under genetically guided and usual care strategies. SIGNIFICANCE This early economic evaluation of a pharmacogenomics panel to guide treatment for drug-resistant epilepsy could potentially be cost-effective in the Australian health care system. Clinical trial evidence is necessary to confirm these findings.
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Affiliation(s)
- Louisa G Gordon
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Nursing and Cancer and Palliative Care Outcomes Centre, Queensland University of Technology, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Thomas M Elliott
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Carmen Bennett
- University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Georgina Hollway
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,genomiQa, Brisbane, Queensland, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,genomiQa, Brisbane, Queensland, Australia
| | - Lata Vadlamudi
- University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
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7
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Trifiletti R, Lachman HM, Manusama O, Zheng D, Spalice A, Chiurazzi P, Schornagel A, Serban AM, van Wijck R, Cunningham JL, Swagemakers S, van der Spek PJ. Identification of ultra-rare genetic variants in pediatric acute onset neuropsychiatric syndrome (PANS) by exome and whole genome sequencing. Sci Rep 2022; 12:11106. [PMID: 35773312 PMCID: PMC9246359 DOI: 10.1038/s41598-022-15279-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/21/2022] [Indexed: 12/13/2022] Open
Abstract
Abrupt onset of severe neuropsychiatric symptoms including obsessive-compulsive disorder, tics, anxiety, mood swings, irritability, and restricted eating is described in children with Pediatric Acute-Onset Neuropsychiatric Syndrome (PANS). Symptom onset is often temporally associated with infections, suggesting an underlying autoimmune/autoinflammatory etiology, although direct evidence is often lacking. The pathological mechanisms are likely heterogeneous, but we hypothesize convergence on one or more biological pathways. Consequently, we conducted whole exome sequencing (WES) on a U.S. cohort of 386 cases, and whole genome sequencing (WGS) on ten cases from the European Union who were selected because of severe PANS. We focused on identifying potentially deleterious genetic variants that were de novo or ultra-rare (MAF) < 0.001. Candidate mutations were found in 11 genes (PPM1D, SGCE, PLCG2, NLRC4, CACNA1B, SHANK3, CHK2, GRIN2A, RAG1, GABRG2, and SYNGAP1) in 21 cases, which included two or more unrelated subjects with ultra-rare variants in four genes. These genes converge into two broad functional categories. One regulates peripheral immune responses and microglia (PPM1D, CHK2, NLRC4, RAG1, PLCG2). The other is expressed primarily at neuronal synapses (SHANK3, SYNGAP1, GRIN2A, GABRG2, CACNA1B, SGCE). Mutations in these neuronal genes are also described in autism spectrum disorder and myoclonus-dystonia. In fact, 12/21 cases developed PANS superimposed on a preexisting neurodevelopmental disorder. Genes in both categories are also highly expressed in the enteric nervous system and the choroid plexus. Thus, genetic variation in PANS candidate genes may function by disrupting peripheral and central immune functions, neurotransmission, and/or the blood-CSF/brain barriers following stressors such as infection.
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Affiliation(s)
| | - Herbert M Lachman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Olivia Manusama
- Department of Immunology, Erasmus MC, Rotterdam, The Netherlands
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alberto Spalice
- Department of Pediatrics, Pediatric Neurology, Sapienza University of Rome, Rome, Italy
| | - Pietro Chiurazzi
- Sezione di Medicina Genomica, Dipartimento Scienze della Vita e Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento Scienze di Laboratorio e Infettivologiche, UOC Genetica Medica, Rome, Italy
| | - Allan Schornagel
- GGZ-Delfland, Kinderpraktijk Zoetermeer, Zoetermeer, The Netherlands
| | - Andreea M Serban
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - Rogier van Wijck
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - Janet L Cunningham
- Department of Neuroscience, Psychiatry, Uppsala University, Uppsala, Sweden
| | - Sigrid Swagemakers
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J van der Spek
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
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Sun JH, Chen J, Ayala Valenzuela FE, Brown C, Masser-Frye D, Jones M, Romero LP, Rinaldi B, Li WL, Li QQ, Wu D, Gerard B, Thorpe E, Bayat A, Shi YS. X-linked neonatal-onset epileptic encephalopathy associated with a gain-of-function variant p.R660T in GRIA3. PLoS Genet 2021; 17:e1009608. [PMID: 34161333 PMCID: PMC8259962 DOI: 10.1371/journal.pgen.1009608] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/06/2021] [Accepted: 05/18/2021] [Indexed: 12/02/2022] Open
Abstract
