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Kim SY, Woo H, Lim BC, Kim KJ, Chae JH. Exploring the Clinical Utility of Targeted MECP2 Testing in Real-World Practice. Pediatr Neurol 2024; 161:28-33. [PMID: 39255539 DOI: 10.1016/j.pediatrneurol.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/06/2024] [Accepted: 08/03/2024] [Indexed: 09/12/2024]
Abstract
BACKGROUND This study aimed to explore the clinical utility of targeted MECP2 testing in a large cohort of females with neurodevelopmental delays. Our aim was to identify suitable candidates for testing based on prevailing diagnostic criteria. METHODS Eligible participants with global developmental delay/arrest or regression before age 36 months underwent MECP2 testing. MECP2-positive patients were further categorized based on Rett syndrome (RTT) diagnostic criteria, including typical, atypical, possible, and unclassified, to assess disease typicality and progression with respect to age. RESULTS Of the 683 patients, 162 (23.7%) were diagnosed with MECP2-related RTT. Global developmental delay was the predominant initial symptom in approximately 75% of the cohort with developmental arrest/regression at testing. Symptoms emerged before age six months in 14 patients (8.6%). The average age at the time of MECP2 testing was 3.7 years, with 31.5% of the patients tested under two years. Of those under two years, 15 were initially categorized into the unclassified group; however, 12 were later reclassified into the typical/atypical RTT groups based on follow-up evaluation. Among the 119 patients monitored beyond age five years, 80% displayed typical RTT symptoms, 10 remained unclassified, and 9.8% had exonic deletions, posing challenges for detection using next-generation sequencing. CONCLUSIONS Targeted MECP2 testing has emerged as a clinically valuable tool with a high diagnostic yield, including the identification of small deletions. Given that younger patients may not always meet the classic RTT criteria, this study recommends targeted MECP2 testing in younger patients without typical RTT features.
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Affiliation(s)
- Soo Yeon Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hyewon Woo
- Department of Pediatrics, Chungbuk National University Hospital, Cheongju, Republic of Korea; Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea; Department of Pediatrics, Pediatric Clinical Neuroscience Center, Seoul National University Children's Hospital, Seoul, Republic of Korea; Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea.
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2
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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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Hung KL. Genetic Diagnosis in Children with Developmental Delay. CHILDREN (BASEL, SWITZERLAND) 2024; 11:669. [PMID: 38929248 PMCID: PMC11201514 DOI: 10.3390/children11060669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 06/28/2024]
Abstract
Developmental delay (DD) has a great impact on children at the developmental stage, and is often manifested by varying degrees of motor delays, intellectual disabilities, and other defects [...].
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Affiliation(s)
- Kun-Long Hung
- Department of Pediatrics, Fu-Jen Catholic University Hospital, New Taipei City 243, Taiwan; or ; Tel.: +886-2-8512-8704; Fax: +886-2-2904-6422
- School of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan
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4
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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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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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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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7
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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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8
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Riquin K, Isidor B, Mercier S, Nizon M, Colin E, Bonneau D, Pasquier L, Odent S, Le Guillou Horn XM, Le Guyader G, Toutain A, Meyer V, Deleuze JF, Pichon O, Doco-Fenzy M, Bézieau S, Cogné B. Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders. J Med Genet 2023; 61:47-56. [PMID: 37495270 DOI: 10.1136/jmg-2023-109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/09/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression. METHODS We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance. RESULTS We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs. CONCLUSION Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.
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Affiliation(s)
- Kevin Riquin
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
| | - Bertrand Isidor
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Sandra Mercier
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Mathilde Nizon
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Estelle Colin
- CHU Angers, Service de Génétique médicale, Angers, France
- UMR CNRS 6214-INSERM 1083, Université d'Angers, Angers, France
| | - Dominique Bonneau
- CHU Angers, Service de Génétique médicale, Angers, France
- UMR CNRS 6214-INSERM 1083, Université d'Angers, Angers, France
| | | | - Sylvie Odent
- Service de Génétique Clinique, ERN ITHACA, Rennes, France
- Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Xavier Maximin Le Guillou Horn
- Service de génétique médicale, CHU de Poitiers, Poitiers, France
- LabCom I3M-Dactim mis/LMA CNRS 7348, Université de Poitiers, Poitiers, France
| | | | - Annick Toutain
- UF de Génétique Médicale, Centre Hospitalier Universitaire, Tours, France
- UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
| | - Olivier Pichon
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Martine Doco-Fenzy
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Stéphane Bézieau
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Benjamin Cogné
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
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9
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Liu N, Li J, Gao K, Perszyk RE, Zhang J, Wang J, Wu Y, Jenkins A, Yuan H, Traynelis SF, Jiang Y. De novo CLPTM1 variants with reduced GABA A R current response in patients with epilepsy. Epilepsia 2023; 64:2968-2981. [PMID: 37577761 PMCID: PMC10840799 DOI: 10.1111/epi.17746] [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: 02/08/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
OBJECTIVE To investigate the clinical features and potential pathogenesis mechanism of de novo CLPTM1 variants associated with epilepsy. METHODS Identify de novo genetic variants associated with epilepsy by reanalyzing trio-based whole-exome sequencing data. We analyzed the clinical characteristics of patients with these variants and performed functional in vitro studies in cells expressing mutant complementary DNA for these variants using whole-cell voltage-clamp current recordings and outside-out patch-clamp recordings from transiently transfected human embryonic kidney (HEK) cells. RESULTS Two de novo missense variants related to epilepsy were identified in the CLPTM1 gene. Functional studies indicated that CLPTM1-p.R454H and CLPTM1-p.R568Q variants reduced the γ-aminobutyric acid A receptor (GABAA R) current response amplitude recorded under voltage clamp compared to the wild-type receptors. These variants also reduced the charge transfer and altered the time course of desensitization and deactivation following rapid removal of GABA. The surface expression of the GABAA R γ2 subunit from the CLPTM1-p.R568Q group was significantly reduced compared to CLPTM1-WT. SIGNIFICANCE This is the first report of functionally relevant variants within the CLPTM1 gene. Patch-clamp recordings showed that these de novo CLPTM1 variants reduce GABAA R currents and charge transfer, which should promote excitation and hypersynchronous activity. This study may provide insights into the molecular mechanisms of the CLPTM1 variants underlying the patients' phenotypes, as well as for exploring potential therapeutic targets for epilepsy.
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Affiliation(s)
- Nana Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Jinliang Li
- Department of Pediatrics, Central People's Hospital of Zhanjiang, Guangdong, China
| | - Kai Gao
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
| | - Riley E Perszyk
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jing Zhang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jingmin Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
- Department of Neurology, Affiliated Children's Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Andrew Jenkins
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pharmaceutical Sciences, University of Saint Joseph, West Hartford, Connecticut, USA
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis and Study on Pediatric Genetic Diseases, Beijing, China
- Children Epilepsy Center, Peking University First Hospital, Beijing, China
- Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
- Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
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10
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Bartolomaeus T, Hentschel J, Jamra RA, Popp B. Re-evaluation and re-analysis of 152 research exomes five years after the initial report reveals clinically relevant changes in 18. Eur J Hum Genet 2023; 31:1154-1164. [PMID: 37460657 PMCID: PMC10545662 DOI: 10.1038/s41431-023-01425-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/16/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023] Open
Abstract
Iterative re-analysis of NGS results is not well investigated for published research cohorts of rare diseases. We revisited a cohort of 152 consanguineous families with developmental disorders (NDD) reported five years ago. We re-evaluated all reported variants according to diagnostic classification guidelines or our candidate gene scoring system (AutoCaSc) and systematically scored the validity of gene-disease associations (GDA). Sequencing data was re-processed using an up-to-date pipeline for case-level re-analysis. In 28/152 (18%) families, we identified a clinically relevant change. Ten previously reported (likely) pathogenic variants were re-classified as VUS/benign. In one case, the GDA (TSEN15) validity was judged as limited, and in five cases GDAs are meanwhile established. We identified 12 new disease causing variants. Two previously reported variants were missed by our updated pipeline due to alignment or reference issues. Our results support the need to re-evaluate screening studies, not only the negative cases but including supposedly solved ones. This also applies in a diagnostic setting. We highlight that the complexity of computational re-analysis for old data should be weighed against the decreasing re-testing costs. Since extensive re-analysis per case is beyond the resources of most institutions, we recommend a screening procedure that would quickly identify the majority (83%) of new variants.
