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Huang J, Sun C, Zhu Q, Wu G, Cao Y, Shi J, He S, Jiang L, Liao J, Li L, Zhong C, Lu Y. Phenotyping of FGF12A V52H mutation in mouse implies a complex FGF12 network. Neurobiol Dis 2024; 200:106637. [PMID: 39142611 DOI: 10.1016/j.nbd.2024.106637] [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: 03/04/2024] [Revised: 06/26/2024] [Accepted: 08/11/2024] [Indexed: 08/16/2024] Open
Abstract
Pathogenic missense mutation of the FGF12 gene is responsible for a variable disease phenotypic spectrum. Disease-specific therapies require precise dissection of the relationship between different mutations and phenotypes. The lack of a proper animal model hinders the investigation of related diseases, such as early-onset epileptic encephalopathy. Here, an FGF12AV52H mouse model was generated using CRISPR/Cas9 technology, which altered the A isoform without affecting the B isoform. The FGF12AV52H mice exhibited seizure susceptibility, while no spontaneous seizures were observed. The increased excitability in dorsal hippocampal CA3 neurons was confirmed by patch-clamp recordings. Furthermore, immunostaining showed that the balance of excitatory/inhibitory neurons in the hippocampus of the FGF12AV52H mice was perturbed. The increases in inhibitory SOM+ neurons and excitatory CaMKII+ neurons were heterogeneous. Moreover, the locomotion, anxiety levels, risk assessment behavior, social behavior, and cognition of the FGF12AV52H mice were investigated by elevated plus maze, open field, three-chamber sociability, and novel object tests, respectively. Cognition deficit, impaired risk assessment, and social behavior with normal social indexes were observed, implying complex consequences of V52H FGF12A in mice. Together, these data suggest that the function of FGF12A in neurons can be immediate or long-term and involves modulation of ion channels and the differentiation and maturation of neurons. The FGF12AV52H mouse model increases the understanding of the function of FGF12A, and it is of great importance for revealing the complex network of the FGF12 gene in physiological and pathological processes.
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Affiliation(s)
- Jianyu Huang
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chongyang Sun
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qian Zhu
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Neurology, Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Ge Wu
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Cao
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiarui Shi
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyu He
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Department of Neurology, Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Luyao Jiang
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianxiang Liao
- Department of Neurology, Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Lin Li
- Department of Neurology, Surgery Division, Epilepsy Center, Shenzhen Children's Hospital, Shenzhen 518038, China.
| | - Cheng Zhong
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yi Lu
- Shenzhen Key Laboratory of Precision Diagnosis and Treatment of Depression, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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Andjelkovic M, Klaassen K, Skakic A, Marjanovic I, Kravljanac R, Djordjevic M, Vucetic Tadic B, Kecman B, Pavlovic S, Stojiljkovic M. Characterization of 13 Novel Genetic Variants in Genes Associated with Epilepsy: Implications for Targeted Therapeutic Strategies. Mol Diagn Ther 2024; 28:645-663. [PMID: 39003674 PMCID: PMC11349789 DOI: 10.1007/s40291-024-00720-2] [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] [Accepted: 05/26/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Childhood epilepsies are caused by heterogeneous underlying disorders where approximately 40% of the origins of epilepsy can be attributed to genetic factors. The application of next-generation sequencing (NGS) has revolutionized molecular diagnostics and has enabled the identification of disease-causing genes and variants in childhood epilepsies. The objective of this study was to use NGS to identify variants in patients with childhood epilepsy, to expand the variant spectrum and discover potential therapeutic targets. METHODS In our study, 55 children with epilepsy of unknown etiology were analyzed by combining clinical-exome and whole-exome sequencing. Novel variants were characterized using various in silico algorithms for pathogenicity and structure prediction. RESULTS The molecular genetic cause of epilepsy was identified in 28 patients and the overall diagnostic success rate was 50.9%. We identified variants in 22 different genes associated with epilepsy that correlate well with the described phenotype. SCN1A gene variants were found in five unrelated patients, while ALDH7A1 and KCNQ2 gene variants were found twice. In the other 19 genes, variants were found only in a single patient. This includes genes such as ASH1L, CSNK2B, RHOBTB2, and SLC13A5, which have only recently been associated with epilepsy. Almost half of diagnosed patients (46.4%) carried novel variants. Interestingly, we identified variants in ALDH7A1, KCNQ2, PNPO, SCN1A, and SCN2A resulting in gene-directed therapy decisions for 11 children from our study, including four children who all carried novel SCN1A genetic variants. CONCLUSIONS Described novel variants will contribute to a better understanding of the European genetic landscape, while insights into the genotype-phenotype correlation will contribute to a better understanding of childhood epilepsies worldwide. Given the expansion of molecular-based approaches, each newly identified genetic variant could become a potential therapeutic target.
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Affiliation(s)
- Marina Andjelkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Anita Skakic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Irena Marjanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Ruzica Kravljanac
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Maja Djordjevic
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Biljana Vucetic Tadic
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bozica Kecman
- Institute for Mother and Child Healthcare of Serbia, "Dr Vukan Cupic", Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042, Belgrade, Serbia.
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3
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Ferreira T, Polavarapu K, Olimpio C, Paramonov I, Lochmüller H, Horvath R. Variants in mitochondrial disease genes are common causes of inherited peripheral neuropathies. J Neurol 2024; 271:3546-3553. [PMID: 38549004 PMCID: PMC11136726 DOI: 10.1007/s00415-024-12319-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: 02/13/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND Peripheral neuropathies in mitochondrial disease are caused by mutations in nuclear genes encoding mitochondrial proteins, or in the mitochondrial genome. Whole exome or genome sequencing enable parallel testing of nuclear and mtDNA genes, and it has significantly advanced the genetic diagnosis of inherited diseases. Despite this, approximately 40% of all Charcot-Marie-Tooth (CMT) cases remain undiagnosed. METHODS The genome-phenome analysis platform (GPAP) in RD-Connect was utilised to create a cohort of 2087 patients with at least one Human Phenotype Ontology (HPO) term suggestive of a peripheral neuropathy, from a total of 10,935 patients. These patients' genetic data were then analysed and searched for variants in known mitochondrial disease genes. RESULTS A total of 1,379 rare variants were identified, 44 of which were included in this study as either reported pathogenic or likely causative in 42 patients from 36 families. The most common genes found to be likely causative for an autosomal dominant neuropathy were GDAP1 and GARS1. We also detected heterozygous likely pathogenic variants in DNA2, MFN2, DNM2, PDHA1, SDHA, and UCHL1. Biallelic variants in SACS, SPG7, GDAP1, C12orf65, UCHL1, NDUFS6, ETFDH and DARS2 and variants in the mitochondrial DNA (mtDNA)-encoded MT-ATP6 and MT-TK were also causative for mitochondrial CMT. Only 50% of these variants were already reported as solved in GPAP. CONCLUSION Variants in mitochondrial disease genes are frequent in patients with inherited peripheral neuropathies. Due to the clinical overlap between mitochondrial disease and CMT, agnostic exome or genome sequencing have better diagnostic yields than targeted gene panels.
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Affiliation(s)
- Tomas Ferreira
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK
| | - Kiran Polavarapu
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Catarina Olimpio
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ida Paramonov
- Centro Nacional de Análisis Genómico, Barcelona, Spain
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Centro Nacional de Análisis Genómico, Barcelona, Spain
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
- Brain and Mind Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Rita Horvath
- Department of Clinical Neurosciences, John Van Geest Centre for Brain Repair, School of Clinical Medicine, University of Cambridge, Robinson Way, Cambridge, CB2 0PY, UK.
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van der Geest MA, Maeckelberghe ELM, van Gijn ME, Lucassen AM, Swertz MA, van Langen IM, Plantinga M. Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications. Eur J Hum Genet 2024; 32:489-497. [PMID: 38480795 PMCID: PMC11061183 DOI: 10.1038/s41431-023-01529-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: 07/26/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 05/02/2024] Open
Abstract
With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.
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Affiliation(s)
- Marije A van der Geest
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Els L M Maeckelberghe
- Institute for Medical Education, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Faculty of Medicine, Clinical Ethics and Law, University of Southampton, Southampton, UK
- Centre for Personalised Medicine, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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5
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Ferrer A, Duffy P, Olson RJ, Meiners MA, Schultz-Rogers L, Macke EL, Safgren S, Morales-Rosado JA, Cousin MA, Oliver GR, Rider D, Williams M, Pichurin PN, Deyle DR, Morava E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Kaiwar C, Vitek CR, McAllister TM, Wick MJ, Schimmenti LA, Lazaridis KN, Vairo FPE, Klee EW. Semiautomated approach focused on new genomic information results in time and effort-efficient reannotation of negative exome data. Hum Genet 2024; 143:649-666. [PMID: 38538918 DOI: 10.1007/s00439-024-02664-3] [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: 07/06/2023] [Accepted: 02/25/2024] [Indexed: 05/18/2024]
Abstract
Most rare disease patients (75-50%) undergoing genomic sequencing remain unsolved, often due to lack of information about variants identified. Data review over time can leverage novel information regarding disease-causing variants and genes, increasing this diagnostic yield. However, time and resource constraints have limited reanalysis of genetic data in clinical laboratories setting. We developed RENEW, (REannotation of NEgative WES/WGS) an automated reannotation procedure that uses relevant new information in on-line genomic databases to enable rapid review of genomic findings. We tested RENEW in an unselected cohort of 1066 undiagnosed cases with a broad spectrum of phenotypes from the Mayo Clinic Center for Individualized Medicine using new information in ClinVar, HGMD and OMIM between the date of previous analysis/testing and April of 2022. 5741 variants prioritized by RENEW were rapidly reviewed by variant interpretation specialists. Mean analysis time was approximately 20 s per variant (32 h total time). Reviewed cases were classified as: 879 (93.0%) undiagnosed, 63 (6.6%) putatively diagnosed, and 4 (0.4%) definitively diagnosed. New strategies are needed to enable efficient review of genomic findings in unsolved cases. We report on a fast and practical approach to address this need and improve overall diagnostic success in patient testing through a recurrent reannotation process.
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Affiliation(s)
- Alejandro Ferrer
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick Duffy
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Michael A Meiners
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Lab Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica L Macke
- The Institute of Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | | | - Joel A Morales-Rosado
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - David Rider
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Megan Williams
- Bioinformatics Systems, Information Technology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Klass J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Carolyn R Vitek
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Myra J Wick
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
- Departments of Otorhinolaryngology, Head and Neck Surgery, Ophthalmology, and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Konstantinos N Lazaridis
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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Robertson AJ, Tran KA, Bennett C, Sullivan C, Stark Z, Vadlamudi L, Waddell N. Clinically significant changes in genes and variants associated with epilepsy over time: implications for re-analysis. Sci Rep 2024; 14:7717. [PMID: 38565608 PMCID: PMC10987647 DOI: 10.1038/s41598-024-57976-1] [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: 12/06/2023] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
Despite the significant advances in understanding the genetic architecture of epilepsy, many patients do not receive a molecular diagnosis after genomic testing. Re-analysing existing genomic data has emerged as a potent method to increase diagnostic yields-providing the benefits of genomic-enabled medicine to more individuals afflicted with a range of different conditions. The primary drivers for these new diagnoses are the discovery of novel gene-disease and variants-disease relationships; however, most decisions to trigger re-analysis are based on the passage of time rather than the accumulation of new knowledge. To explore how our understanding of a specific condition changes and how this impacts re-analysis of genomic data from epilepsy patients, we developed Vigelint. This approach combines the information from PanelApp and ClinVar to characterise how the clinically relevant genes and causative variants available to laboratories change over time, and this approach to five clinical-grade epilepsy panels. Applying the Vigelint pipeline to these panels revealed highly variable patterns in new, clinically relevant knowledge becoming publicly available. This variability indicates that a more dynamic approach to re-analysis may benefit the diagnosis and treatment of epilepsy patients. Moreover, this work suggests that Vigelint can provide empirical data to guide more nuanced, condition-specific approaches to re-analysis.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia.