The X-linked GRIA3 gene encodes the GLUA3 subunit of AMPA-type glutamate receptors. Pathogenic variants in this gene were previously reported in neurodevelopmental diseases, mostly in male patients but rarely in females. Here we report a de novo pathogenic missense variant in GRIA3 (c.1979G>C; p. R660T) identified in a 1-year-old female patient with severe epilepsy and global developmental delay. When exogenously expressed in human embryonic kidney (HEK) cells, GLUA3_R660T showed slower desensitization and deactivation kinetics compared to wildtype (wt) GLUA3 receptors. Substantial non-desensitized currents were observed with the mutant but not for wt GLUA3 with prolonged exposure to glutamate. When co-expressed with GLUA2, the decay kinetics were similarly slowed in GLUA2/A3_R660T with non-desensitized steady state currents. In cultured cerebellar granule neurons, miniature excitatory postsynaptic currents (mEPSCs) were significantly slower in R660T transfected cells than those expressing wt GLUA3. When overexpressed in hippocampal CA1 neurons by in utero electroporation, the evoked EPSCs and mEPSCs were slower in neurons expressing R660T mutant compared to those expressing wt GLUA3. Therefore our study provides functional evidence that a gain of function (GoF) variant in GRIA3 may cause epileptic encephalopathy and global developmental delay in a female subject by enhancing synaptic transmission. Glutamate is the excitatory neurotransmitter in brain, abnormality of which causes excitotoxicity and diseases. Here we identified a pathogenic missense variant in GRIA3 gene in a female patient with severe epilepsy and global developmental delay. The X-linked GRIA3 gene encodes GLUA3, a subunit of glutamate receptors. Through electrophysiological analysis of the mutant GLUA3 in a cell line and mouse neurons, we found this mutant makes strengthened glutamate receptors. This study thus indicates that the variant causes epileptic encephalopathy and global developmental delay by enhancing glutamate signaling in brain.
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Affiliation(s)
- Jia-Hui Sun
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Department of Neurology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Jiang Chen
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Department of Neurology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | | | - Carolyn Brown
- Illumina Inc., San Diego, California, United States of America
| | - Diane Masser-Frye
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children’s Hospital, San Diego, California, United States of America
| | - Marilyn Jones
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children’s Hospital, San Diego, California, United States of America
| | - Leslie Patron Romero
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana, Mexico
| | - Berardo Rinaldi
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Wenhui Laura Li
- Breakthrough Genomics Inc., Irvine, California, United States of America
| | - Qing-Qing Li
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Department of Neurology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Dan Wu
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Department of Neurology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Benedicte Gerard
- Laboratoires de diagnostic génétique, Institut Medical d’Alsace, Hôpitaux Universitaire de Strasbourg, Strasbourg, France
| | - Erin Thorpe
- Illumina Inc., San Diego, California, United States of America
- * E-mail: (ET); (AB); (YSS)
| | - Allan Bayat
- Department for Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services Research, University of Southern Denmark, Odense, Denmark
- * E-mail: (ET); (AB); (YSS)
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Department of Neurology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Nanjing University, Nanjing, China
- Institute for Brain Sciences, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
- * E-mail: (ET); (AB); (YSS)
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Varesio C, Gana S, Asaro A, Ballante E, Cabini RF, Tartara E, Bagnaschi M, Pasca L, Valente M, Orcesi S, Cereda C, Veggiotti P, Borgatti R, Valente EM, De Giorgis V. Diagnostic Yield and Cost-Effectiveness of "Dynamic" Exome Analysis in Epilepsy with Neurodevelopmental Disorders: A Tertiary-Center Experience in Northern Italy. Diagnostics (Basel) 2021; 11:diagnostics11060948. [PMID: 34070668 PMCID: PMC8228291 DOI: 10.3390/diagnostics11060948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 02/02/2023] Open
Abstract
Background: The advent of next-generation sequencing (NGS) techniques in clinical practice led to a significant advance in gene discovery. We aimed to describe diagnostic yields of a “dynamic” exome-based approach in a cohort of patients with epilepsy associated with neurodevelopmental disorders. Methods: We conducted a retrospective, observational study on 72 probands. All patients underwent a first diagnostic level of a 135 gene panel, a second of 297 genes for inconclusive cases, and finally, a whole-exome sequencing for negative cases. Diagnostic yields at each step and cost-effectiveness were the objects of statistical analysis. Results: Overall diagnostic yield in our cohort was 37.5%: 29% of diagnoses derived from the first step analysis, 5.5% from the second step, and 3% from the third. A significant difference emerged between the three diagnostic steps (p < 0.01), between the first and second (p = 0.001), and the first and third (p << 0.001). The cost-effectiveness plane indicated that our exome-based “dynamic” approach was better in terms of cost savings and higher diagnostic rate. Conclusions: Our findings suggested that “dynamic” NGS techniques applied to well-phenotyped individuals can save both time and resources. In patients with unexplained epilepsy comorbid with NDDs, our approach might maximize the number of diagnoses achieved.