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Affiliation(s)
- Tobias Bartolomaeus
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, 04103, Germany.
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Center of Functional Genomics, Hessische Straße 4A, 10115, Berlin, Germany.
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11
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Barili V, Ambrosini E, Uliana V, Bellini M, Vitetta G, Martorana D, Cannizzaro IR, Taiani A, De Sensi E, Caggiati P, Hilton S, Banka S, Percesepe A. Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond. Genes (Basel) 2023; 14:1241. [PMID: 37372421 DOI: 10.3390/genes14061241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.
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Affiliation(s)
- Valeria Barili
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Enrico Ambrosini
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Vera Uliana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Melissa Bellini
- Department of Pediatrics and Neonatology, Guglielmo da Saliceto Hospital, 29121 Piacenza, Italy
| | - Giulia Vitetta
- Medical Genetics, University of Bologna, 40138 Bologna, Italy
| | - Davide Martorana
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
| | - Ilenia Rita Cannizzaro
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Antonietta Taiani
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Erika De Sensi
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | | | - Sarah Hilton
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Manchester M13 9PL, UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Antonio Percesepe
- Medical Genetics, Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
- Medical Genetics, University Hospital of Parma, 43126 Parma, Italy
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12
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Grether A, Ivanovski I, Russo M, Begemann A, Steindl K, Abela L, Papik M, Zweier M, Oneda B, Joset P, Rauch A. The current benefit of genome sequencing compared to exome sequencing in patients with developmental or epileptic encephalopathies. Mol Genet Genomic Med 2023; 11:e2148. [PMID: 36785910 PMCID: PMC10178799 DOI: 10.1002/mgg3.2148] [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: 08/26/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND As the technology of next generation sequencing rapidly develops and costs are constantly reduced, the clinical availability of whole genome sequencing (WGS) increases. Thereby, it remains unclear what exact advantage WGS offers in comparison to whole exome sequencing (WES) for the diagnosis of genetic diseases using current technologies. METHODS Trio-WGS was conducted for 20 patients with developmental or epileptic encephalopathies who remained undiagnosed after WES and chromosomal microarray analysis. RESULTS A diagnosis was reached for four patients (20%). However, retrospectively all pathogenic variants could have been detected in a WES analysis conducted with today's methods and knowledge. CONCLUSION The additional diagnostic yield of WGS versus WES is currently largely explained by new scientific insights and the general technological progress. Nevertheless, it is noteworthy that whole genome sequencing has greater potential for the analysis of small copy number and copy number neutral variants not seen with WES as well as variants in noncoding regions, especially as potentially more knowledge of the function of noncoding regions arises. We, therefore, conclude that even though today the added value of WGS versus WES seems to be limited, it may increase substantially in the future.
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Affiliation(s)
- Anna Grether
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Ivan Ivanovski
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Martina Russo
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Anaïs Begemann
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | | | - Lucia Abela
- Division of Child NeurologyUniversity Children's Hospital ZurichZurichSwitzerland
| | - Michael Papik
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Markus Zweier
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Beatrice Oneda
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and PathologyUniversity Hospital BaselBaselSwitzerland
| | - Anita Rauch
- Institute of Medical GeneticsUniversity of ZurichZurichSwitzerland
- University Children's Hospital ZurichZurichSwitzerland
- University of Zurich Clinical Research Priority Program (CRPP) Praeclare – Personalized prenatal and reproductive medicineZurichSwitzerland
- University of Zurich Research Priority Program (URPP) AdaBD: Adaptive Brain Circuits in Development and LearningZurichSwitzerland
- University of Zurich Research Priority Program (URPP) ITINERARE: Innovative Therapies in Rare DiseasesZurichSwitzerland
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13
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [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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14
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Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities—A Narrative Review. CHILDREN 2023; 10:children10030501. [PMID: 36980059 PMCID: PMC10047410 DOI: 10.3390/children10030501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Unexplained global developmental delay (GDD) and intellectual disabilities (ID) together affect nearly 2% of the pediatric population. Establishing an etiologic diagnosis is crucial for disease management, prognostic evaluation, and provision of physical and psychological support for both the patient and the family. Advancements in genome sequencing have allowed rapid accumulation of gene–disorder associations and have accelerated the search for an etiologic diagnosis for unexplained GDD/ID. We reviewed recent studies that utilized genome-wide analysis technologies, and we discussed their diagnostic yield, strengths, and limitations. Overall, exome sequencing (ES) and genome sequencing (GS) outperformed chromosomal microarrays and targeted panel sequencing. GS provides coverage for both ES and chromosomal microarray regions, providing the maximal diagnostic potential, and the cost of ES and reanalysis of ES-negative results is currently still lower than that of GS alone. Therefore, singleton or trio ES is the more cost-effective option for the initial investigation of individuals with GDD/ID in clinical practice compared to a staged approach or GS alone. Based on these updated evidence, we proposed an evaluation algorithm with ES as the first-tier evaluation for unexplained GDD/ID.
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Boonsimma P, Ittiwut C, Kamolvisit W, Ittiwut R, Chetruengchai W, Phokaew C, Srichonthong C, Poonmaksatit S, Desudchit T, Suphapeetiporn K, Shotelersuk V. Exome sequencing as first-tier genetic testing in infantile-onset pharmacoresistant epilepsy: diagnostic yield and treatment impact. Eur J Hum Genet 2023; 31:179-187. [PMID: 36198807 PMCID: PMC9905506 DOI: 10.1038/s41431-022-01202-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Pharmacoresistant epilepsy presenting during infancy poses both diagnostic and therapeutic challenges. We aim to identify diagnostic yield and treatment implications of exome sequencing (ES) as first-tier genetic testing for infantile-onset pharmacoresistant epilepsy. From June 2016 to December 2020, we enrolled patients with infantile-onset (age ≤ 12 months) pharmacoresistant epilepsy. 103 unrelated patients underwent ES. Clinical characteristics and changes in management due to the molecular diagnosis were studied. 42% (43/103) had epilepsy onset within the first month of life. After ES as first-tier genetic testing, 62% (64/103) of the cases were solved. Two partially solved cases (2%; 2/103) with heterozygous variants identified in ALDH7A1 known to cause autosomal recessive pyridoxine dependent epilepsy underwent genome sequencing (GS). Two novel large deletions in ALDH7A1 were detected in both cases. ES identified 66 pathogenic and likely pathogenic single nucleotide variants (SNVs) in 27 genes. 19 variants have not been previously reported. GS identified two additional copy number variations (CNVs). The most common disease-causing genes are SCN1A (13%; 13/103) and KCNQ2 (8%; 8/103). Eight percent (8/103) of the patients had treatable disorders and specific treatments were provided resulting in seizure freedom. Pyridoxine dependent epilepsy was the most common treatable epilepsy (6%; 6/103). Furthermore, 35% (36/103) had genetic defects which guided gene-specific treatments. Altogether, the diagnostic yield is 64%. Molecular diagnoses change management in 43% of the cases. This study substantiates the use of next generation sequencing (NGS) as the first-tier genetic investigation in infantile-onset pharmacoresistant epilepsy.
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Affiliation(s)
- Ponghatai Boonsimma
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wuttichart Kamolvisit
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Rungnapa Ittiwut
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chalurmpon Srichonthong
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sathida Poonmaksatit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tayard Desudchit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
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Tran Mau-Them F, Overs A, Bruel AL, Duquet R, Thareau M, Denommé-Pichon AS, Vitobello A, Sorlin A, Safraou H, Nambot S, Delanne J, Moutton S, Racine C, Engel C, De Giraud d’Agay M, Lehalle D, Goldenberg A, Willems M, Coubes C, Genevieve D, Verloes A, Capri Y, Perrin L, Jacquemont ML, Lambert L, Lacaze E, Thevenon J, Hana N, Van-Gils J, Dubucs C, Bizaoui V, Gerard-Blanluet M, Lespinasse J, Mercier S, Guerrot AM, Maystadt I, Tisserant E, Faivre L, Philippe C, Duffourd Y, Thauvin-Robinet C. Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis. Front Genet 2023; 14:1122985. [PMID: 37152996 PMCID: PMC10157399 DOI: 10.3389/fgene.2023.1122985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction: Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. Patients and methods: We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. Results: After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.