- The Genomic Institute, Department of Health, Queensland Government, Brisbane, Australia.
| | - Khoa A Tran
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
| | - Carmen Bennett
- UQ Centre for Clinical Research, Herston, Brisbane, QLD, 4029, Australia
- Department of Neurology, Royal Brisbane & Women's Hospital, Herston, Brisbane, QLD, 4029, Australia
| | - Clair Sullivan
- Faculty of Medicine, University of Queensland, Brisbane, Australia
- Queensland Digital Health Centre, University of Queensland, Brisbane, Australia
- Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Woolloongabba, Australia
- Department of Health, Metro North Hospital and Health Service, Queensland Government, Brisbane, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Australian Genomics, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
| | - Lata Vadlamudi
- UQ Centre for Clinical Research, Herston, Brisbane, QLD, 4029, Australia
- Department of Neurology, Royal Brisbane & Women's Hospital, Herston, Brisbane, QLD, 4029, Australia
| | - Nicola Waddell
- Faculty of Medicine, University of Queensland, Brisbane, Australia.
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
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7
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Krenn M, Wagner M, Zulehner G, Weng R, Jäger F, Keritam O, Sener M, Brücke C, Milenkovic I, Langer A, Buchinger D, Habersam R, Mayerhanser K, Brugger M, Brunet T, Jacob M, Graf E, Berutti R, Cetin H, Hoefele J, Winkelmann J, Zimprich F, Rath J. Next-generation sequencing and comprehensive data reassessment in 263 adult patients with neuromuscular disorders: insights into the gray zone of molecular diagnoses. J Neurol 2024; 271:1937-1946. [PMID: 38127101 PMCID: PMC10972933 DOI: 10.1007/s00415-023-12101-6] [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: 09/20/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Neuromuscular disorders (NMDs) are heterogeneous conditions with a considerable fraction attributed to monogenic defects. Despite the advancements in genomic medicine, many patients remain without a diagnosis. Here, we investigate whether a comprehensive reassessment strategy improves the diagnostic outcomes. METHODS We analyzed 263 patients with NMD phenotypes that underwent diagnostic exome or genome sequencing at our tertiary referral center between 2015 and 2023. We applied a comprehensive reassessment encompassing variant reclassification, re-phenotyping and NGS data reanalysis. Multivariable logistic regression was performed to identify predictive factors associated with a molecular diagnosis. RESULTS Initially, a molecular diagnosis was identified in 53 cases (20%), while an additional 23 (9%) had findings of uncertain significance. Following comprehensive reassessment, the diagnostic yield increased to 23%, revealing 44 distinct monogenic etiologies. Reasons for newly obtained molecular diagnoses were variant reclassifications in 7 and NGS data reanalysis in 3 cases including one recently described disease-gene association (DNAJB4). Male sex reduced the odds of receiving a molecular diagnosis (OR 0.42; 95%CI 0.21-0.82), while a positive family history (OR 5.46; 95%CI 2.60-11.76) and a myopathy phenotype (OR 2.72; 95%CI 1.11-7.14) increased the likelihood. 7% were resolved through targeted genetic testing or classified as acquired etiologies. CONCLUSION Our findings reinforce the use of NGS in NMDs of suspected monogenic origin. We show that a comprehensive reassessment enhances diagnostic accuracy. However, one needs to be aware that genetic diagnoses are often made with uncertainty and can even be downgraded based on new evidence.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Gudrun Zulehner
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Rosa Weng
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Fiona Jäger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Omar Keritam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Merve Sener
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christof Brücke
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Ivan Milenkovic
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Agnes Langer
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Dominic Buchinger
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Richard Habersam
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Katharina Mayerhanser
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Dr. Von Hauner's Children's Hospital, University of Munich, Munich, Germany
| | - Maureen Jacob
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Hakan Cetin
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Klinikum Rechts Der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Jakob Rath
- Department of Neurology, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria.
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8
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Ji J, Leung ML. Clinical Utility and Long-Term Feasibility of Exome and Genome Reanalysis: From the Perspectives of a Clinical Laboratory. J Appl Lab Med 2024; 9:162-167. [PMID: 38167756 DOI: 10.1093/jalm/jfad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/28/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Jianling Ji
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, United States
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Marco L Leung
- Department of Pathology and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, United States
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9
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van Slobbe M, van Haeringen A, Vissers LELM, Bijlsma EK, Rutten JW, Suerink M, Nibbeling EAR, Ruivenkamp CAL, Koene S. Reanalysis of whole-exome sequencing (WES) data of children with neurodevelopmental disorders in a standard patient care context. Eur J Pediatr 2024; 183:345-355. [PMID: 37889289 PMCID: PMC10858114 DOI: 10.1007/s00431-023-05279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/20/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
This study aims to inform future genetic reanalysis management by evaluating the yield of whole-exome sequencing (WES) reanalysis in standard patient care in the Netherlands. Single-center data of 159 patients with a neurodevelopmental disorder (NDD), in which WES analysis and reanalysis were performed between January 1, 2014, and December 31, 2021, was retrospectively collected. Patients were included if they were under the age of 18 years at initial analysis and if this initial analysis did not result in a diagnosis. Demographic, phenotypic, and genotypic characteristics of patients were collected and analyzed. The primary outcomes of our study were (i) diagnostic yield at reanalysis, (ii) reasons for detecting a new possibly causal variant at reanalysis, (iii) unsolicited findings, and (iv) factors associated with positive result of reanalysis. In addition, we conducted a questionnaire study amongst the 7 genetic department in the Netherlands creating an overview of used techniques, yield, and organization of WES reanalysis. The single-center data show that in most cases, WES reanalysis was initiated by the clinical geneticist (65%) or treating physician (30%). The mean time between initial WES analysis and reanalysis was 3.7 years. A new (likely) pathogenic variant or VUS with a clear link to the phenotype was found in 20 initially negative cases, resulting in a diagnostic yield of 12.6%. In 75% of these patients, the diagnosis had clinical consequences, as for example, a screening plan for associated signs and symptoms could be devised. Most (32%) of the (likely) causal variants identified at WES reanalysis were discovered due to a newly described gene-disease association. In addition to the 12.6% diagnostic yield based on new diagnoses, reclassification of a variant of uncertain significance found at initial analysis led to a definite diagnosis in three patients. Diagnostic yield was higher in patients with dysmorphic features compared to patients without clear dysmorphic features (yield 27% vs. 6%; p = 0.001). CONCLUSIONS Our results show that WES reanalysis in patients with NDD in standard patient care leads to a substantial increase in genetic diagnoses. In the majority of newly diagnosed patients, the diagnosis had clinical consequences. Knowledge about the clinical impact of WES reanalysis, clinical characteristics associated with higher yield, and the yield per year after a negative WES in larger clinical cohorts is warranted to inform guidelines for genetic reanalysis. These guidelines will be of great value for pediatricians, pediatric rehabilitation specialists, and pediatric neurologists in daily care of patients with NDD. WHAT IS KNOWN • Whole exome sequencing can cost-effectively identify a genetic cause of intellectual disability in about 30-40% of patients. • WES reanalysis in a research setting can lead to a definitive diagnosis in 10-20% of previously exome negative cases. WHAT IS NEW • WES reanalysis in standard patient care resulted in a diagnostic yield of 13% in previously exome negative children with NDD. • The presence of dysmorphic features is associated with an increased diagnostic yield of WES reanalysis.
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Affiliation(s)
- Michelle van Slobbe
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julie W Rutten
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
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10
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Saglia C, Bracciamà V, Trotta L, Mioli F, Faini AC, Brach Del Prever GM, Kalantari S, Luca M, Romeo CM, Scolari C, Peruzzi L, Calvo PL, Mussa A, Fenoglio R, Roccatello D, Alberti C, Carli D, Amoroso A, Deaglio S, Vaisitti T. Relevance of next generation sequencing (NGS) data re-analysis in the diagnosis of monogenic diseases leading to organ failure. BMC Med Genomics 2023; 16:303. [PMID: 38012624 PMCID: PMC10680258 DOI: 10.1186/s12920-023-01747-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: 09/20/2023] [Accepted: 11/21/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND In 2018, our center started a program to offer genetic diagnosis to patients with kidney and liver monogenic rare conditions, potentially eligible for organ transplantation. We exploited a clinical exome sequencing approach, followed by analyses of in silico gene panels tailored to clinical suspicions, obtaining detection rates in line with what reported in literature. However, a percentage of patients remains without a definitive genetic diagnosis. This work aims to evaluate the utility of NGS data re-analysis for those patients with an inconclusive or negative genetic test at the time of first analysis considering that (i) the advance of alignment and variant calling processes progressively improve the detection rate, limiting false positives and false negatives; (ii) gene panels are periodically updated and (iii) variant annotation may change over time. METHODS 114 patients, recruited between 2018 and 2020, with an inconclusive or negative NGS report at the time of first analysis, were included in the study. Re-alignment and variant calling of previously generated sequencing raw data were performed using the GenomSys Variant Analyzer software. RESULTS 21 previously not reported potentially causative variants were identified in 20 patients. In most cases (n = 19), causal variants were retrieved out of the re-classification from likely benign to variants of unknown significance (VUS). In one case, the variant was included because of inclusion in the analysis of a newly disease-associated gene, not present in the original gene panel, and in another one due to the improved data alignment process. Whenever possible, variants were validated with Sanger sequencing and family segregation studies. As of now, 16 out of 20 patients have been analyzed and variants confirmed in 8 patients. Specifically, in two pediatric patients, causative variants were de novo mutations while in the others, the variant was present also in other affected relatives. In the remaining patients, variants were present also in non-affected parents, raising questions on their re-classification. CONCLUSIONS Overall, these data indicate that periodic and systematic re-analysis of negative or inconclusive NGS data reports can lead to new variant identification or reclassification in a small but significant proportion of cases, with benefits for patients' management.
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Affiliation(s)
- Claudia Saglia
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valeria Bracciamà
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Fiorenza Mioli
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Angelo Corso Faini
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Giulia Margherita Brach Del Prever
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Kalantari
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Maria Luca
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Carmelo Maria Romeo
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Scolari
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Licia Peruzzi
- Pediatric Nephrology Dialysis and Transplantation Unit, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
| | - Pier Luigi Calvo
- Pediatric Gastroenterology Unit, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
| | - Alessandro Mussa
- Pediatric Clinical Genetics, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Roberta Fenoglio
- Nephrology and Dialysis Unit, Center of Research on Immunopathology and Rare Diseases, CMID, San Giovanni Bosco Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Dario Roccatello
- Nephrology and Dialysis Unit, Center of Research on Immunopathology and Rare Diseases, CMID, San Giovanni Bosco Hospital, Turin, Italy
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | | | - Diana Carli
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Antonio Amoroso
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tiziana Vaisitti
- Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino", Turin, Italy.
- Department of Medical Sciences, University of Turin, Turin, Italy.
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11
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Price E, Fedida LM, Pugacheva EM, Ji YJ, Loukinov D, Lobanenkov VV. An updated catalog of CTCF variants associated with neurodevelopmental disorder phenotypes. Front Mol Neurosci 2023; 16:1185796. [PMID: 37324587 PMCID: PMC10264798 DOI: 10.3389/fnmol.2023.1185796] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction CTCF-related disorder (CRD) is a neurodevelopmental disorder (NDD) caused by monoallelic pathogenic variants in CTCF. The first CTCF variants in CRD cases were documented in 2013. To date, 76 CTCF variants have been further described in the literature. In recent years, due to the increased application of next-generation sequencing (NGS), growing numbers of CTCF variants are being identified, and multiple genotype-phenotype databases cataloging such variants are emerging. Methods In this study, we aimed to expand the genotypic spectrum of CRD, by cataloging NDD phenotypes associated with reported CTCF variants. Here, we systematically reviewed all known CTCF variants reported in case studies and large-scale exome sequencing cohorts. We also conducted a meta-analysis using public variant data from genotype-phenotype databases to identify additional CTCF variants, which we then curated and annotated. Results From this combined approach, we report an additional 86 CTCF variants associated with NDD phenotypes that have not yet been described in the literature. Furthermore, we describe and explain inconsistencies in the quality of reported variants, which impairs the reuse of data for research of NDDs and other pathologies. Discussion From this integrated analysis, we provide a comprehensive and annotated catalog of all currently known CTCF mutations associated with NDD phenotypes, to aid diagnostic applications, as well as translational and basic research.