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Affiliation(s)
- Costanza Varesio
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, 27100 Pavia, Italy; (L.P.); (S.O.); (R.B.); (V.D.G.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
- Correspondence: ; Tel.: +39-0382-380289
| | - Simone Gana
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (S.G.); (A.A.); (M.V.); (E.M.V.)
| | - Alessia Asaro
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (S.G.); (A.A.); (M.V.); (E.M.V.)
| | - Elena Ballante
- BioData Science Center, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Department of Mathematics, University of Pavia, 27100 Pavia, Italy;
| | - Raffaella Fiamma Cabini
- Department of Mathematics, University of Pavia, 27100 Pavia, Italy;
- Istituto Nazionale di Fisica Nucleare Section of Pavia, 27100 Pavia, Italy
| | - Elena Tartara
- Epilepsy Center, IRCCS Mondino Foundation, 27100 Pavia, Italy;
| | - Michela Bagnaschi
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Ludovica Pasca
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, 27100 Pavia, Italy; (L.P.); (S.O.); (R.B.); (V.D.G.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Marialuisa Valente
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (S.G.); (A.A.); (M.V.); (E.M.V.)
- Laboratory of Clinical Pathology Microbiology and Genetics, SS. Annunziata, 74100 Taranto, Italy
| | - Simona Orcesi
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, 27100 Pavia, Italy; (L.P.); (S.O.); (R.B.); (V.D.G.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Cristina Cereda
- Molecular Genetics and Cytogenetics Section, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Pierangelo Veggiotti
- Pediatric Neurology Unit, Vittore Buzzi Hospital, 20100 Milano, Italy;
- Biomedical and Clinical Sciences Department, Luigi Sacco Hospital, University of Milan, 20100 Milano, Italy
| | - Renato Borgatti
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, 27100 Pavia, Italy; (L.P.); (S.O.); (R.B.); (V.D.G.)
- Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy;
| | - Enza Maria Valente
- Medical Genetics Unit, IRCCS Mondino Foundation, 27100 Pavia, Italy; (S.G.); (A.A.); (M.V.); (E.M.V.)
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Valentina De Giorgis
- Department of Child Neurology and Psychiatry, IRCCS Mondino Foundation, 27100 Pavia, Italy; (L.P.); (S.O.); (R.B.); (V.D.G.)
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Sun H, Shen XR, Fang ZB, Jiang ZZ, Wei XJ, Wang ZY, Yu XF. Next-Generation Sequencing Technologies and Neurogenetic Diseases. Life (Basel) 2021; 11:life11040361. [PMID: 33921670 PMCID: PMC8072598 DOI: 10.3390/life11040361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/05/2021] [Accepted: 04/16/2021] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) technology has led to great advances in understanding the causes of Mendelian and complex neurological diseases. Owing to the complexity of genetic diseases, the genetic factors contributing to many rare and common neurological diseases remain poorly understood. Selecting the correct genetic test based on cost-effectiveness, coverage area, and sequencing range can improve diagnosis, treatments, and prevention. Whole-exome sequencing and whole-genome sequencing are suitable methods for finding new mutations, and gene panels are suitable for exploring the roles of specific genes in neurogenetic diseases. Here, we provide an overview of the classifications, applications, advantages, and limitations of NGS in research on neurological diseases. We further provide examples of NGS-based explorations and insights of the genetic causes of neurogenetic diseases, including Charcot-Marie-Tooth disease, spinocerebellar ataxias, epilepsy, and multiple sclerosis. In addition, we focus on issues related to NGS-based analyses, including interpretations of variants of uncertain significance, de novo mutations, congenital genetic diseases with complex phenotypes, and single-molecule real-time approaches.
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Affiliation(s)
| | | | | | | | | | | | - Xue-Fan Yu
- Correspondence: ; Tel.: +86-157-5430-1836
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