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Affiliation(s)
- Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- *Correspondence: Frédéric Tran Mau-Them,
| | - Alexis Overs
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Romain Duquet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Mylene Thareau
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Arthur Sorlin
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Caroline Racine
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Camille Engel
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | | | - Daphne Lehalle
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Rouen, France
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Marjolaine Willems
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Christine Coubes
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - David Genevieve
- Département de Génétique Médicale Maladies Rares et Médecine Personnalisée, Centre de Référence Maladies Rares Anomalies du Développement, Hôpital Arnaud de Villeneuve, Université Montpellier, Montpellier, France
| | - Alain Verloes
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Department of Medical Genetics, AP-HPNord- Université de Paris, Hôpital Robert Debré, Paris, France
- INSERM UMR 1141, Paris, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Laurence Perrin
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pole Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | | | - Elodie Lacaze
- Unité de Génétique Médicale, Groupe Hospitalier du Havre, Le Havre, France
| | - Julien Thevenon
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Nadine Hana
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat, Paris, France
- INSERM U1148, Laboratory for Vascular Translational Science, Université Paris de Paris, Hôpital Bichat, Paris, France
| | - Julien Van-Gils
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Charlotte Dubucs
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Varoona Bizaoui
- Service de Génétique, Centre Hospitalier Universitaire Caen Normandie, Caen, France
| | | | | | - Sandra Mercier
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandie Univ, UNIROUEN, CHU Rouen, Rouen, France
- Inserm U1245, FHU G4 Génomique, Rouen, France
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Emilie Tisserant
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Yannis Duffourd
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon, Dijon, France
- INSERM UMR1231 GAD, Dijon, France
- Centre de Référence Maladies Rares “Anomalies du développement et syndromes malformatifs”, Centre de Génétique, FHUTRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
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Hagihara H, Shoji H, Kuroiwa M, Graef IA, Crabtree GR, Nishi A, Miyakawa T. Forebrain-specific conditional calcineurin deficiency induces dentate gyrus immaturity and hyper-dopaminergic signaling in mice. Mol Brain 2022; 15:94. [PMID: 36414974 PMCID: PMC9682671 DOI: 10.1186/s13041-022-00981-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022] Open
Abstract
Calcineurin (Cn), a phosphatase important for synaptic plasticity and neuronal development, has been implicated in the etiology and pathophysiology of neuropsychiatric disorders, including schizophrenia, intellectual disability, autism spectrum disorders, epilepsy, and Alzheimer's disease. Forebrain-specific conditional Cn knockout mice have been known to exhibit multiple behavioral phenotypes related to these disorders. In this study, we investigated whether Cn mutant mice show pseudo-immaturity of the dentate gyrus (iDG) in the hippocampus, which we have proposed as an endophenotype shared by these disorders. Expression of calbindin and GluA1, typical markers for mature DG granule cells (GCs), was decreased and that of doublecortin, calretinin, phospho-CREB, and dopamine D1 receptor (Drd1), markers for immature GC, was increased in Cn mutants. Phosphorylation of cAMP-dependent protein kinase (PKA) substrates (GluA1, ERK2, DARPP-32, PDE4) was increased and showed higher sensitivity to SKF81297, a Drd1-like agonist, in Cn mutants than in controls. While cAMP/PKA signaling is increased in the iDG of Cn mutants, chronic treatment with rolipram, a selective PDE4 inhibitor that increases intracellular cAMP, ameliorated the iDG phenotype significantly and nesting behavior deficits with nominal significance. Chronic rolipram administration also decreased the phosphorylation of CREB, but not the other four PKA substrates examined, in Cn mutants. These results suggest that Cn deficiency induces pseudo-immaturity of GCs and that cAMP signaling increases to compensate for this maturation abnormality. This study further supports the idea that iDG is an endophenotype shared by certain neuropsychiatric disorders.
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Affiliation(s)
- Hideo Hagihara
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192 Japan
| | - Hirotaka Shoji
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192 Japan
| | - Mahomi Kuroiwa
- Department of Pharmacology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011 Japan
| | - Isabella A. Graef
- Department of Pathology, Stanford University of Medicine, Stanford, CA 94305 USA
| | - Gerald R. Crabtree
- Department of Pathology, Stanford University of Medicine, Stanford, CA 94305 USA
| | - Akinori Nishi
- Department of Pharmacology, Kurume University School of Medicine, Kurume, Fukuoka 830-0011 Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi 470-1192 Japan
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18
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Li J, Cao J. Case report: A novel PPP3CA truncating mutation within the regulatory domain causes severe developmental and epileptic encephalopathy in a Chinese patient. Front Neurol 2022; 13:889167. [PMID: 36158964 PMCID: PMC9491239 DOI: 10.3389/fneur.2022.889167] [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: 03/03/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction Developmental and epileptic encephalopathy 91 (DEE91; OMIM#617711) is a severe neurodevelopmental disorder caused by heterozygous PPP3CA variants. To the best of our knowledge, only a few DEE91 cases have been reported. Results This study reports a boy who experienced recurrent afebrile convulsions and spasms at the age of 2 months. After being given multiple antiepileptic treatments with levetiracetam, adrenocorticotropic hormone (ACTH), prednisone, topiramate, and clonazepam, his seizures were not completely relieved. At the age of 4 months, the patient exhibited delayed neuromotor development and difficulty in feeding; at the age of 6 months, he was diagnosed with developmental regression with recurrent spasms and myoclonic seizures that could respond to vigabatrin. At the age of 1 year and 4 months, the patient showed profound global developmental delay (GDD) with intermittent absence seizures. Whole-exome sequencing (WES) identified a novel loss-of-function variant c.1258_1259insAGTG (p. Val420Glufs*32) in PPP3CA. Conclusion This finding expands the genetic spectrum of the PPP3CA gene and reinforces the theory that DEE91-associated truncating variants cluster within a 26-amino acid region in the regulatory domain (RD) of PPP3CA.
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Affiliation(s)
- Jieling Li
- Department of Medical General Ward, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Cao
- Department of Medical General Ward, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
- Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Jie Cao
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19
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Lesca G, Baumgartner T, Monin P, De Dominicis A, Kunz WS, Specchio N. Genetic causes of rare and common epilepsies: What should the epileptologist know? Eur J Med Genet 2022; 65:104570. [PMID: 35850153 DOI: 10.1016/j.ejmg.2022.104570] [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: 01/15/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
In past decades, the identification of genes involved in epileptic disorders has grown exponentially. The pace of gene identification in epileptic disorders began to accelerate in the late 2000s, driven by new technologies such as molecular cytogenetics and next-generation sequencing (NGS). These technologies have also been applied to genetic diagnostics, with different configurations, such as gene panels, whole-exome sequencing and whole-genome sequencing. The clinician must be aware that any technology has its limitations and complementary techniques must still be used to establish a diagnosis for specific diseases. In addition, increasing the amount of genetic information available in a larger patient sample also increases the need for rigorous interpretation steps, when taking into account the clinical, electroclinical, and when available, functional data. Local, multidisciplinary discussions have proven valuable in difficult diagnostic situations, especially in cases where precision medicine is being considered. They also serve to improve genetic counseling in complex situations. In this article, we will briefly review the genetic basis of rare and common epilepsies, the current strategies used for molecular diagnosis, including their limitations, and some pitfalls for data interpretation, in the context of etiological diagnosis and genetic counseling.