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12
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Oliver KL, Scheffer IE, Bennett MF, Grinton BE, Bahlo M, Berkovic SF. Genes4Epilepsy: An epilepsy gene resource. Epilepsia 2023; 64:1368-1375. [PMID: 36808730 PMCID: PMC10952165 DOI: 10.1111/epi.17547] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023]
Abstract
OBJECTIVE "How many epilepsy genes are there?" is a frequently asked question. We sought to (1) provide a curated list of genes that cause monogenic epilepsies, and (2) compare and contrast epilepsy gene panels from multiple sources. METHODS We compared genes included on the epilepsy panels (as of July 29, 2022) of four clinical diagnostic providers: Invitae, GeneDx, Fulgent Genetics, and Blueprint Genetics; and two research resources: PanelApp Australia and ClinGen. A master list of all unique genes was supplemented by additional genes identified via PubMed searches up until August 15, 2022, using the search terms "genetics" AND/OR "epilepsy" AND/OR "seizures". Evidence supporting a monogenic role for all genes was manually reviewed; those with limited or disputed evidence were excluded. All genes were annotated according to inheritance pattern and broad epilepsy phenotype. RESULTS The comparison of genes included on epilepsy clinical panels revealed high heterogeneity in both number of genes (range: 144-511) and content. Just 111 genes (15.5%) were included on all four clinical panels. Subsequent manual curation of all "epilepsy genes" identified >900 monogenic etiologies. Almost 90% of genes were associated with developmental and epileptic encephalopathies. By comparison only 5% of genes were associated with monogenic causes of "common epilepsies" (i.e., generalized and focal epilepsy syndromes). Autosomal recessive genes were most frequent (56% of genes); however, this varied according to the associated epilepsy phenotype(s). Genes associated with common epilepsy syndromes were more likely to be dominantly inherited and associated with multiple epilepsy types. SIGNIFICANCE Our curated list of monogenic epilepsy genes is publicly available: github.com/bahlolab/genes4epilepsy and will be regularly updated. This gene resource can be utilized to target genes beyond those included on clinical gene panels, for gene enrichment methods and candidate gene prioritization. We invite ongoing feedback and contributions from the scientific community via genes4-epilepsy@unimelb.edu.au.
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Affiliation(s)
- Karen L. Oliver
- Department of Medicine, Epilepsy Research CentreUniversity of Melbourne, Austin HealthMelbourneVictoriaAustralia
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Ingrid E. Scheffer
- Department of Medicine, Epilepsy Research CentreUniversity of Melbourne, Austin HealthMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthHeidelbergVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Mark F. Bennett
- Department of Medicine, Epilepsy Research CentreUniversity of Melbourne, Austin HealthMelbourneVictoriaAustralia
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Bronwyn E. Grinton
- Department of Medicine, Epilepsy Research CentreUniversity of Melbourne, Austin HealthMelbourneVictoriaAustralia
| | - Melanie Bahlo
- Population Health and Immunity DivisionThe Walter and Eliza Hall Institute of Medical ResearchParkvilleVictoriaAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Samuel F. Berkovic
- Department of Medicine, Epilepsy Research CentreUniversity of Melbourne, Austin HealthMelbourneVictoriaAustralia
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13
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Spillmann RC, Tan QKG, Reuter C, Schoch K, Kohler J, Bonner D, Zastrow D, Alkelai A, Baugh E, Cope H, Marwaha S, Wheeler MT, Bernstein JA, Shashi V. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med 2023; 25:100353. [PMID: 36481303 PMCID: PMC10506157 DOI: 10.1016/j.gim.2022.12.001] [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: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice. METHODS A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data. RESULTS In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection. CONCLUSION The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.
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Affiliation(s)
- Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Chloe Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Anna Alkelai
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Evan Baugh
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
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14
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Denommé-Pichon AS, Matalonga L, de Boer E, Jackson A, Benetti E, Banka S, Bruel AL, Ciolfi A, Clayton-Smith J, Dallapiccola B, Duffourd Y, Ellwanger K, Fallerini C, Gilissen C, Graessner H, Haack TB, Havlovicova M, Hoischen A, Jean-Marçais N, Kleefstra T, López-Martín E, Macek M, Mencarelli MA, Moutton S, Pfundt R, Pizzi S, Posada M, Radio FC, Renieri A, Rooryck C, Ryba L, Safraou H, Schwarz M, Tartaglia M, Thauvin-Robinet C, Thevenon J, Tran Mau-Them F, Trimouille A, Votypka P, de Vries BBA, Willemsen MH, Zurek B, Verloes A, Philippe C, Vitobello A, Vissers LELM, Faivre L. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing. Genet Med 2023; 25:100018. [PMID: 36681873 DOI: 10.1016/j.gim.2023.100018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. METHODS Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. RESULTS We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). CONCLUSION The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock.
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Affiliation(s)
- Anne-Sophie Denommé-Pichon
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France.
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation," The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Elisa Benetti
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Ange-Line Bruel
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Andrea Ciolfi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, United Kingdom
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Yannis Duffourd
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Kornelia Ellwanger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Chiara Fallerini
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy
| | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radbound University, Nijmegen, The Netherlands
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Marketa Havlovicova
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Alexander Hoischen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radbound University, Nijmegen, The Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Nolwenn Jean-Marçais
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, The Netherlands
| | - Estrella López-Martín
- Institute of Rare Diseases Research, Spanish Undiagnosed Rare Diseases Cases Program (SpainUDP) & Undiagnosed Diseases Network International, Instituto de Salud Carlos III, Madrid, Spain
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | | | - Sébastien Moutton
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Simone Pizzi
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Manuel Posada
- Institute of Rare Diseases Research, Spanish Undiagnosed Rare Diseases Cases Program (SpainUDP) & Undiagnosed Diseases Network International, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Alessandra Renieri
- MedBiotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy; Medical Genetics, University of Siena, Siena, Italy; Medical Genetics, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Caroline Rooryck
- MRGM INSERM U1211, University of Bordeaux, Medical Genetics Department, Bordeaux University Hospital, Bordeaux, France
| | - Lukas Ryba
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Hana Safraou
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Martin Schwarz
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Christel Thauvin-Robinet
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France
| | - Julien Thevenon
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Frédéric Tran Mau-Them
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Aurélien Trimouille
- Molecular Genetics Laboratory, Medical Genetics Department, Bordeaux University Hospital - Hôpital Pellegrin, Bordeaux, France
| | - Pavel Votypka
- Department of Biology and Medical Genetics, Second Faculty of Medicine of Charles University and Motol University Hospital, Prague, Czech Republic
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Birte Zurek
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; Centre for Rare Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Alain Verloes
- Department of Genetics, Assistance Publique-Hôpitaux de Paris - Université de Paris, Paris, France; INSERM UMR 1141 "NeuroDiderot," Hôpital Robert Debré, Paris, France
| | - Christophe Philippe
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, The Netherlands
| | - Laurence Faivre
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, FHU-TRANSLAD and GIMI Institute, Dijon Bourgogne University Hospital, Dijon, France.
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15
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Sun S, Wang H. Clocking Epilepsies: A Chronomodulated Strategy-Based Therapy for Rhythmic Seizures. Int J Mol Sci 2023; 24:4223. [PMID: 36835631 PMCID: PMC9962262 DOI: 10.3390/ijms24044223] [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: 12/19/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Epilepsy is a neurological disorder characterized by hypersynchronous recurrent neuronal activities and seizures, as well as loss of muscular control and sometimes awareness. Clinically, seizures have been reported to display daily variations. Conversely, circadian misalignment and circadian clock gene variants contribute to epileptic pathogenesis. Elucidation of the genetic bases of epilepsy is of great importance because the genetic variability of the patients affects the efficacies of antiepileptic drugs (AEDs). For this narrative review, we compiled 661 epilepsy-related genes from the PHGKB and OMIM databases and classified them into 3 groups: driver genes, passenger genes, and undetermined genes. We discuss the potential roles of some epilepsy driver genes based on GO and KEGG analyses, the circadian rhythmicity of human and animal epilepsies, and the mutual effects between epilepsy and sleep. We review the advantages and challenges of rodents and zebrafish as animal models for epileptic studies. Finally, we posit chronomodulated strategy-based chronotherapy for rhythmic epilepsies, integrating several lines of investigation for unraveling circadian mechanisms underpinning epileptogenesis, chronopharmacokinetic and chronopharmacodynamic examinations of AEDs, as well as mathematical/computational modeling to help develop time-of-day-specific AED dosing schedules for rhythmic epilepsy patients.
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Affiliation(s)
- Sha Sun
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China
- School of Biology and Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou 215123, China
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16
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Smith L, Malinowski J, Ceulemans S, Peck K, Walton N, Sheidley BR, Lippa N. Genetic testing and counseling for the unexplained epilepsies: An evidence‐based practice guideline of the National Society of Genetic Counselors. J Genet Couns 2022; 32:266-280. [PMID: 36281494 DOI: 10.1002/jgc4.1646] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/27/2022] [Accepted: 10/01/2022] [Indexed: 11/10/2022]
Abstract
Epilepsy, defined by the occurrence of two or more unprovoked seizures or one unprovoked seizure with a propensity for others, affects 0.64% of the population and can lead to significant morbidity and mortality. A majority of unexplained epilepsy (seizures not attributed to an acquired etiology, such as trauma or infection) is estimated to have an underlying genetic etiology. Despite rapid progress in understanding of the genetic underpinnings of the epilepsies, there are no recent evidence-based guidelines for genetic testing and counseling for this population. This practice guideline provides evidence-based recommendations for approaching genetic testing in the epilepsies using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Evidence to Decision framework. We used evidence from a recent systematic evidence review and meta-analysis of diagnostic yield of genetic tests in patients with epilepsy. We also compiled data from other sources, including recently submitted conference abstracts and peer-reviewed journal articles. We identified and prioritized outcomes of genetic testing as critical, important or not important and based our recommendations on outcomes deemed critical and important. We considered the desirable and undesirable effects, value and acceptability to relevant stakeholders, impact on health equity, cost-effectiveness, certainty of evidence, and feasibility of the interventions in individuals with epilepsy. Taken together, we generated two clinical recommendations: (1) Genetic testing is strongly recommended for all individuals with unexplained epilepsy, without limitation of age, with exome/genome sequencing and/or a multi-gene panel (>25 genes) as first-tier testing followed by chromosomal microarray, with exome/genome sequencing conditionally recommended over multi-gene panel. (2) It is strongly recommended that genetic tests be selected, ordered, and interpreted by a qualified healthcare provider in the setting of appropriate pre-test and post-test genetic counseling. Incorporation of genetic counselors into neurology practices and/or referral to genetics specialists are both useful models for supporting providers without genetics expertise to implement these recommendations.
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Affiliation(s)
- Lacey Smith
- Epilepsy Genetics Program, Department of Neurology Boston Children's Hospital Boston Massachusetts USA
| | | | - Sophia Ceulemans
- Department of Genetics, Department of Neurology Rady Children's Hospital San Diego California USA
| | - Katlin Peck
- Department of Laboratory Management eviCore Healthcare Bluffton South Carolina USA
| | - Nephi Walton
- Intermountain Precision Genomics Intermountain Healthcare St. George Utah USA
| | - Beth Rosen Sheidley
- Epilepsy Genetics Program, Department of Neurology Boston Children's Hospital Boston Massachusetts USA
| | - Natalie Lippa
- Instititute for Genomic Medicine Columbia University Irving Medical Center New York New York USA
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17
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Alsubhi S, Osterman B, Chrestian N, Dubeau F, Buhas D, Srour M. Case report: PLPHP deficiency, a rare but important cause of B6-responsive disorders: A report of three novel individuals and review of 51 cases. Front Neurol 2022; 13:913652. [PMID: 36324377 PMCID: PMC9618642 DOI: 10.3389/fneur.2022.913652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
PLPHP (pyridoxal-phosphate homeostasis protein) deficiency is caused by biallelic pathogenic variants in PLPBP and is a rare cause of pyridoxine-responsive disorders. We describe three French-Canadian individuals with PLPHP deficiency, including one with unusual paroxysmal episodes lacking EEG correlation with a suspicious movement disorder, rarely reported in B6RDs. In addition, we review the clinical features and treatment responses of all 51 previously published individuals with PLPHP deficiency. Our case series underlines the importance of considering PLPBP mutations in individuals with partially B6-responsive seizures and highlights the presence of a founder effect in the French-Canadian population.