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Affiliation(s)
- Gaetan Lesca
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France.
| | - Tobias Baumgartner
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Pauline Monin
- Department of Medical Genetics and Department of Paedaitric Clinical Epileptology, Member of the ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France; University Claude Bernard Lyon 1, Lyon, France
| | - Angela De Dominicis
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Wolfram S Kunz
- Department of Epileptology, University Hospital Bonn, Member of the ERN EpiCARE, Bonn, Germany
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Full Member of European Reference Network EpiCARE, Rome, Italy
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20
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Sánchez-Luquez KY, Carpena MX, Karam SM, Tovo-Rodrigues L. The contribution of whole-exome sequencing to intellectual disability diagnosis and knowledge of underlying molecular mechanisms: A systematic review and meta-analysis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108428. [PMID: 35905832 DOI: 10.1016/j.mrrev.2022.108428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 01/01/2023]
Abstract
Whole-exome sequencing (WES) is useful for molecular diagnosis, family genetic counseling, and prognosis of intellectual disability (ID). However, ID molecular diagnosis ascertainment based on WES is highly dependent on de novo mutations (DNMs) and variants of uncertain significance (VUS). The quantification of DNM frequency in ID molecular diagnosis ascertainment and the biological mechanisms common to genes with VUS may provide objective information about WES use in ID diagnosis and etiology. We aimed to investigate and estimate the rate of ID molecular diagnostic assessment by WES, quantify the contribution of DNMs to this rate, and biologically and functionally characterize the genes whose mutations were identified through WES. A PubMed/Medline, Web of Science, Scopus, Science Direct, BIREME, and PsycINFO systematic review and meta-analysis was performed, including studies published between 2010 and 2022. Thirty-seven articles with data on ID molecular diagnostic yield using the WES approach were included in the review. WES testing accounted for an overall diagnostic rate of 42% (Confidence interval (CI): 35-50%), while the estimate restricted to DNMs was 11% (CI: 6-18%). Genetic information on mutations and genes was extracted and split into two groups: (1) genes whose mutation was used for positive molecular diagnosis, and (2) genes whose mutation led to uncertain molecular diagnosis. After functional enrichment analysis, in addition to their expected roles in neurodevelopment, genes from the first group were enriched in epigenetic regulatory mechanisms, immune system regulation, and circadian rhythm control. Genes from uncertain diagnosis cases were enriched in the renin angiotensin pathway. Taken together, our results support WES as an important approach to the molecular diagnosis of ID. The results also indicated relevant pathways that may underlie the pathogenesis of ID with the renin-angiotensin pathway being suggested to be a potential pathway underlying the pathogenesis of ID.
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Affiliation(s)
| | - Marina Xavier Carpena
- Postgraduate Program in Epidemiology, Universidade Federal de Pelotas, Pelotas, Brazil.
| | - Simone M Karam
- Postgraduate Program in Public Health, Universidade Federal do Rio Grande, Rio Grande, Brazil.
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21
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Schobers G, Schieving JH, Yntema HG, Pennings M, Pfundt R, Derks R, Hofste T, de Wijs I, Wieskamp N, van den Heuvel S, Galbany JC, Gilissen C, Nelen M, Brunner HG, Kleefstra T, Kamsteeg EJ, Willemsen MAAP, Vissers LELM. Reanalysis of exome negative patients with rare disease: a pragmatic workflow for diagnostic applications. Genome Med 2022; 14:66. [PMID: 35710456 PMCID: PMC9204949 DOI: 10.1186/s13073-022-01069-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Background Approximately two third of patients with a rare genetic disease remain undiagnosed after exome sequencing (ES). As part of our post-test counseling procedures, patients without a conclusive diagnosis are advised to recontact their referring clinician to discuss new diagnostic opportunities in due time. We performed a systematic study of genetically undiagnosed patients 5 years after their initial negative ES report to determine the efficiency of diverse reanalysis strategies. Methods We revisited a cohort of 150 pediatric neurology patients originally enrolled at Radboud University Medical Center, of whom 103 initially remained genetically undiagnosed. We monitored uptake of physician-initiated routine clinical and/or genetic re-evaluation (ad hoc re-evaluation) and performed systematic reanalysis, including ES-based resequencing, of all genetically undiagnosed patients (systematic re-evaluation). Results Ad hoc re-evaluation was initiated for 45 of 103 patients and yielded 18 diagnoses (including 1 non-genetic). Subsequent systematic re-evaluation identified another 14 diagnoses, increasing the diagnostic yield in our cohort from 31% (47/150) to 53% (79/150). New genetic diagnoses were established by reclassification of previously identified variants (10%, 3/31), reanalysis with enhanced bioinformatic pipelines (19%, 6/31), improved coverage after resequencing (29%, 9/31), and new disease-gene associations (42%, 13/31). Crucially, our systematic study also showed that 11 of the 14 further conclusive genetic diagnoses were made in patients without a genetic diagnosis that did not recontact their referring clinician. Conclusions We find that upon re-evaluation of undiagnosed patients, both reanalysis of existing ES data as well as resequencing strategies are needed to identify additional genetic diagnoses. Importantly, not all patients are routinely re-evaluated in clinical care, prolonging their diagnostic trajectory, unless systematic reanalysis is facilitated. We have translated our observations into considerations for systematic and ad hoc reanalysis in routine genetic care. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01069-z.
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Affiliation(s)
- Gaby Schobers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Jolanda H Schieving
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje Pennings
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilse de Wijs
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nienke Wieskamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michèl A A P Willemsen
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Pediatric Neurology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
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22
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Tian MQ, Chen XX, Li L, Lang CH, Li J, Chen J, Yu XH, Shu XM. [Progressive psychomotor regression for 2.5 years in a boy aged 5 years]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2022; 24:699-704. [PMID: 35762438 PMCID: PMC9250405 DOI: 10.7499/j.issn.1008-8830.2201048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
A boy, aged 5 years, attended the hospital due to progressive psychomotor regression for 2.5 years. Motor function regression was the main manifestation in the early stage, and brain MRI and whole-exome sequencing (WES) of the family showed no abnormalities. After the age of 4 years and 9 months, the boy developed cognitive function regression, and brain MRI showed cerebellar atrophy. The reanalysis of WES results revealed a compound heterozygous mutation, [NM_000520, c.784C>T(p.His262Tyr]), c.1412C>T(p.Pro471Leu)], in the HEXA gene. The enzyme activity detection showed a significant reduction in the level of β-hexosaminidase encoded by this gene. The boy was diagnosed with juvenile Tay-Sachs disease (TSD). TSD has strong clinical heterogeneity, and cerebellar atrophy may be an important clue for the diagnosis of juvenile TSD. The reanalysis of genetic data when appropriate based on disease evolution may improve the positive rate of WES.
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Affiliation(s)
| | - Xiao-Xi Chen
- Department of Pediatrics, Guizhou Children's Hospital/Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563003, China
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23
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Lavelle TA, Feng X, Keisler M, Cohen JT, Neumann PJ, Prichard D, Schroeder BE, Salyakina D, Espinal PS, Weidner SB, Maron JL. Cost-effectiveness of exome and genome sequencing for children with rare and undiagnosed conditions. Genet Med 2022; 24:1349-1361. [PMID: 35396982 DOI: 10.1016/j.gim.2022.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE This study aimed to estimate the cost-effectiveness of exome sequencing (ES) and genome sequencing (GS) for children. METHODS We modeled costs, diagnoses, and quality-adjusted life years (QALYs) for diagnostic strategies for critically ill infants (aged <1 year) and children (aged <18 years) with suspected genetic conditions: (1) standard of care (SOC) testing, (2) ES, (3) GS, (4) SOC followed by ES, (5) SOC followed by GS, (6) ES followed by GS, and (7) SOC followed by ES followed by GS. We calculated the 10-year incremental cost per additional diagnosis, and lifetime incremental cost per QALY gained, from a health care perspective. RESULTS First-line GS costs $15,048 per diagnosis vs SOC for infants and $27,349 per diagnosis for children. If GS is unavailable, ES represents the next most efficient option compared with SOC ($15,543 per diagnosis for infants and $28,822 per diagnosis for children). Other strategies provided the same or fewer diagnoses at a higher incremental cost per diagnosis. Lifetime results depend on the patient's assumed long-term prognosis after diagnosis. For infants, GS ranged from cost-saving (vs all alternatives) to $18,877 per QALY (vs SOC). For children, GS (vs SOC) ranged from $119,705 to $490,047 per QALY. CONCLUSION First-line GS may be the most cost-effective strategy for diagnosing infants with suspected genetic conditions. For all children, GS may be cost-effective under certain assumptions. ES is nearly as efficient as GS and hence is a viable option when GS is unavailable.
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Affiliation(s)
- Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA.
| | - Xue Feng
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Marlena Keisler
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Joshua T Cohen
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Peter J Neumann
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | | | | | - Daria Salyakina
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Paula S Espinal
- Personalized Medicine and Health Outcomes Research, Nicklaus Children's Hospital, Miami, FL
| | - Samuel B Weidner
- Center for the Evaluation of Value and Risk in Health (CEVR), Tufts Medical Center, Boston, MA
| | - Jill L Maron
- Women & Infants Hospital of Rhode Island, Care New England Health System, Providence, RI
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24
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The Emerging Roles of Long Non-Coding RNAs in Intellectual Disability and Related Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116118. [PMID: 35682796 PMCID: PMC9181295 DOI: 10.3390/ijms23116118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 02/05/2023] Open
Abstract
In the human brain, long non-coding RNAs (lncRNAs) are widely expressed in an exquisitely temporally and spatially regulated manner, thus suggesting their contribution to normal brain development and their probable involvement in the molecular pathology of neurodevelopmental disorders (NDD). Bypassing the classic protein-centric conception of disease mechanisms, some studies have been conducted to identify and characterize the putative roles of non-coding sequences in the genetic pathogenesis and diagnosis of complex diseases. However, their involvement in NDD, and more specifically in intellectual disability (ID), is still poorly documented and only a few genomic alterations affecting the lncRNAs function and/or expression have been causally linked to the disease endophenotype. Considering that a significant fraction of patients still lacks a genetic or molecular explanation, we expect that a deeper investigation of the non-coding genome will unravel novel pathogenic mechanisms, opening new translational opportunities. Here, we present evidence of the possible involvement of many lncRNAs in the etiology of different forms of ID and NDD, grouping the candidate disease-genes in the most frequently affected cellular processes in which ID-risk genes were previously collected. We also illustrate new approaches for the identification and prioritization of NDD-risk lncRNAs, together with the current strategies to exploit them in diagnosis.
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25
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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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26
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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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27
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The Genetic Diagnosis of Ultrarare DEEs: An Ongoing Challenge. Genes (Basel) 2022; 13:genes13030500. [PMID: 35328054 PMCID: PMC8953579 DOI: 10.3390/genes13030500] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Epileptic encephalopathies (EEs) and developmental and epileptic encephalopathies (DEEs) are a group of severe early-onset neurodevelopmental disorders (NDDs). In recent years, next-generation equencing (NGS) technologies enabled the discovery of numerous genes involved in these conditions. However, more than 50% of patients remained undiagnosed. A major obstacle lies in the high degree of genetic heterogeneity and the wide phenotypic variability that has characterized these disorders. Interpreting a large amount of NGS data is also a crucial challenge. This study describes a dynamic diagnostic procedure used to investigate 17 patients with DEE or EE with previous negative or inconclusive genetic testing by whole-exome sequencing (WES), leading to a definite diagnosis in about 59% of participants. Biallelic mutations caused most of the diagnosed cases (50%), and a pathogenic somatic mutation resulted in 10% of the subjects. The high diagnostic yield reached highlights the relevance of the scientific approach, the importance of the reverse phenotyping strategy, and the involvement of a dedicated multidisciplinary team. The study emphasizes the role of recessive and somatic variants, new genetic mechanisms, and the complexity of genotype–phenotype associations. In older patients, WES results could end invasive diagnostic procedures and allow a more accurate transition. Finally, an early pursued diagnosis is essential for comprehensive care of patients, precision approach, knowledge of prognosis, patient and family planning, and quality of life.
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28
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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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29
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Tran Mau-Them F, Duffourd Y, Vitobello A, Bruel AL, Denommé-Pichon AS, Nambot S, Delanne J, Moutton S, Sorlin A, Couturier V, Bourgeois V, Chevarin M, Poe C, Mosca-Boidron AL, Callier P, Safraou H, Faivre L, Philippe C, Thauvin-Robinet C. Interest of exome sequencing trio-like strategy based on pooled parental DNA for diagnosis and translational research in rare diseases. Mol Genet Genomic Med 2021; 9:e1836. [PMID: 34716697 PMCID: PMC8683640 DOI: 10.1002/mgg3.1836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/22/2021] [Accepted: 10/01/2021] [Indexed: 11/10/2022] Open
Abstract
Background Exome sequencing (ES) has become the most powerful and cost‐effective molecular tool for deciphering rare diseases with a diagnostic yield approaching 30%–40% in solo‐ES and 50% in trio‐ES. We applied an innovative parental DNA pooling method to reduce the parental sequencing cost while maintaining the diagnostic yield of trio‐ES. Methods We pooled six (Agilent‐CRE‐v2–100X) or five parental DNA (TWIST‐HCE–70X) aiming to detect allelic balance around 8–10% for heterozygous status. The strategies were applied as second‐tier (74 individuals after negative solo‐ES) and first‐tier approaches (324 individuals without previous ES). Results The allelic balance of parental‐pool variants was around 8.97%. Sanger sequencing uncovered false positives in 1.5% of sporadic variants. In the second‐tier approach, we evaluated than two thirds of the Sanger validations performed after solo‐ES (41/59–69%) would have been saved if the parental‐pool segregations had been available from the start. The parental‐pool strategy identified a causative diagnosis in 18/74 individuals (24%) in the second‐tier and in 116/324 individuals (36%) in the first‐tier approaches, including 19 genes newly associated with human disorders. Conclusions Parental‐pooling is an efficient alternative to trio‐ES. It provides rapid segregation and extension to translational research while reducing the cost of parental and Sanger sequencing.
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Affiliation(s)
- Frederic Tran Mau-Them
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Yannis Duffourd
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Sophie Nambot
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Julian Delanne
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Sebastien Moutton
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Arthur Sorlin
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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- FHU-TRANSLAD, Dijon, France
| | - Victor Couturier
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Valentin Bourgeois
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Martin Chevarin
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Charlotte Poe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | | | - Patrick Callier
- Laboratoire de Génétique Chromosomique et Moléculaire, CHU de Dijon, France
| | - Hana Safraou
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Laurence Faivre
- Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Unité Fonctionnelle 6254 d'Innovation en Diagnostique Génomique des Maladies Rares, Pôle de Biologie, CHU Dijon Bourgogne, Dijon, France.,Inserm - Université de Bourgogne UMR1231 GAD, FHU-TRANSLAD, Dijon, France.,FHU-TRANSLAD, Dijon, France.,Centre de Référence Maladies Rares «Déficiences Intellectuelles de Causes Rares», Hôpital d'Enfants, CHU Dijon Bourgogne, Dijon, France
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30
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Klau J, Abou Jamra R, Radtke M, Oppermann H, Lemke JR, Beblo S, Popp B. Exome first approach to reduce diagnostic costs and time - retrospective analysis of 111 individuals with rare neurodevelopmental disorders. Eur J Hum Genet 2021; 30:117-125. [PMID: 34690354 PMCID: PMC8738730 DOI: 10.1038/s41431-021-00981-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/09/2022] Open
Abstract
This single-center study aims to determine the time, diagnostic procedure, and cost saving potential of early exome sequencing in a cohort of 111 individuals with genetically confirmed neurodevelopmental disorders. We retrospectively collected data regarding diagnostic time points and procedures from the individuals' medical histories and developed criteria for classifying diagnostic procedures in terms of requirement, followed by a cost allocation. All genetic variants were re-evaluated according to ACMG recommendations and considering the individuals' phenotype. Individuals who developed first symptoms of their underlying genetic disorder when Next Generation Sequencing (NGS) diagnostics were already available received a diagnosis significantly faster than individuals with first symptoms before this cutoff. The largest amount of potentially dispensable diagnostics was found in genetic, metabolic, and cranial magnetic resonance imaging examinations. Out of 407 performed genetic examinations, 296 (72.7%) were classified as potentially dispensable. The same applied to 36 (27.9%) of 129 cranial magnetic resonance imaging and 111 (31.8%) of 349 metabolic examinations. Dispensable genetic examinations accounted 302,947.07€ (90.2%) of the total 335,837.49€ in potentially savable costs in this cohort. The remaining 32,890.42€ (9.8%) are related to non-required metabolic and cranial magnetic resonance imaging diagnostics. On average, the total potentially savable costs in our study amount to €3,025.56 per individual. Cost savings by first tier exome sequencing lie primarily in genetic, metabolic, and cMRI testing in this German cohort, underscoring the utility of performing exome sequencing at the beginning of the diagnostic pathway and the potential for saving diagnostic costs and time.