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Affiliation(s)
- Sarah Alsubhi
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Bradley Osterman
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Nicolas Chrestian
- Department of Pediatric Neurology, Pediatric Neuromuscular Disorder, Centre Mère Enfant Soleil, Laval University, Quebec City, QC, Canada
| | - François Dubeau
- Department of Neurology and Neurosurgery McGill University, Montreal, QC, Canada
| | - Daniela Buhas
- Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Center, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Myriam Srour
- Division of Pediatric Neurology, Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery McGill University, Montreal, QC, Canada
- Child Health and Human Development Program (CHHD), McGill University Health Center Research Institute, Montreal, QC, Canada
- *Correspondence: Myriam Srour
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18
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Knowles JK, Helbig I, Metcalf CS, Lubbers LS, Isom LL, Demarest S, Goldberg EM, George AL, Lerche H, Weckhuysen S, Whittemore V, Berkovic SF, Lowenstein DH. Precision medicine for genetic epilepsy on the horizon: Recent advances, present challenges, and suggestions for continued progress. Epilepsia 2022; 63:2461-2475. [PMID: 35716052 PMCID: PMC9561034 DOI: 10.1111/epi.17332] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 01/18/2023]
Abstract
The genetic basis of many epilepsies is increasingly understood, giving rise to the possibility of precision treatments tailored to specific genetic etiologies. Despite this, current medical therapy for most epilepsies remains imprecise, aimed primarily at empirical seizure reduction rather than targeting specific disease processes. Intellectual and technological leaps in diagnosis over the past 10 years have not yet translated to routine changes in clinical practice. However, the epilepsy community is poised to make impressive gains in precision therapy, with continued innovation in gene discovery, diagnostic ability, and bioinformatics; increased access to genetic testing and counseling; fuller understanding of natural histories; agility and rigor in preclinical research, including strategic use of emerging model systems; and engagement of an evolving group of stakeholders (including patient advocates, governmental resources, and clinicians and scientists in academia and industry). In each of these areas, we highlight notable examples of recent progress, new or persistent challenges, and future directions. The future of precision medicine for genetic epilepsy looks bright if key opportunities on the horizon can be pursued with strategic and coordinated effort.
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Affiliation(s)
- Juliet K. Knowles
- Department of Neurology, Division of Child Neurology, Stanford University School of Medicine, Stanford, California, USA
| | - Ingo Helbig
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Cameron S. Metcalf
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | - Laura S. Lubbers
- Citizens United for Research in Epilepsy, Chicago, Illinois, USA
| | - Lori L. Isom
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Scott Demarest
- Department of Pediatrics and Neurology, University of Colorado, School of Medicine, Aurora, Colorado, USA
| | - Ethan M. Goldberg
- Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Sarah Weckhuysen
- Division of Neurology, University Hospital Antwerp, Antwerp, Belgium
- Applied and Translational Neurogenomics Group, Vlaams Instituut voor Biotechnologie Center for Molecular Neurology, Antwerp, Belgium
- Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium
- μNEURO Research Center of Excellence, University of Antwerp, Antwerp, Belgium
| | - Vicky Whittemore
- Division of Neuroscience, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Rockville, Maryland, USA
| | - Samuel F. Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel H. Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
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19
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Mahdiannasser M, Rashidi-Nezhad A, Badv RS, Akrami SM. Exploring the genetic etiology of drug-resistant epilepsy: incorporation of exome sequencing into practice. Acta Neurol Belg 2022; 122:1457-1468. [PMID: 36127562 DOI: 10.1007/s13760-022-02095-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND By affecting about 50 million people worldwide, epilepsy is considered a global concern in neurology. Intolerable enough, up to ¼ of all patients do not respond to antiepileptic drugs and have recurring seizures. Therefore, revealing the underlying etiology is quite demanding in a clinical context to improve diagnosis and disease management. METHODS Initially, 85 patients suspected of epilepsy underwent thorough clinical and paraclinical evaluation and 24 individuals with drug-resistant epilepsy entered the study. Using whole-exome sequencing, the genetic etiology of drug-resistant epilepsy was investigated and discerned whether this method could facilitate the management of drug-resistant epilepsy through personalized medicine. Eventually, functional annotation was performed and drug-gene interaction networks were constructed to find potential therapeutic targets. RESULTS We found eleven novel variants in various genes including IRF2BPL, ST3GAL3, and GPAA1, for which a few epilepsy-related variants are available in public databases. The overall diagnostic yield for likely pathogenic and pathogenic variants and the detection rate of novel variants were 25% and 84.6%, respectively. Based on the results, two patients were considered potential candidates for personalized medicine. The highest number of interaction with drugs was demonstrated for SCN1A, SCN2A, and GRIN2A genes. CONCLUSIONS This study highlighted the importance of consanguineous marriage in drug-resistant epilepsy and suggested the possibility of reduced penetrance and variable expressivity in some of the autosomal dominant cases. We also suggest that whole-exome sequencing could facilitate personalized management of drug-resistant epilepsy. Regarding drug-gene interactions, some genes such as SCN1A and SCN2A might serve as therapeutic targets in drug-resistant epilepsy.
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Affiliation(s)
- Mojdeh Mahdiannasser
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Poursina St., P.O. Box:14176-13151, Tehran, Iran
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Poursina St., P.O. Box:14176-13151, Tehran, Iran.
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20
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Park S, Jang SS, Lee S, Kim M, Sim H, Jeon H, Hong SE, Lee J, Lee J, Jeon EY, Lee J, Lee CR, Kim SY, Kim MJ, Yoon JG, Lim BC, Kim WJ, Kim KJ, Ko JM, Cho A, Lee JS, Choi M, Chae JH. Systematic analysis of inheritance pattern determination in genes that cause rare neurodevelopmental diseases. Front Genet 2022; 13:990015. [PMID: 36212160 PMCID: PMC9533195 DOI: 10.3389/fgene.2022.990015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023] Open
Abstract
Despite recent advancements in our understanding of genetic etiology and its molecular and physiological consequences, it is not yet clear what genetic features determine the inheritance pattern of a disease. To address this issue, we conducted whole exome sequencing analysis to characterize genetic variants in 1,180 Korean patients with neurological symptoms. The diagnostic yield for definitive pathogenic variant findings was 50.8%, after including 33 cases (5.9%) additionally diagnosed by reanalysis. Of diagnosed patients, 33.4% carried inherited variants. At the genetic level, autosomal recessive-inherited genes were characterized by enrichments in metabolic process, muscle organization and metal ion homeostasis pathways. Transcriptome and interactome profiling analyses revealed less brain-centered expression and fewer protein-protein interactions for recessive genes. The majority of autosomal recessive genes were more tolerant of variation, and functional prediction scores of recessively-inherited variants tended to be lower than those of dominantly-inherited variants. Additionally, we were able to predict the rates of carriers for recessive variants. Our results showed that genes responsible for neurodevelopmental disorders harbor different molecular mechanisms and expression patterns according to their inheritance patterns. Also, calculated frequency rates for recessive variants could be utilized to pre-screen rare neurodevelopmental disorder carriers.
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Affiliation(s)
- Soojin Park
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Seungbok Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Minsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyungtai Sim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeongseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Eun Hong
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jean Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongeun Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Eun Young Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeongha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Cho-Rong Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,Rare Disease Center, Seoul National University Hospital, Seoul, South Korea
| | - Jihoon G. Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Woo Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Anna Cho
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Hospital Child Cancer and Rare Disease Administration, Seoul National University Children’s Hospital, Seoul, South Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University College of Medicine, Seoul National University Children’s Hospital, Seoul, South Korea,Department of Genomic Medicine, Seoul National University Hospital, Seoul, South Korea,*Correspondence: Murim Choi, ; Jong-Hee Chae,
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21
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Dai P, Honda A, Ewans L, McGaughran J, Burnett L, Law M, Phan TG. Recommendations for next generation sequencing data reanalysis of unsolved cases with suspected Mendelian disorders: A systematic review and meta-analysis. Genet Med 2022; 24:1618-1629. [PMID: 35550369 DOI: 10.1016/j.gim.2022.04.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The study aimed to determine the diagnostic yield, optimal timing, and methodology of next generation sequencing data reanalysis in suspected Mendelian disorders. METHODS We conducted a systematic review and meta-analysis of studies that conducted data reanalysis in patients with suspected Mendelian disorders. Random effects model was used to pool the estimated outcome with subgroup analysis stratified by timing, sequencing methodology, sample size, segregation, use of research validation, and artificial intelligence (AI) variant curation tools. RESULTS A search of PubMed, Embase, Scopus, and Web of Science between 2007 and 2021 yielded 9327 articles, of which 29 were selected. Significant heterogeneity was noted between studies. Reanalysis had an overall diagnostic yield of 0.10 (95% CI = 0.06-0.13). Literature updates accounted for most new diagnoses. Diagnostic yield was higher after 24 months, although this was not statistically significant. Increased diagnoses were obtained with research validation and data sharing. AI-based tools did not adversely affect reanalysis diagnostic rate. CONCLUSION Next generation sequencing data reanalysis can improve diagnostic yield. Owing to the heterogeneity of the studies, the optimal time to reanalysis and the impact of AI-based tools could not be determined with confidence. We propose standardized guidelines for future studies to reduce heterogeneity and improve the quality of the conclusions.
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Affiliation(s)
- Pei Dai
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Andrew Honda
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Lisa Ewans
- Department of Clinical Genetics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
| | - Julie McGaughran
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Leslie Burnett
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia; The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Genetic Medicine Program, Northern Clinical School, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Matthew Law
- Biostatistics and Databases Program, The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Tri Giang Phan
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia; Clinical Immunogenomics Research Consortium Australasia (CIRCA), Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
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22
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Robertson AJ, Tan NB, Spurdle AB, Metke-Jimenez A, Sullivan C, Waddell N. Re-analysis of genomic data: An overview of the mechanisms and complexities of clinical adoption. Genet Med 2022; 24:798-810. [PMID: 35065883 DOI: 10.1016/j.gim.2021.12.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022] Open
Abstract
Re-analyzing genomic information from a patient suspected of having an underlying genetic condition can improve the diagnostic yield of sequencing tests, potentially providing significant benefits to the patient and to the health care system. Although a significant number of studies have shown the clinical potential of re-analysis, less work has been performed to characterize the mechanisms responsible for driving the increases in diagnostic yield. Complexities surrounding re-analysis have also emerged. The terminology itself represents a challenge because "re-analysis" can refer to a range of different concepts. Other challenges include the increased workload that re-analysis demands of curators, adequate reimbursement pathways for clinical and diagnostic services, and the development of systems to handle large volumes of data. Re-analysis also raises ethical implications for patients and families, most notably when re-classification of a variant alters diagnosis, treatment, and prognosis. This review highlights the possibilities and complexities associated with the re-analysis of existing clinical genomic data. We propose a terminology that builds on the foundation presented in a recent statement from the American College of Medical Genetics and Genomics and describes each re-analysis process. We identify mechanisms for increasing diagnostic yield and provide perspectives on the range of challenges that must be addressed by health care systems and individual patients.
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Affiliation(s)
- Alan J Robertson
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; The Genomic Institute, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Natalie B Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia; Department of Paediatrics, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Clair Sullivan
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Queensland Digital Health Research Network, Global Change Institute, The University of Queensland, Brisbane, Queensland, Australia; Centre for Health Services Research, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Metro North Hospital and Health Service, Department of Health, Queensland Government, Brisbane, Queensland, Australia
| | - Nicola Waddell
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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23
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Cummings CT, Rowley MJ. Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment. Genes (Basel) 2022; 13:583. [PMID: 35456389 PMCID: PMC9030571 DOI: 10.3390/genes13040583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Properly organizing DNA within the nucleus is critical to ensure normal downstream nuclear functions. CTCF and cohesin act as major architectural proteins, working in concert to generate thousands of high-intensity chromatin loops. Due to their central role in loop formation, a massive research effort has been dedicated to investigating the mechanism by which CTCF and cohesin create these loops. Recent results lead to questioning the direct impact of CTCF loops on gene expression. Additionally, results of controlled depletion experiments in cell lines has indicated that genome architecture may be somewhat resistant to incomplete deficiencies in CTCF or cohesin. However, heterozygous human genetic deficiencies in CTCF and cohesin have illustrated the importance of their dosage in genome architecture, cellular processes, animal behavior, and disease phenotypes. Thus, the importance of considering CTCF or cohesin levels is especially made clear by these heterozygous germline variants that characterize genetic syndromes, which are increasingly recognized in clinical practice. Defined primarily by developmental delay and intellectual disability, the phenotypes of CTCF and cohesin deficiency illustrate the importance of architectural proteins particularly in neurodevelopment. We discuss the distinct roles of CTCF and cohesin in forming chromatin loops, highlight the major role that dosage of each protein plays in the amplitude of observed effects on gene expression, and contrast these results to heterozygous mutation phenotypes in murine models and clinical patients. Insights highlighted by this comparison have implications for future research into these newly emerging genetic syndromes.