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Affiliation(s)
- Julia Klau
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Radtke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.,Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Skadi Beblo
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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31
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Salinas V, Martínez N, Maturo JP, Rodriguez-Quiroga SA, Zavala L, Medina N, Amartino H, Sfaello I, Agosta G, Serafín EM, Morón DG, Kauffman MA, Vega P. Clinical next generation sequencing in developmental and epileptic encephalopathies: Diagnostic relevance of data re-analysis and variants re-interpretation. Eur J Med Genet 2021; 64:104363. [PMID: 34673242 DOI: 10.1016/j.ejmg.2021.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 09/24/2021] [Accepted: 10/08/2021] [Indexed: 11/26/2022]
Abstract
Developmental and epileptic encephalopathies (DEE) are complex pediatric epilepsies, in which heterogeneous pathogenic factors play an important role. Next-generation-sequencing based tools have shown excellent effectiveness. The constant increase in the number of new genotype-phenotype associations suggests the periodic need for re-interpretation and re-analysis of genetic studies without positive results. In this study, we report the diagnostic utility of targeted gene panel sequencing and whole exome sequencing in 55 Argentine subjects with DEE, focusing on the utility of re-interpretation and re-analysis of undetermined and negative genetic diagnoses. The new information in biomedical literature and databases was used for the re-interpretation. For re-analysis, sequencing data processing was repeated using updated bioinformatics tools. Initially, pathogenic variants were detected in 21 subjects (38%). After an average time of 29 months, 25% of the subjects without a genetic diagnosis were re-categorized as diagnosed. Finally, the overall diagnostic yield increased to 53% (29 subjects). In consequence of the re-interpretation and re-analysis, we identified novel variants in the genes: CHD2, COL4A1, FOXG1, GABRA1, GRIN2B, HNRNPU, KCNQ2, MECP2, PCDH19, SCN1A, SCN2A, SCN8A, SLC6A1, STXBP1 and WWOX. Our results expand the diagnostic yield of this subgroup of infantile and childhood seizures and demonstrate the importance of re-evaluation of genetic tests in subjects without an identified causative etiology.
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Affiliation(s)
- Valeria Salinas
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Nerina Martínez
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Josefina Pérez Maturo
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | | | - Lucia Zavala
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Nancy Medina
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
| | - Hernán Amartino
- Paediatric Neurology Unit, Hospital Universitario Austral, Buenos Aires, Argentina.
| | - Ignacio Sfaello
- CETES, Instituto de Neurología Infanto-Juvenil, Córdoba, Argentina.
| | - Guillermo Agosta
- Paediatric Neurology Unit, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.
| | | | | | - Marcelo A Kauffman
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina; Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute-CONICET, Faculty of Biomedical Sciences, Universidad Austral, Buenos Aires, Argentina.
| | - Patricia Vega
- Neurogenetics Unit, Hospital JM Ramos Mejía, Buenos Aires, Argentina.
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32
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Teng H, Liang C, Liang D, Li Z, Wu L. Novel variants in OSGEP leading to Galloway-Mowat syndrome by altering its subcellular localization. Clin Chim Acta 2021; 523:297-303. [PMID: 34666032 DOI: 10.1016/j.cca.2021.10.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 10/20/2022]
Abstract
Galloway-Mowat syndrome (GAMOS) is an extremely rare clinically heterogeneous autosomal or X-linked inherited recessive disease characterized by early-onset steroid-resistant nephrotic syndrome (SRNS), microcephaly and neurological impairment. In this study, two siblings mainly presenting with decreased head circumference, hypotonia, gross motor delay, and dysmorphic features were initially detected without pathogenic variants by karyotyping, SNP-array and WES. After a 3 year's follow-up, the proband manifested additional proteinuria, hematuria and "deeper sulci" with a sign of brain atrophy. By reanalysis on the proband's previous WES data, two novel compound heterozygous variants of OSGEP (c.133dupA; c.608C > T) were identified. Furthermore, functional studies showed that the variants reduced the expression of OSGEP protein and activated the DNA damage response (DDR) signaling in the lymphoblastoid cell lines (LCLs) obtained from the patient. The analysis of protein localization with confocal microscopy revealed that the EGFP-tagged/HA-tagged mutant OSGEP proteins were abnormal aggregation or retained inside the cytosol, respectively. Our study not only expanded the pathogenic variant spectrum of OSGEP but also carried on regular follow-up for kidney involvement and established a strategy for evaluation on the function of mutant OSGFP by subcellular localization assay.
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Affiliation(s)
- Hua Teng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Chen Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.
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33
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Technological Improvements in the Genetic Diagnosis of Rett Syndrome Spectrum Disorders. Int J Mol Sci 2021; 22:ijms221910375. [PMID: 34638716 PMCID: PMC8508637 DOI: 10.3390/ijms221910375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 11/17/2022] Open
Abstract
Rett syndrome (RTT) is a severe neurodevelopmental disorder that constitutes the second most common cause of intellectual disability in females worldwide. In the past few years, the advancements in genetic diagnosis brought by next generation sequencing (NGS), have made it possible to identify more than 90 causative genes for RTT and significantly overlapping phenotypes (RTT spectrum disorders). Therefore, the clinical entity known as RTT is evolving towards a spectrum of overlapping phenotypes with great genetic heterogeneity. Hence, simultaneous multiple gene testing and thorough phenotypic characterization are mandatory to achieve a fast and accurate genetic diagnosis. In this review, we revise the evolution of the diagnostic process of RTT spectrum disorders in the past decades, and we discuss the effectiveness of state-of-the-art genetic testing options, such as clinical exome sequencing and whole exome sequencing. Moreover, we introduce recent technological advancements that will very soon contribute to the increase in diagnostic yield in patients with RTT spectrum disorders. Techniques such as whole genome sequencing, integration of data from several “omics”, and mosaicism assessment will provide the tools for the detection and interpretation of genomic variants that will not only increase the diagnostic yield but also widen knowledge about the pathophysiology of these disorders.
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A Novel De Novo TUBB3 Variant Causing Developmental Delay, Epilepsy and Mild Ophthalmological Symptoms in a Chinese Child. J Mol Neurosci 2021; 72:37-44. [PMID: 34562182 DOI: 10.1007/s12031-021-01909-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
Heterozygous missense mutations in TUBB3 have been implicated in various neurological disorders encompassing either isolated congenital fibrosis of the extraocular muscles type 3 (CFEOM3) or complex cortical dysplasia with other brain malformations 1 (CDCBM1). The description of seizures in patients with TUBB3 mutations is rare. Here, we reported a patient who had febrile seizures before and focal seizure this time, which was diagnosed as epilepsy in combination with an abnormal EEG. MRI showed hypoplastic corpus callosum. Mutation analysis showed a novel de novo heterozygous variant of the TUBB3 gene (NM_006086), c.763G > A (p.V255I). The patient had global developmental delay, photophobia and elliptic pupils, but lacking extraocular muscle involvement and malformations of cortical development, which might be a less severe phenotype of TUBB3 mutations. This is the first report of elliptic pupils in a patient with TUBB3 mutations and expands the spectrum of TUBB3 phenotypes. It indicates that the phenotypic range of TUBB3 mutations might exist on more of a continuum than as a discrete entity, with severity ranging from mild to severe. Further studies are needed to elucidate the complete spectrum of TUBB3-related phenotypes.