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Affiliation(s)
- Christopher T. Cummings
- Munroe-Meyer Institute, Department of Genetic Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - M. Jordan Rowley
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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24
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Leung ML, Ji J, Baker S, Buchan JG, Sivakumaran TA, Krock BL, Hutchins R, Bayrak-Toydemir P, Pfeifer J, Cremona ML, Funke B, Santani AB. A Framework of Critical Considerations in Clinical Exome Reanalyses by Clinical and Laboratory Standards Institute. J Mol Diagn 2022; 24:177-188. [PMID: 35074075 DOI: 10.1016/j.jmoldx.2021.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022] Open
Abstract
Exome reanalysis is useful for providing molecular diagnoses for previously uninformative samples. However, challenges exist in implementing a practical solution for clinicians and laboratories. This study complements the current literature by providing practical considerations for patient-level and cohort-level reanalyses. The Clinical and Laboratory Standards Institute assembled the Document Development Committee and an interpretation working group that developed the framework for reevaluation of exome-based data. We describe two distinct but complementary approaches toward exome reanalyses: clinician-initiated patient-level reanalysis, and laboratory-initiated cohort-level reanalysis. We highlight the advantages and constraints for both approaches, and provide a high-level conceptual guide for ordering clinicians and laboratories through the critical decision pathways. Because clinical exome sequencing continues to be the standard of care in genetics, exome reanalysis would be critical in increasing the overall diagnostic yield. A systematic guide will facilitate the efficient adoption of reevaluation of exome data for laboratories, health care professionals, genetic counselors, and clinicians.
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Affiliation(s)
- Marco L Leung
- Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio; The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Jianling Ji
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California; Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Samuel Baker
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jillian G Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Theru A Sivakumaran
- Division of Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, Arizona
| | | | | | - Pinar Bayrak-Toydemir
- Department of Pathology, The University of Utah, Salt Lake City, Utah; ARUP Laboratories, Salt Lake City, Utah
| | - John Pfeifer
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | | | | | - Avni B Santani
- Center for Applied Genomics, Children's Hospital of Philadelphia, Pennsylvania; Veritas Genetics, Boston, Massachusetts.
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25
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Freyberger F, Kokotović T, Krnjak G, Frković SH, Nagy V. Expanding the known phenotype of Mullegama-Klein-Martinez syndrome in male patients. Hum Genome Var 2021; 8:37. [PMID: 34580287 PMCID: PMC8476567 DOI: 10.1038/s41439-021-00169-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 02/02/2023] Open
Abstract
Here, we report a novel case of a male patient with a hemizygous missense variant in STAG2 (p.Tyr159His) resulting in Mullegama–Klein–Martinez syndrome (MKMS), a rare X-linked cohesinopathy. He shares distinct clinical features with a previously reported male patient carrying the STAG2 variant p.Tyr159Cys, suggesting that this phenotype is determined by the position of the mutation. Additionally, our patient exhibits symptoms not previously associated with MKMS, expanding the known clinical phenotype of this rare disease.
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Affiliation(s)
- Fiona Freyberger
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria.,CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Goran Krnjak
- Department of Pediatrics, Varazdin General Hospital, Varazdin, Croatia
| | - Sanda Huljev Frković
- Department of Paediatrics, Division for Genetics and Metabolism, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria. .,Department of Neurology, Medical University of Vienna, Vienna, Austria. .,CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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26
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Tian Q, Li H, Shu L, Wang H, Peng Y, Fang H, Mao X. Effective treatments for FGF12-related early-onset epileptic encephalopathies patients. Brain Dev 2021; 43:851-856. [PMID: 34020858 DOI: 10.1016/j.braindev.2021.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND FGF12 (FHF1) gene encodes voltage-gated sodium channel (Nav)-binding protein fibroblast growth factor homologous factor 1, which could cause seizures by regulating voltage dependence of Nav fast inactivation and neuron excitability. The most common pathogenic variant FGF12 c.341G > A related early-onset epileptic encephalopathies (EOEE) was characterized by intractable seizures and developmental disabilities. RESULTS Using whole exome sequencing, a de novo hotspot variant c.341G > A (NM_021032.4) of FGF12 was identified in three unrelated EOEE probands. All probands were seizure free after a combination treatment of valproic acid (VPA) and topiramate (TPM). The motor and cognitive skills in two probands were improved due to the early and effective treatment. In order to compare the effectiveness of different treatment strategies for the disease, a review of treatments for FGF12-related epilepsy was made. CONCLUSION We reported three FGF12 c.341G > A related EOEE patients responded well to a combination antiepileptic therapy of VPA and TPM. The current study is the first to describe the combination therapy of VPA and TPM in FGF12 c.341G > A related EOEE patients. This study may contribute to future medication consultation for intractable epilepsy with FGF12 hotspot variants.
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Affiliation(s)
- Qi Tian
- Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China; National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China
| | - Haoyu Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China; Center for Molecular Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li Shu
- Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China; National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China
| | - Hua Wang
- Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China; National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China
| | - Ying Peng
- Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China.
| | - Hongjun Fang
- Department of Neurology, Hunan Children's Hospital, University of South China, Changsha 410007, China.
| | - Xiao Mao
- Department of Medical Genetics, Maternal, Child Health Hospital of Hunan Province, Changsha Hunan 410008, China; National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China.
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27
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Abstract
Novel gene-disease discoveries, rapid advancements in technology, and improved bioinformatics tools all have the potential to yield additional molecular diagnoses through the reanalysis of exome sequencing data. Collaborations between clinical laboratories, ordering physicians, and researchers are also driving factors that can contribute to these new insights. Automation in ongoing natural history collection, evolving phenotype updates, advancements in processing next-generation sequencing data, and up-to-date variant-gene-disease databases are increasingly needed for systematic exome reanalysis. Here, we review some of the advantages and challenges for clinician-initiated and laboratory-initiated exome reanalysis, and we propose a model for the future that could potentially maximize the clinical utility of exome reanalysis by integrating information from electronic medical records and knowledge databases into routine clinical workflows.
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28
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Harvey S, King MD, Gorman KM. Paroxysmal Movement Disorders. Front Neurol 2021; 12:659064. [PMID: 34177764 PMCID: PMC8232056 DOI: 10.3389/fneur.2021.659064] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 11/13/2022] Open
Abstract
Paroxysmal movement disorders (PxMDs) are a clinical and genetically heterogeneous group of movement disorders characterized by episodic involuntary movements (dystonia, dyskinesia, chorea and/or ataxia). Historically, PxMDs were classified clinically (triggers and characteristics of the movements) and this directed single-gene testing. With the advent of next-generation sequencing (NGS), how we classify and investigate PxMDs has been transformed. Next-generation sequencing has enabled new gene discovery (RHOBTB2, TBC1D24), expansion of phenotypes in known PxMDs genes and a better understanding of disease mechanisms. However, PxMDs exhibit phenotypic pleiotropy and genetic heterogeneity, making it challenging to predict genotype based on the clinical phenotype. For example, paroxysmal kinesigenic dyskinesia is most commonly associated with variants in PRRT2 but also variants identified in PNKD, SCN8A, and SCL2A1. There are no radiological or biochemical biomarkers to differentiate genetic causes. Even with NGS, diagnosis rates are variable, ranging from 11 to 51% depending on the cohort studied and technology employed. Thus, a large proportion of patients remain undiagnosed compared to other neurological disorders such as epilepsy, highlighting the need for further genomic research in PxMDs. Whole-genome sequencing, deep-sequencing, copy number variant analysis, detection of deep-intronic variants, mosaicism and repeat expansions, will improve diagnostic rates. Identifying the underlying genetic cause has a significant impact on patient care, modification of treatment, long-term prognostication and genetic counseling. This paper provides an update on the genetics of PxMDs, description of PxMDs classified according to causative gene rather than clinical phenotype, highlighting key clinical features and providing an algorithm for genetic testing of PxMDs.
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Affiliation(s)
- Susan Harvey
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland
| | - Mary D King
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Kathleen M Gorman
- Department of Paediatric Neurology and Clinical Neurophysiology, Children's Health Ireland at Temple Street, Dublin, Ireland.,School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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29
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Phenotypic analysis of catastrophic childhood epilepsy genes. Commun Biol 2021; 4:680. [PMID: 34083748 PMCID: PMC8175701 DOI: 10.1038/s42003-021-02221-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/17/2021] [Indexed: 01/06/2023] Open
Abstract
Genetic engineering techniques have contributed to the now widespread use of zebrafish to investigate gene function, but zebrafish-based human disease studies, and particularly for neurological disorders, are limited. Here we used CRISPR-Cas9 to generate 40 single-gene mutant zebrafish lines representing catastrophic childhood epilepsies. We evaluated larval phenotypes using electrophysiological, behavioral, neuro-anatomical, survival and pharmacological assays. Local field potential recordings (LFP) were used to screen ∼3300 larvae. Phenotypes with unprovoked electrographic seizure activity (i.e., epilepsy) were identified in zebrafish lines for 8 genes; ARX, EEF1A, GABRB3, GRIN1, PNPO, SCN1A, STRADA and STXBP1. We also created an open-source database containing sequencing information, survival curves, behavioral profiles and representative electrophysiology data. We offer all zebrafish lines as a resource to the neuroscience community and envision them as a starting point for further functional analysis and/or identification of new therapies. Griffin et al used CRISPR-Cas9 to generate 40 single-gene mutant zebrafish lines representing childhood epilepsies for which they evaluated larval phenotypes using electrophysiological, behavioral, neuro-anatomical, survival and pharmacological assays. Their study provides a useful resource for the future functional analysis and/or identification of potential anti-epileptic therapies.
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30
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Gillentine MA, Wang T, Hoekzema K, Rosenfeld J, Liu P, Guo H, Kim CN, De Vries BBA, Vissers LELM, Nordenskjold M, Kvarnung M, Lindstrand A, Nordgren A, Gecz J, Iascone M, Cereda A, Scatigno A, Maitz S, Zanni G, Bertini E, Zweier C, Schuhmann S, Wiesener A, Pepper M, Panjwani H, Torti E, Abid F, Anselm I, Srivastava S, Atwal P, Bacino CA, Bhat G, Cobian K, Bird LM, Friedman J, Wright MS, Callewaert B, Petit F, Mathieu S, Afenjar A, Christensen CK, White KM, Elpeleg O, Berger I, Espineli EJ, Fagerberg C, Brasch-Andersen C, Hansen LK, Feyma T, Hughes S, Thiffault I, Sullivan B, Yan S, Keller K, Keren B, Mignot C, Kooy F, Meuwissen M, Basinger A, Kukolich M, Philips M, Ortega L, Drummond-Borg M, Lauridsen M, Sorensen K, Lehman A, Lopez-Rangel E, Levy P, Lessel D, Lotze T, Madan-Khetarpal S, Sebastian J, Vento J, Vats D, Benman LM, Mckee S, Mirzaa GM, Muss C, Pappas J, Peeters H, Romano C, Elia M, Galesi O, Simon MEH, van Gassen KLI, Simpson K, Stratton R, Syed S, Thevenon J, Palafoll IV, Vitobello A, Bournez M, Faivre L, Xia K, Earl RK, Nowakowski T, Bernier RA, Eichler EE. Rare deleterious mutations of HNRNP genes result in shared neurodevelopmental disorders. Genome Med 2021; 13:63. [PMID: 33874999 PMCID: PMC8056596 DOI: 10.1186/s13073-021-00870-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/16/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND With the increasing number of genomic sequencing studies, hundreds of genes have been implicated in neurodevelopmental disorders (NDDs). The rate of gene discovery far outpaces our understanding of genotype-phenotype correlations, with clinical characterization remaining a bottleneck for understanding NDDs. Most disease-associated Mendelian genes are members of gene families, and we hypothesize that those with related molecular function share clinical presentations. METHODS We tested our hypothesis by considering gene families that have multiple members with an enrichment of de novo variants among NDDs, as determined by previous meta-analyses. One of these gene families is the heterogeneous nuclear ribonucleoproteins (hnRNPs), which has 33 members, five of which have been recently identified as NDD genes (HNRNPK, HNRNPU, HNRNPH1, HNRNPH2, and HNRNPR) and two of which have significant enrichment in our previous meta-analysis of probands with NDDs (HNRNPU and SYNCRIP). Utilizing protein homology, mutation analyses, gene expression analyses, and phenotypic characterization, we provide evidence for variation in 12 HNRNP genes as candidates for NDDs. Seven are potentially novel while the remaining genes in the family likely do not significantly contribute to NDD risk. RESULTS We report 119 new NDD cases (64 de novo variants) through sequencing and international collaborations and combined with published clinical case reports. We consider 235 cases with gene-disruptive single-nucleotide variants or indels and 15 cases with small copy number variants. Three hnRNP-encoding genes reach nominal or exome-wide significance for de novo variant enrichment, while nine are candidates for pathogenic mutations. Comparison of HNRNP gene expression shows a pattern consistent with a role in cerebral cortical development with enriched expression among radial glial progenitors. Clinical assessment of probands (n = 188-221) expands the phenotypes associated with HNRNP rare variants, and phenotypes associated with variation in the HNRNP genes distinguishes them as a subgroup of NDDs. CONCLUSIONS Overall, our novel approach of exploiting gene families in NDDs identifies new HNRNP-related disorders, expands the phenotypes of known HNRNP-related disorders, strongly implicates disruption of the hnRNPs as a whole in NDDs, and supports that NDD subtypes likely have shared molecular pathogenesis. To date, this is the first study to identify novel genetic disorders based on the presence of disorders in related genes. We also perform the first phenotypic analyses focusing on related genes. Finally, we show that radial glial expression of these genes is likely critical during neurodevelopment. This is important for diagnostics, as well as developing strategies to best study these genes for the development of therapeutics.
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Affiliation(s)
- Madelyn A Gillentine
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA
| | - Jill Rosenfeld
- Baylor Genetics Laboratories, Houston, TX, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Hui Guo
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Bert B A De Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magnus Nordenskjold
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jozef Gecz
- School of Medicine and the Robinson Research Institute, the University of Adelaide at the Women's and Children's Hospital, Adelaide, South Australia, Australia.,Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia.,South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Maria Iascone
- Laboratorio di Genetica Medica - ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Agnese Scatigno
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Genetic Unit, Department of Pediatrics, Fondazione MBBM S. Gerardo Hospital, Monza, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department Neurosciences, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sarah Schuhmann
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Antje Wiesener
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Micah Pepper
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | - Heena Panjwani
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA
| | | | - Farida Abid
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Siddharth Srivastava
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paldeep Atwal
- The Atwal Clinic: Genomic & Personalized Medicine, Jacksonville, FL, USA
| | - Carlos A Bacino
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gifty Bhat
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Katherine Cobian
- Department of Pediatrics, Section of Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.,Department of Neurosciences, University of California San Diego, San Diego, CA, USA
| | - Meredith S Wright
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bert Callewaert
- Department of Biomolecular Medicine, Ghent University Hospital, Ghent, Belgium
| | - Florence Petit
- Clinique de Génétique, Hôpital Jeanne de Flandre, Bâtiment Modulaire, CHU, 59037, Lille Cedex, France
| | - Sophie Mathieu
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexandra Afenjar
- Sorbonne Universités, Centre de Référence déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, AP-HP, Paris, France
| | - Celenie K Christensen
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kerry M White
- Department of Medical and Molecular Genetics, IU Health, Indianapolis, IN, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Itai Berger
- Pediatric Neurology, Assuta-Ashdod University Hospital, Ashdod, Israel.,Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Edward J Espineli
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Susan Hughes
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA.,The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- The University of Missouri-Kansas City, School of Medicine, Kansas City, MO, USA.,Children's Mercy Kansas City, Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Bonnie Sullivan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Shuang Yan
- Division of Clinical Genetics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Kory Keller
- Oregon Health & Science University, Corvallis, OR, USA
| | - Boris Keren
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Cyril Mignot
- Department of Genetics, Hópital Pitié-Salpêtrière, Paris, France
| | - Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Marije Meuwissen
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Alice Basinger
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Mary Kukolich
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Meredith Philips
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | - Lucia Ortega
- Genetics Department, Cook Children's Hospital, Fort Worth, TX, USA
| | | | - Mathilde Lauridsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kristina Sorensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,BC Children's Hospital and BC Women's Hospital, Vancouver, BC, Canada
| | | | - Elena Lopez-Rangel
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Division of Developmental Pediatrics, Department of Pediatrics, BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada.,Sunny Hill Health Centre for Children, Vancouver, BC, Canada
| | - Paul Levy
- Department of Pediatrics, The Children's Hospital at Montefiore, Bronx, NY, USA
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Lotze
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Suneeta Madan-Khetarpal
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA.,UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jodie Vento
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Divya Vats
- Kaiser Permanente Southern California, Los Angeles, CA, USA
| | | | - Shane Mckee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Candace Muss
- Al Dupont Hospital for Children, Wilmington, DE, USA
| | - John Pappas
- NYU Grossman School of Medicine, Department of Pediatrics, Clinical Genetic Services, New York, NY, USA
| | - Hilde Peeters
- Center for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | | | | | | | - Marleen E H Simon
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Kara Simpson
- Rare Disease Institute, Children's National Health System, Washington, DC, USA
| | - Robert Stratton
- Department of Genetics, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Sabeen Syed
- Department of Pediatric Gastroenterology, Driscoll Children's Hospital, Corpus Christi, TX, USA
| | - Julien Thevenon
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebrón, Barcelona, Spain
| | | | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne and INSERM UMR1231 GAD, Université de Bourgogne Franche-Comté, F-21000, Dijon, France.,INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France
| | - Marie Bournez
- Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes malformatifs » Université Bourgogne Franche-Comté, Dijon, France
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Rachel K Earl
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Tomasz Nowakowski
- Department of Anatomy, University of California, San Francisco, CA, USA.,Department of Psychiatry, University of California, San Francisco, CA, USA.,Weill Institute for Neurosciences, University of California at San Francisco, San Francisco, CA, USA.,The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Raphael A Bernier
- Center on Human Development and Disability, University of Washington, Seattle, WA, USA.,Seattle Children's Autism Center, Seattle, WA, USA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Ave NE S413A, Box 355065, Seattle, WA, 981095-5065, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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31
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Gannamani R, van der Veen S, van Egmond M, de Koning TJ, Tijssen MAJ. Challenges in Clinicogenetic Correlations: One Phenotype - Many Genes. Mov Disord Clin Pract 2021; 8:311-321. [PMID: 33816658 PMCID: PMC8015914 DOI: 10.1002/mdc3.13163] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 12/11/2022] Open
Abstract
Background In the field of movement disorders, what you see (phenotype) is seldom what you get (genotype). Whereas 1 phenotype was previously associated to 1 gene, the advent of next‐generation sequencing (NGS) has facilitated an exponential increase in disease‐causing genes and genotype–phenotype correlations, and the “one‐phenotype‐many‐genes” paradigm has become prominent. Objectives To highlight the “one‐phenotype‐many‐genes” paradigm by discussing the main challenges, perspectives on how to address them, and future directions. Methods We performed a scoping review of the various aspects involved in identifying the underlying molecular cause of a movement disorder phenotype. Results The notable challenges are (1) the lack of gold standards, overlap in clinical spectrum of different movement disorders, and variability in the interpretation of classification systems; (2) selecting which patients benefit from genetic tests and the choice of genetic testing; (3) problems in the variant interpretation guidelines; (4) the filtering of variants associated with disease; and (5) the lack of standardized, complete, and up‐to‐date gene lists. Perspectives to address these include (1) deep phenotyping and genotype–phenotype integration, (2) adherence to phenotype‐specific diagnostic algorithms, (3) implementation of current and complementary bioinformatic tools, (4) a clinical‐molecular diagnosis through close collaboration between clinicians and genetic laboratories, and (5) ongoing curation of gene lists and periodic reanalysis of genetic sequencing data. Conclusions Despite the rapidly emerging possibilities of NGS, there are still many steps to take to improve the genetic diagnostic yield. Future directions, including post‐NGS phenotyping and cohort analyses enriched by genotype–phenotype integration and gene networks, ought to be pursued to accelerate identification of disease‐causing genes and further improve our understanding of disease biology.
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Affiliation(s)
- Rahul Gannamani
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Department of Genetics University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Sterre van der Veen
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Martje van Egmond
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
| | - Tom J de Koning
- Department of Genetics University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands.,Pediatrics, Department of Clinical Sciences Lund University Lund Sweden
| | - Marina A J Tijssen
- Department of Neurology University of Groningen, University Medical Centre Groningen Groningen The Netherlands.,Expertise Centre Movement Disorders Groningen University Medical Centre Groningen Groningen The Netherlands
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32
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Palmer EE, Sachdev R, Macintosh R, Melo US, Mundlos S, Righetti S, Kandula T, Minoche AE, Puttick C, Gayevskiy V, Hesson L, Idrisoglu S, Shoubridge C, Thai MHN, Davis RL, Drew AP, Sampaio H, Andrews PI, Lawson J, Cardamone M, Mowat D, Colley A, Kummerfeld S, Dinger ME, Cowley MJ, Roscioli T, Bye A, Kirk E. Diagnostic Yield of Whole Genome Sequencing After Nondiagnostic Exome Sequencing or Gene Panel in Developmental and Epileptic Encephalopathies. Neurology 2021; 96:e1770-e1782. [PMID: 33568551 DOI: 10.1212/wnl.0000000000011655] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE). METHODS We performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray and either research ES (n = 15) or diagnostic MGP (n = 15). RESULTS Eight diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants, which now had additional evidence for pathogenicity. Eleven diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n = 10) involved genes not included in the panel, particularly in individuals with postneonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features, or multiorgan involvement. A total of 42% of diagnoses were autosomal recessive or X-chromosome linked. CONCLUSION WGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n = 3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel noncoding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.
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Affiliation(s)
- Elizabeth Emma Palmer
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia.
| | - Rani Sachdev
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Rebecca Macintosh
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Uirá Souto Melo
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Stefan Mundlos
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Righetti
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tejaswi Kandula
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Andre E Minoche
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Clare Puttick
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Velimir Gayevskiy
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Luke Hesson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Senel Idrisoglu
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Cheryl Shoubridge
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Monica Hong Ngoc Thai
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ryan L Davis
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alexander P Drew
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Hugo Sampaio
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Peter Ian Andrews
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - John Lawson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Michael Cardamone
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - David Mowat
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alison Colley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Kummerfeld
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Marcel E Dinger
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Mark J Cowley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tony Roscioli
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ann Bye
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Edwin Kirk
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
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Jiang YL, Song C, Wang Y, Zhao J, Yang F, Gao Q, Leng X, Man Y, Jiang W. Clinical Utility of Exome Sequencing and Reinterpreting Genetic Test Results in Children and Adults With Epilepsy. Front Genet 2020; 11:591434. [PMID: 33391346 PMCID: PMC7775549 DOI: 10.3389/fgene.2020.591434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
The clinical utility of genetic testing for epilepsy has been enhanced with the advancement of next-generation sequencing (NGS) technology along with the rapid updating of publicly available databases. The aim of this study was to evaluate the diagnostic yield of NGS and assess the value of reinterpreting genetic test results in children and adults with epilepsy. We performed genetic testing on 200 patients, including 82 children and 118 adults. The results were classified into three categories: positive, inconclusive, or negative. The reinterpretation of inconclusive results was conducted in April 2020. Overall, we identified disease-causing variants in 12% of the patients in the original analysis, and 14.5% at reinterpretation. The diagnostic yield for adults with epilepsy was similar to that for children (11 vs. 19.5%, p = 0.145). After reinterpretation, 9 of the 86 patients who initially had inconclusive results obtained a clinically significant change in diagnosis. Among these nine revised cases, five obtained positive diagnoses, representing a diagnosis rate of 5.8% (5/86). Manual searches for additional evidence of pathogenicity for candidate variants and updated patient clinical information were the main reasons for diagnostic reclassification. This study emphasizes the diagnostic potential of combining NGS and reinterpretation of inconclusive genetic test reports in children and adults with epilepsy.