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35
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de Boer E, Ockeloen CW, Matalonga L, Horvath R, Rodenburg RJ, Coenen MJH, Janssen M, Henssen D, Gilissen C, Steyaert W, Paramonov I, Trimouille A, Kleefstra T, Verloes A, Vissers LELM. A MT-TL1 variant identified by whole exome sequencing in an individual with intellectual disability, epilepsy, and spastic tetraparesis. Eur J Hum Genet 2021; 29:1359-1368. [PMID: 34075211 PMCID: PMC8440635 DOI: 10.1038/s41431-021-00900-2] [Citation(s) in RCA: 3] [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: 10/13/2020] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022] Open
Abstract
The genetic etiology of intellectual disability remains elusive in almost half of all affected individuals. Within the Solve-RD consortium, systematic re-analysis of whole exome sequencing (WES) data from unresolved cases with (syndromic) intellectual disability (n = 1,472 probands) was performed. This re-analysis included variant calling of mitochondrial DNA (mtDNA) variants, although mtDNA is not specifically targeted in WES. We identified a functionally relevant mtDNA variant in MT-TL1 (NC_012920.1:m.3291T > C; NC_012920.1:n.62T > C), at a heteroplasmy level of 22% in whole blood, in a 23-year-old male with severe intellectual disability, epilepsy, episodic headaches with emesis, spastic tetraparesis, brain abnormalities, and feeding difficulties. Targeted validation in blood and urine supported pathogenicity, with heteroplasmy levels of 23% and 58% in index, and 4% and 17% in mother, respectively. Interestingly, not all phenotypic features observed in the index have been previously linked to this MT-TL1 variant, suggesting either broadening of the m.3291T > C-associated phenotype, or presence of a co-occurring disorder. Hence, our case highlights the importance of underappreciated mtDNA variants identifiable from WES data, especially for cases with atypical mitochondrial phenotypes and their relatives in the maternal line.
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Affiliation(s)
- Elke de Boer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Leslie Matalonga
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, John Van Geest Cambridge Centre for Brain Repair, Cambridge, UK
| | - Richard J Rodenburg
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marieke J H Coenen
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mirian Janssen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dylan Henssen
- Department of Medical Imaging, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wouter Steyaert
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aurélien Trimouille
- Service de Génétique Médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
- MRGM, Maladies Rares: Génétique et Métabolisme, lNSERM U1211, Université de Bordeaux, Bordeaux, France
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alain Verloes
- Département de Génétique, APHP Robert DEBRE University Hospital and INSERM U1141, Paris, France
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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36
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Perea-Romero I, Blanco-Kelly F, Sanchez-Navarro I, Lorda-Sanchez I, Tahsin-Swafiri S, Avila-Fernandez A, Martin-Merida I, Trujillo-Tiebas MJ, Lopez-Rodriguez R, Rodriguez de Alba M, Iancu IF, Romero R, Quinodoz M, Hakonarson H, Garcia-Sandova B, Minguez P, Corton M, Rivolta C, Ayuso C. NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases. Hum Genet 2021; 140:1665-1678. [PMID: 34448047 PMCID: PMC8553673 DOI: 10.1007/s00439-021-02343-7] [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: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.
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Affiliation(s)
- I Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - F Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Sanchez-Navarro
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - S Tahsin-Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - A Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M J Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Rodriguez de Alba
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I F Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca Garcia-Sandova
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - P Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - C Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - C Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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37
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Zaganas I, Vorgia P, Spilioti M, Mathioudakis L, Raissaki M, Ilia S, Giorgi M, Skoula I, Chinitrakis G, Michaelidou K, Paraskevoulakos E, Grafakou O, Kariniotaki C, Psyllou T, Zafeiris S, Tzardi M, Briassoulis G, Dinopoulos A, Mitsias P, Evangeliou A. Genetic cause of epilepsy in a Greek cohort of children and young adults with heterogeneous epilepsy syndromes. Epilepsy Behav Rep 2021; 16:100477. [PMID: 34568804 PMCID: PMC8449081 DOI: 10.1016/j.ebr.2021.100477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/01/2022] Open
Abstract
We describe a cohort of 10 unrelated Greek patients (4 females, 6 males; median age 6.5 years, range 2-18 years) with heterogeneous epilepsy syndromes with a genetic basis. In these patients, causative genetic variants, including two novel ones, were identified in 9 known epilepsy-related genes through whole exome sequencing. A patient with glycine encephalopathy was a compound heterozygote for the p.Arg222Cys and the p.Ser77Leu AMT variant. A patient affected with Lafora disease carried the homozygous p.Arg171His EPM2A variant. A de novo heterozygous variant in the GABRG2 gene (p.Pro282Thr) was found in one patient and a pathogenic variant in the GRIN2B gene (p.Gly820Val) in another patient. Infantile-onset lactic acidosis with seizures was associated with the p.Arg446Ter PDHX gene variant in one patient. In two additional epilepsy patients, the p.Ala1662Val and the novel non-sense p.Phe1330Ter SCN1A gene variants were found. Finally, in 3 patients we observed a novel heterozygous missense variant in SCN2A (p.Ala1874Thr), a heterozygous splice site variant in SLC2A1 (c.517-2A>G), as a cause of Glut1 deficiency syndrome, and a pathogenic variant in STXBP1 (p.Arg292Leu), respectively. In half of our cases (patients with variants in the GRIN2B, SCN1A, SCN2A and SLC2A1 genes), a genetic cause with potential management implications was identified.
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Affiliation(s)
- Ioannis Zaganas
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
- Neurology Department, University Hospital of Heraklion, Crete, Greece
| | - Pelagia Vorgia
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Martha Spilioti
- AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lambros Mathioudakis
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Maria Raissaki
- Department of Radiology, University Hospital of Heraklion, Crete, Greece
| | - Stavroula Ilia
- Pediatric Intensive Care Unit, University Hospital of Heraklion, Crete, Greece
| | | | - Irene Skoula
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | | | - Kleita Michaelidou
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | | | - Olga Grafakou
- Pediatric Department, Venizelion General Hospital, Heraklio, Crete, Greece
| | - Chariklia Kariniotaki
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Thekla Psyllou
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Spiros Zafeiris
- Neurology Department, University Hospital of Heraklion, Crete, Greece
| | - Maria Tzardi
- Pathology Department, Medical School, University of Crete, Greece
| | - George Briassoulis
- Pediatric Intensive Care Unit, University Hospital of Heraklion, Crete, Greece
| | | | - Panayiotis Mitsias
- Neurology Department, University Hospital of Heraklion, Crete, Greece
- Department of Neurology, Henry Ford Hospital/Wayne State University, Detroit, MI, USA
| | - Athanasios Evangeliou
- Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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38
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Panneerselvam S, Wang J, Zhu W, Dai H, Pappas JG, Rabin R, Low KJ, Rosenfeld JA, Emrick L, Xiao R, Xia F, Yang Y, Eng CM, Anderson A, Chau V, Soler-Alfonso C, Streff H, Lalani SR, Mercimek-Andrews S, Bi W. PPP3CA truncating variants clustered in the regulatory domain cause early-onset refractory epilepsy. Clin Genet 2021; 100:227-233. [PMID: 33963760 DOI: 10.1111/cge.13979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/27/2022]
Abstract
PPP3CA encodes the catalytic subunit of calcineurin, a calcium-calmodulin-regulated serine-threonine phosphatase. Loss-of-function (LoF) variants in the catalytic domain have been associated with epilepsy, while gain-of-function (GoF) variants in the auto-inhibitory domain cause multiple congenital abnormalities. We herein report five new patients with de novo PPP3CA variants. Interestingly, the two frameshift variants in this study and the six truncating variants reported previously are all located within a 26-amino acid region in the regulatory domain (RD). Patients with a truncating variant had more severe earlier onset seizures compared to patients with a LoF missense variant, while autism spectrum disorder was a more frequent feature in the latter. Expression studies of a truncating variant showed apparent RNA expression from the mutant allele, but no detectable mutant protein. Our data suggest that PPP3CA truncating variants clustered in the RD, causing more severe early-onset refractory epilepsy and representing a type of variants distinct from LoF or GoF missense variants.