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Affiliation(s)
- Yong-Li Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Changgeng Song
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yuanyuan Wang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Jingjing Zhao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Fang Yang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Qiong Gao
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiuxiu Leng
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yulin Man
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Wen Jiang
- Department of Neurology, Comprehensive Epilepsy Center, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Stefanski A, Calle-López Y, Leu C, Pérez-Palma E, Pestana-Knight E, Lal D. Clinical sequencing yield in epilepsy, autism spectrum disorder, and intellectual disability: A systematic review and meta-analysis. Epilepsia 2020; 62:143-151. [PMID: 33200402 PMCID: PMC7839709 DOI: 10.1111/epi.16755] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022]
Abstract
Objective Clinical genetic sequencing is frequently utilized to diagnose individuals with neurodevelopmental disorders (NDDs). Here we perform a meta‐analysis and systematic review of the success rate (diagnostic yield) of clinical sequencing through next‐generation sequencing (NGS) across NDDs. We compare the genetic testing yield across NDD subtypes and sequencing technology. Methods We performed a systematic review of the PubMed literature until May 2020. We included clinical sequencing studies that utilized NGS in individuals with epilepsy, autism spectrum disorder (ASD), or intellectual disability (ID). Data were extracted, reviewed, and categorized according to the Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) guidelines. Two investigators performed clinical evaluation and grouping following the International League Against Epilepsy (ILAE) guidelines. Pooled rates of the diagnostic yield and 95% confidence intervals were estimated with a random‐effects model. Results We identified 103 studies (epilepsy, N = 72; ASD, N = 14; ID, N = 21) across 32,331 individuals. Targeted gene panel sequencing was used in 73, and exome sequencing in 36 cohorts. Given highly selected patient cohorts, the diagnostic yield was 17.1% for ASD, 24% for epilepsy, and 28.2% for ID (23.7% overall). The highest diagnostic yield for epilepsy subtypes was observed in individuals with ID (27.9%) and early onset seizures (36.8%). The diagnostic yield for exome sequencing was higher than for panel sequencing, even though not statistically significant (27.2% vs 22.6%, P = .071). We observed that clinical sequencing studies are performed predominantly in countries with a high Inequality‐adjusted Human Development Index (IHDI) (countries with sequencing studies: IHDI median = 0.84, interquartile range [IQR] = 0.09 vs countries without sequencing studies: IHDI median = 0.56, IQR = 0.3). No studies from Africa, India, or Latin America were identified, indicating potential barriers to genetic testing. Significance This meta‐analysis and systematic review provides a comprehensive overview of clinical sequencing studies of NDDs and will help guide policymaking and steer decision‐making in patient management.
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Yamile Calle-López
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Program, Neuroclinica, University of Antioquia, Medellín, CO, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA.,Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK
| | - Eduardo Pérez-Palma
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Elia Pestana-Knight
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
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35
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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36
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Aoi H, Lei M, Mizuguchi T, Nishioka N, Goto T, Miyama S, Suzuki T, Iwama K, Uchiyama Y, Mitsuhashi S, Itakura A, Takeda S, Matsumoto N. Nonsense variants of STAG2 result in distinct congenital anomalies. Hum Genome Var 2020; 7:26. [PMID: 33014403 PMCID: PMC7501222 DOI: 10.1038/s41439-020-00114-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022] Open
Abstract
Herein, we report two female cases with novel nonsense mutations of STAG2 at Xq25, encoding stromal antigen 2, a component of the cohesion complex. Exome analysis identified c.3097 C>T, p.(Arg1033*) in Case 1 (a fetus with multiple congenital anomalies) and c.2229 G>A, p.(Trp743*) in Case 2 (a 7-year-old girl with white matter hypoplasia and cleft palate). X inactivation was highly skewed in both cases.
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Affiliation(s)
- Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuko Nishioka
- Department of Obstetrics and Gynecology, Koshigaya Municipal Hospital, Saitama, Japan
| | - Tomohide Goto
- Department of Neurology, Kanagawa Children’s Medical Center, Kanagawa, Japan
| | - Sahoko Miyama
- Department of Neurology, Tokyo Metropolitan Children’s Medical Center, Fuchu, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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37
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A three-year follow-up study evaluating clinical utility of exome sequencing and diagnostic potential of reanalysis. NPJ Genom Med 2020; 5:37. [PMID: 32963807 PMCID: PMC7484757 DOI: 10.1038/s41525-020-00144-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/14/2020] [Indexed: 01/05/2023] Open
Abstract
Exome sequencing (ES) has become one of the important diagnostic tools in clinical genetics with a reported diagnostic rate of 25–58%. Many studies have illustrated the diagnostic and immediate clinical impact of ES. However, up to 75% of individuals remain undiagnosed and there is scarce evidence supporting clinical utility beyond a follow-up period of >1 year. This is a 3-year follow-up analysis to our previous publication by Mak et al. (NPJ Genom. Med. 3:19, 2018), to evaluate the long-term clinical utility of ES and the diagnostic potential of exome reanalysis. The diagnostic yield of the initial study was 41% (43/104). Exome reanalysis in 46 undiagnosed individuals has achieved 12 new diagnoses. The additional yield compared with the initial analysis was at least 12% (increased from 41% to at least 53%). After a median follow-up period of 3.4 years, change in clinical management was observed in 72.2% of the individuals (26/36), leading to positive change in clinical outcome in four individuals (11%). There was a minimum healthcare cost saving of HKD$152,078 (USD$19,497; €17,282) annually for these four individuals. There were a total of six pregnancies from five families within the period. Prenatal diagnosis was performed in four pregnancies; one fetus was affected and resulted in termination. None of the parents underwent preimplantation genetic diagnosis. This 3-year follow-up study demonstrated the long-term clinical utility of ES at individual, familial and health system level, and the promising diagnostic potential of subsequent reanalysis. This highlights the benefits of implementing ES and regular reanalysis in the clinical setting.
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38
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Trivisano M, Ferretti A, Bebin E, Huh L, Lesca G, Siekierska A, Takeguchi R, Carneiro M, De Palma L, Guella I, Haginoya K, Shi RM, Kikuchi A, Kobayashi T, Jung J, Lagae L, Milh M, Mathieu ML, Minassian BA, Novelli A, Pietrafusa N, Takeshita E, Tartaglia M, Terracciano A, Thompson ML, Cooper GM, Vigevano F, Villard L, Villeneuve N, Buyse GM, Demos M, Scheffer IE, Specchio N. Defining the phenotype of FHF1 developmental and epileptic encephalopathy. Epilepsia 2020; 61:e71-e78. [PMID: 32645220 DOI: 10.1111/epi.16582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/18/2020] [Accepted: 05/26/2020] [Indexed: 01/25/2023]
Abstract
Fibroblast growth-factor homologous factor (FHF1) gene variants have recently been associated with developmental and epileptic encephalopathy (DEE). FHF1 encodes a cytosolic protein that modulates neuronal sodium channel gating. We aim to refine the electroclinical phenotypic spectrum of patients with pathogenic FHF1 variants. We retrospectively collected clinical, genetic, neurophysiologic, and neuroimaging data of 17 patients with FHF1-DEE. Sixteen patients had recurrent heterozygous FHF1 missense variants: 14 had the recurrent p.Arg114His variant and two had a novel likely pathogenic variant p.Gly112Ser. The p.Arg114His variant is associated with an earlier onset and more severe phenotype. One patient carried a chromosomal microduplication involving FHF1. Twelve patients carried a de novo variant, five (29.5%) inherited from parents with gonadic or somatic mosaicism. Seizure onset was between 1 day and 41 months; in 76.5% it was within 30 days. Tonic seizures were the most frequent seizure type. Twelve patients (70.6%) had drug-resistant epilepsy, 14 (82.3%) intellectual disability, and 11 (64.7%) behavioral disturbances. Brain magnetic resonance imaging (MRI) showed mild cerebral and/or cerebellar atrophy in nine patients (52.9%). Overall, our findings expand and refine the clinical, EEG, and imaging phenotype of patients with FHF1-DEE, which is characterized by early onset epilepsy with tonic seizures, associated with moderate to severe ID and psychiatric features.
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Affiliation(s)
- Marina Trivisano
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
| | - Alessandro Ferretti
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
| | - Elizabeth Bebin
- Department of Pediatric Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Linda Huh
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS, UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | | | - Ryo Takeguchi
- Department of Pediatrics, Asahikawa Medical University, Asahikawa, Japan
| | - Maryline Carneiro
- Department of Pediatric Neurology, Femme Mère Enfant Hospital, Hospices Civils de Lyon, Lyon, France
| | - Luca De Palma
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
| | - Ilaria Guella
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Ruo Ming Shi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Pediatrics, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Hospital, Sendai, Japan
| | - Tomoko Kobayashi
- Division of Child Development, Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Julien Jung
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Institut Neuromyogène, Equipe Métabolisme énergétique et développement neuronal, CNRS, UMR 5310, INSERM U1217, Université Lyon 1, Lyon, France
| | - Lieven Lagae
- Department of Development and Regeneration, University Hospitals KU Leuven, Leuven, Belgium
| | - Mathieu Milh
- Department of Pediatric Neurology, Femme Mère Enfant Hospital, Hospices Civils de Lyon, Lyon, France
| | - Marie L Mathieu
- Department of Pediatric Neurology, Femme Mère Enfant Hospital, Hospices Civils de Lyon, Lyon, France
| | - Berge A Minassian
- Department of Pediatrics, University of Texas Southwestern, Dallas, TX, USA
| | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Nicola Pietrafusa
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Alessandra Terracciano
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | | | - Federico Vigevano
- Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
| | | | - Nathalie Villeneuve
- Department of Pediatric Neurology, APHM, Hopital de la Timone, Marseille, France
| | - Gunnar M Buyse
- Pediatric Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Ingrid E Scheffer
- Austin Health, and Royal Children's Hospital, Florey and Murdoch Institutes, University of Melbourne, Melbourne, Australia
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital IRCCS, Member of European Reference Network EpiCARE, Rome, Italy
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Rockowitz S, LeCompte N, Carmack M, Quitadamo A, Wang L, Park M, Knight D, Sexton E, Smith L, Sheidley B, Field M, Holm IA, Brownstein CA, Agrawal PB, Kornetsky S, Poduri A, Snapper SB, Beggs AH, Yu TW, Williams DA, Sliz P. Children's rare disease cohorts: an integrative research and clinical genomics initiative. NPJ Genom Med 2020; 5:29. [PMID: 32655885 PMCID: PMC7338382 DOI: 10.1038/s41525-020-0137-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
While genomic data is frequently collected under distinct research protocols and disparate clinical and research regimes, there is a benefit in streamlining sequencing strategies to create harmonized databases, particularly in the area of pediatric rare disease. Research hospitals seeking to implement unified genomics workflows for research and clinical practice face numerous challenges, as they need to address the unique requirements and goals of the distinct environments and many stakeholders, including clinicians, researchers and sequencing providers. Here, we present outcomes of the first phase of the Children’s Rare Disease Cohorts initiative (CRDC) that was completed at Boston Children’s Hospital (BCH). We have developed a broadly sharable database of 2441 exomes from 15 pediatric rare disease cohorts, with major contributions from early onset epilepsy and early onset inflammatory bowel disease. All sequencing data is integrated and combined with phenotypic and research data in a genomics learning system (GLS). Phenotypes were both manually annotated and pulled automatically from patient medical records. Deployment of a genomically-ordered relational database allowed us to provide a modular and robust platform for centralized storage and analysis of research and clinical data, currently totaling 8516 exomes and 112 genomes. The GLS integrates analytical systems, including machine learning algorithms for automated variant classification and prioritization, as well as phenotype extraction via natural language processing (NLP) of clinical notes. This GLS is extensible to additional analytic systems and growing research and clinical collections of genomic and other types of data.
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Affiliation(s)
- Shira Rockowitz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Nicholas LeCompte
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Mary Carmack
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Andrew Quitadamo
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Lily Wang
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
| | - Meredith Park
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Devon Knight
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Emma Sexton
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Lacey Smith
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Beth Sheidley
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Ingrid A Holm
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Catherine A Brownstein
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Pankaj B Agrawal
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115 USA
| | - Susan Kornetsky
- Research Administration, Boston Children's Hospital, Boston, MA 02115 USA
| | - Annapurna Poduri
- Harvard Medical School, Boston, MA 02115 USA.,Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115 USA.,Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, MA 02115 USA
| | - Scott B Snapper
- Harvard Medical School, Boston, MA 02115 USA.,Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA 02115 USA
| | - Alan H Beggs
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - Timothy W Yu
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115 USA
| | - David A Williams
- Harvard Medical School, Boston, MA 02115 USA.,Division of Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115 USA
| | - Piotr Sliz
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115 USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115 USA.,Harvard Medical School, Boston, MA 02115 USA
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Yang S, Shen X, Kang Q, Kuang X, Ning Z, Liu S, Liao H, Cao Z, Yang L. Clinical and Genetic Study on a Chinese Patient with Infantile Onset Epileptic Encephalopathy carrying a PPP3CA Null Variant: a case report. BMC Pediatr 2020; 20:315. [PMID: 32593294 PMCID: PMC7320544 DOI: 10.1186/s12887-020-02213-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 06/17/2020] [Indexed: 02/06/2023] Open
Abstract
Background PPP3CA gene encodes the catalytic subunit A of a calcium-dependent protein phosphatase called calcineurin. However, two distinct mechanisms in PPP3CA deficiency would cause two clinically different diseases. Gain-of-function mutations in the autoinhibitory domain at the C-terminus would cause ACCIID that stands for arthrogryposis, cleft palate, craniosynostosis and impaired intellectual development. While loss-of-function mutations in PPP3CA would cause infantile or early childhood onset epileptic encephalopathy1, named as IECEE1. IECEE1 is a severe epileptic neurodevelopmental disorder and mainly characterized by psychomotor delay. Here, we report a Chinese patient who was clinically and genetically diagnosed as IECEE1. We also extensively analyzed electroencephalogram (EEG) features of the patient in this study. Case presentation A 2-year-old Chinese patient who had recurrent polymorphic seizures was clinically and genetically diagnosed as IECEE1. A frameshift variant c.1283insC (p.T429NfsX22) was identified in this case. Multiple types of abnormal features were observed in the EEG, comparing with the previous reports. Conclusions These findings could expand the spectrum of PPP3CA mutations and might also support the diagnosis and further study of IECEE1.
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Affiliation(s)
- Sai Yang
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Xiang Shen
- Running Gene Inc., Haohai Mansion, No.7 Shangdi 5th Street, Haidian District, Beijing, China
| | - Qingyun Kang
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Xiaojun Kuang
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Zeshu Ning
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Shulei Liu
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Hongmei Liao
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Zhenhua Cao
- Running Gene Inc., Haohai Mansion, No.7 Shangdi 5th Street, Haidian District, Beijing, China
| | - Liming Yang
- Department of Pediatrics, Hunan Children's Hospital, No.86 Ziyuan Road, Changsha, 410007, Hunan, China.
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Krenn M, Wagner M, Hotzy C, Graf E, Weber S, Brunet T, Lorenz-Depiereux B, Kasprian G, Aull-Watschinger S, Pataraia E, Stogmann E, Zimprich A, Strom TM, Meitinger T, Zimprich F. Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes. J Med Genet 2020; 57:624-633. [PMID: 32086284 DOI: 10.1136/jmedgenet-2019-106658] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND The genetic architecture of non-acquired focal epilepsies (NAFEs) becomes increasingly unravelled using genome-wide sequencing datasets. However, it remains to be determined how this emerging knowledge can be translated into a diagnostic setting. To bridge this gap, we assessed the diagnostic outcomes of exome sequencing (ES) in NAFE. METHODS 112 deeply phenotyped patients with NAFE were included in the study. Diagnostic ES was performed, followed by a screen to detect variants of uncertain significance (VUSs) in 15 well-established focal epilepsy genes. Explorative gene prioritisation was used to identify possible novel candidate aetiologies with so far limited evidence for NAFE. RESULTS ES identified pathogenic or likely pathogenic (ie, diagnostic) variants in 13/112 patients (12%) in the genes DEPDC5, NPRL3, GABRG2, SCN1A, PCDH19 and STX1B. Two pathogenic variants were microdeletions involving NPRL3 and PCDH19. Nine of the 13 diagnostic variants (69%) were found in genes of the GATOR1 complex, a potentially druggable target involved in the mammalian target of rapamycin (mTOR) signalling pathway. In addition, 17 VUSs in focal epilepsy genes and 6 rare variants in candidate genes (MTOR, KCNA2, RBFOX1 and SCN3A) were detected. Five patients with reported variants had double hits in different genes, suggesting a possible (oligogenic) role of multiple rare variants. CONCLUSION This study underscores the molecular heterogeneity of NAFE with GATOR1 complex genes representing the by far most relevant genetic aetiology known to date. Although the diagnostic yield is lower compared with severe early-onset epilepsies, the high rate of VUSs and candidate variants suggests a further increase in future years.
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Affiliation(s)
- Martin Krenn
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Bayern, Germany.,Institute of Neurogenomics, Helmholtz Center Munich, Neuherberg, Bayern, Germany
| | - Christoph Hotzy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Bayern, Germany
| | - Sandrina Weber
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Bayern, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Bayern, Germany
| | | | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | - Tim M Strom
- Institute of Human Genetics, Technical University Munich, Munich, Bayern, Germany.,Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Bayern, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Bayern, Germany.,Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Bayern, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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Rochtus A, Olson HE, Smith L, Keith LG, El Achkar C, Taylor A, Mahida S, Park M, Kelly M, Shain C, Rockowitz S, Sheidley BR, Poduri A. Genetic diagnoses in epilepsy: The impact of dynamic exome analysis in a pediatric cohort. Epilepsia 2020; 61:249-258. [PMID: 31957018 PMCID: PMC7404709 DOI: 10.1111/epi.16427] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 12/18/2019] [Accepted: 12/20/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE We evaluated the yield of systematic analysis and/or reanalysis of whole exome sequencing (WES) data from a cohort of well-phenotyped pediatric patients with epilepsy and suspected but previously undetermined genetic etiology. METHODS We identified and phenotyped 125 participants with pediatric epilepsy. Etiology was unexplained at the time of enrollment despite clinical testing, which included chromosomal microarray (57 patients), epilepsy gene panel (n = 48), both (n = 28), or WES (n = 8). Clinical epilepsy diagnoses included developmental and epileptic encephalopathy (DEE), febrile infection-related epilepsy syndrome, Rasmussen encephalitis, and other focal and generalized epilepsies. We analyzed WES data and compared the yield in participants with and without prior clinical genetic testing. RESULTS Overall, we identified pathogenic or likely pathogenic variants in 40% (50/125) of our study participants. Nine patients with DEE had genetic variants in recently published genes that had not been recognized as epilepsy-related at the time of clinical testing (FGF12, GABBR1, GABBR2, ITPA, KAT6A, PTPN23, RHOBTB2, SATB2), and eight patients had genetic variants in candidate epilepsy genes (CAMTA1, FAT3, GABRA6, HUWE1, PTCHD1). Ninety participants had concomitant or subsequent clinical genetic testing, which was ultimately explanatory for 26% (23/90). Of the 67 participants whose molecular diagnoses were "unsolved" through clinical genetic testing, we identified pathogenic or likely pathogenic variants in 17 (25%). SIGNIFICANCE Our data argue for early consideration of WES with iterative reanalysis for patients with epilepsy, particularly those with DEE or epilepsy with intellectual disability. Rigorous analysis of WES data of well-phenotyped patients with epilepsy leads to a broader understanding of gene-specific phenotypic spectra as well as candidate disease gene identification. We illustrate the dynamic nature of genetic diagnosis over time, with analysis and in some cases reanalysis of exome data leading to the identification of disease-associated variants among participants with previously nondiagnostic results from a variety of clinical testing strategies.
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Affiliation(s)
- Anne Rochtus
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, University of Leuven, Leuven, Belgium
| | - Heather E. Olson
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Lacey Smith
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Louisa G. Keith
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Christelle El Achkar
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Alan Taylor
- Department of Genomics, Al Jalila Children’s Specialty Hospital, Dubai, UAE
| | - Sonal Mahida
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Meredith Park
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - McKenna Kelly
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Catherine Shain
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Shira Rockowitz
- Information Services Department, Boston Children’s Hospital, Boston, MA, USA
| | - Beth Rosen Sheidley
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
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Ware TL, Huskins SR, Grinton BE, Liu Y, Bennett MF, Harvey M, McMahon J, Andreopoulos‐Malikotsinas D, Bahlo M, Howell KB, Hildebrand MS, Damiano JA, Rosenfeld A, Mackay MT, Mandelstam S, Leventer RJ, Harvey AS, Freeman JL, Scheffer IE, Jones DL, Berkovic SF. Epidemiology and etiology of infantile developmental and epileptic encephalopathies in Tasmania. Epilepsia Open 2019; 4:504-510. [PMID: 31440733 PMCID: PMC6698683 DOI: 10.1002/epi4.12350] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 06/19/2019] [Accepted: 06/27/2019] [Indexed: 12/22/2022] Open
Abstract
We sought to determine incidence, etiologies, and yield of genetic testing in infantile onset developmental and epileptic encephalopathies (DEEs) in a population isolate, with an intensive multistage approach. Infants born in Tasmania between 2011 and 2016, with seizure onset <2 years of age, epileptiform EEG, frequent seizures, and developmental impairment, were included. Following review of EEG databases, medical records, brain MRIs, and other investigations, clinical genetic testing was undertaken with subsequent research interrogation of whole exome sequencing (WES) in unsolved cases. The incidence of infantile DEEs was 0.44/1000 per year (95% confidence interval 0.25 to 0.71), with 16 cases ascertained. The etiology was structural in 5/16 cases. A genetic basis was identified in 6 of the remaining 11 cases (3 gene panel, 3 WES). In two further cases, WES identified novel variants with strong in silico data; however, paternal DNA was not available to support pathogenicity. The etiology was not determined in 3/16 (19%) cases, with a candidate gene identified in one of these. Pursuing clinical imaging and genetic testing followed by WES at an intensive research level can give a high diagnostic yield in the infantile DEEs, providing a solid base for prognostic and genetic counseling.
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Affiliation(s)
- Tyson L. Ware
- Department of PaediatricsRoyal Hobart HospitalHobartTasmaniaAustralia
| | | | - Bronwyn E. Grinton
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | - Yu‐Chi Liu
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Mark F. Bennett
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michael Harvey
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | - Jacinta McMahon
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | | | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical ResearchMelbourneVictoriaAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVictoriaAustralia
| | - Katherine B. Howell
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
- Department of PediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - Michael S. Hildebrand
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | - John A. Damiano
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | - Alexander Rosenfeld
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
| | - Mark T. Mackay
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
| | - Simone Mandelstam
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
- Department of PediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Department of RadiologyUniversity of MelbourneMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthParkvilleVictoriaAustralia
| | - Richard J. Leventer
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
- Department of PediatricsUniversity of MelbourneMelbourneVictoriaAustralia
| | - A. Simon Harvey
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
| | - Jeremy L. Freeman
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
| | - Ingrid E. Scheffer
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
- Royal Children’s HospitalMelbourneVictoriaAustralia
- Murdoch Children’s Research InstituteParkvilleVictoriaAustralia
- Department of PediatricsUniversity of MelbourneMelbourneVictoriaAustralia
- Florey Institute of Neuroscience and Mental HealthParkvilleVictoriaAustralia
| | - Dean L. Jones
- School of MedicineUniversity of TasmaniaHobartTasmaniaAustralia
- Department of NeurologyRoyal Hobart HospitalHobartTasmaniaAustralia
| | - Samuel F. Berkovic
- Department of MedicineAustin Health, University of MelbourneHeidelbergVictoriaAustralia
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The Epilepsy Genetics Initiative: Systematic reanalysis of diagnostic exomes increases yield. Epilepsia 2019; 60:797-806. [PMID: 30951195 PMCID: PMC6519344 DOI: 10.1111/epi.14698] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The Epilepsy Genetics Initiative (EGI) was formed in 2014 to create a centrally managed database of clinically generated exome sequence data. EGI performs systematic research-based reanalysis to identify new molecular diagnoses that were not possible at the time of initial sequencing and to aid in novel gene discovery. Herein we report on the efficacy of this approach 3 years after inception. METHODS One hundred sixty-six individuals with epilepsy who underwent diagnostic whole exome sequencing (WES) were enrolled, including 139 who had not received a genetic diagnosis. Sequence data were transferred to the EGI and periodically reevaluated on a research basis. RESULTS Eight new diagnoses were made as a result of updated annotations or the discovery of novel epilepsy genes after the initial diagnostic analysis was performed. In five additional cases, we provided new evidence to support or contradict the likelihood of variant pathogenicity reported by the laboratory. One novel epilepsy gene was discovered through dual interrogation of research and clinically generated WES. SIGNIFICANCE EGI's diagnosis rate of 5.8% represents a considerable increase in diagnostic yield and demonstrates the value of periodic reinterrogation of whole exome data. The initiative's contributions to gene discovery underscore the importance of data sharing and the value of collaborative enterprises.
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