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Affiliation(s)
- Sugi Panneerselvam
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Julia Wang
- Medical Scientist Training Program and Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Wenmiao Zhu
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - John G Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, New York, USA
| | - Rachel Rabin
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, New York, USA
| | - Karen J Low
- University Hospital Bristol NHS Foundation Trust, Bristol, UK
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lisa Emrick
- Texas Children's Hospital, Houston, Texas, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Anne Anderson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Vann Chau
- Division of Neurology, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudia Soler-Alfonso
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Genetics, University of Alberta, Stollery Children's Hospital, Edmonton, Alberta, Canada
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
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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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40
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Comparison of the diagnostic yield of aCGH and genome-wide sequencing across different neurodevelopmental disorders. NPJ Genom Med 2021; 6:25. [PMID: 33767182 PMCID: PMC7994713 DOI: 10.1038/s41525-021-00188-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Most consensus recommendations for the genetic diagnosis of neurodevelopmental disorders (NDDs) do not include the use of next generation sequencing (NGS) and are still based on chromosomal microarrays, such as comparative genomic hybridization array (aCGH). This study compares the diagnostic yield obtained by aCGH and clinical exome sequencing in NDD globally and its spectrum of disorders. To that end, 1412 patients clinically diagnosed with NDDs and studied with aCGH were classified into phenotype categories: global developmental delay/intellectual disability (GDD/ID); autism spectrum disorder (ASD); and other NDDs. These categories were further subclassified based on the most frequent accompanying signs and symptoms into isolated forms, forms with epilepsy; forms with micro/macrocephaly and syndromic forms. Two hundred and forty-five patients of the 1412 were subjected to clinical exome sequencing. Diagnostic yield of aCGH and clinical exome sequencing, expressed as the number of solved cases, was compared for each phenotype category and subcategory. Clinical exome sequencing was superior than aCGH for all cases except for isolated ASD, with no additional cases solved by NGS. Globally, clinical exome sequencing solved 20% of cases (versus 5.7% by aCGH) and the diagnostic yield was highest for all forms of GDD/ID and lowest for Other NDDs (7.1% versus 1.4% by aCGH) and ASD (6.1% versus 3% by aCGH). In the majority of cases, diagnostic yield was higher in the phenotype subcategories than in the mother category. These results suggest that NGS could be used as a first-tier test in the diagnostic algorithm of all NDDs followed by aCGH when necessary.
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41
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Klee EW, Cousin MA, Pinto E Vairo F, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN. Impact of integrated translational research on clinical exome sequencing. Genet Med 2021; 23:498-507. [PMID: 33144682 DOI: 10.1038/s41436-020-01005-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing. METHODS From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses. RESULTS The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient. CONCLUSION Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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Affiliation(s)
- Eric W Klee
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
| | - Margot A Cousin
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Joel A Morales-Rosado
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - W Garrett Jenkinson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ashley N Sigafoos
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Tanya L Schwab
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Raul A Urrutia
- Division of Research, Department of Surgery and the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Aditi Gupta
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Patrick R Blackburn
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Nicole J Boczek
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carri A Prochnow
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rebecca J Lowy
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tammy M McAllister
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Stacy L Aoudia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Teresa M Kruisselbrink
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Jennifer L Kemppainen
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Laura J Fisher
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Megan M Hager
- Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Nicole L Bertsch
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Katherine E Agre
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Laura M Rust
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Scott A Beck
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Marissa S Ellingson
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kristen J Rasmussen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Carrie A Lahner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Zhiyv Niu
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Matthew J Ferber
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Cherisse A Marcou
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Karl J Clark
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Pavel N Pichurin
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - David R Deyle
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eva Morava-Kozicz
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Ralitza H Gavrilova
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Radhika Dhamija
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Scottsdale, AZ, USA
| | - Klaas J Wierenga
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA.,Center for Individualized Medicine, Mayo Clinic, Jacksonville, FL, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Gianrico Farrugia
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lisa A Schimmenti
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Konstantinos N Lazaridis
- Center for Individualized Medicine, College of Medicine, Mayo Clinic, Rochester, MN, USA. .,Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN, USA.
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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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43
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Kim SY, Jang SS, Kim H, Hwang H, Choi JE, Chae JH, Kim KJ, Lim BC. Genetic diagnosis of infantile-onset epilepsy in the clinic: Application of whole-exome sequencing following epilepsy gene panel testing. Clin Genet 2021; 99:418-424. [PMID: 33349918 DOI: 10.1111/cge.13903] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022]
Abstract
This study aimed to evaluate the clinical utility of whole-exome sequencing in a group of infantile-onset epilepsy patients who tested negative for epilepsy using a gene panel test. Whole-exome sequencing was performed on 59 patients who tested negative on customized epilepsy gene panel testing. We identified eight pathogenic or likely pathogenic sequence variants in eight different genes (FARS2, YWHAG, KCNC1, DYRK1A, SMC1A, PIGA, OGT, and FGF12), one pathogenic structural variant (8.6 Mb-sized deletion on chromosome X [140 994 419-149 630 805]), and three putative low-frequency mosaic variants from three different genes (GABBR2, MTOR, and CUX1). Subsequent whole-exome sequencing revealed an additional 8% of diagnostic yield with genetic confirmation of epilepsy in 55.4% (62/112) of our cohort. Three genes (YWHAG, KCNC1, and FGF12) were identified as epilepsy-causing genes after the original gene panel was designed. The others were initially linked with mitochondrial encephalopathy or different neurodevelopmental disorders, although an epilepsy phenotype was listed as one of the clinical features. Application of whole-exome sequencing following epilepsy gene panel testing provided 8% of additional diagnostic yield in an infantile-onset epilepsy cohort. Whole-exome sequencing could provide an opportunity to reanalyze newly recognized epilepsy-linked genes without updating the gene panel design.
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Affiliation(s)
- Soo Yeon Kim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul National University Children's Hospital, Seoul, South Korea.,Rare Diseases Center, Seoul National University Hospital, Seoul, South Korea
| | - Se Song Jang
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul National University Children's Hospital, Seoul, South Korea
| | - Hunmin Kim
- Department of Pediatrics, Seoul National University Bundang Hospital, Gyeonggi-do, South Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University Bundang Hospital, Gyeonggi-do, South Korea
| | - Ji Eun Choi
- Department of Pediatrics, Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul National University Children's Hospital, Seoul, South Korea.,Rare Diseases Center, Seoul National University Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Ki Joong Kim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul National University Children's Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Byung Chan Lim
- Department of Pediatrics, Pediatric Neuroscience Center, Seoul National University Children's Hospital, Seoul National University Children's Hospital, Seoul, South Korea.,Rare Diseases Center, Seoul National University Hospital, Seoul, South Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
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44
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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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45
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Tan NB, Stapleton R, Stark Z, Delatycki MB, Yeung A, Hunter MF, Amor DJ, Brown NJ, Stutterd CA, McGillivray G, Yap P, Regan M, Chong B, Fanjul Fernandez M, Marum J, Phelan D, Pais LS, White SM, Lunke S, Tan TY. Evaluating systematic reanalysis of clinical genomic data in rare disease from single center experience and literature review. Mol Genet Genomic Med 2020; 8:e1508. [PMID: 32969205 PMCID: PMC7667328 DOI: 10.1002/mgg3.1508] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/15/2020] [Accepted: 08/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Our primary aim was to evaluate the systematic reanalysis of singleton exome sequencing (ES) data for unsolved cases referred for any indication. A secondary objective was to undertake a literature review of studies examining the reanalysis of genomic data from unsolved cases. Methods We examined data from 58 unsolved cases referred between June 2016 and March 2017. First reanalysis at 4–13 months after the initial report considered genes newly associated with disease since the original analysis; second reanalysis at 9–18 months considered all disease‐associated genes. At 25–34 months we reviewed all cases and the strategies which solved them. Results Reanalysis of existing ES data alone at two timepoints did not yield new diagnoses. Over the same timeframe, 10 new diagnoses were obtained (17%) from additional strategies, such as microarray detection of copy number variation, repeat sequencing to improve coverage, and trio sequencing. Twenty‐seven peer‐reviewed articles were identified on the literature review, with a median new diagnosis rate via reanalysis of 15% and median reanalysis timeframe of 22 months. Conclusion Our findings suggest that an interval of greater than 18 months from the original report may be optimal for reanalysis. We also recommend a multi‐faceted strategy for cases remaining unsolved after singleton ES.
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Affiliation(s)
- Natalie B Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Rachel Stapleton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - David J Amor
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.,Royal Children's Hospital, Parkville, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - Chloe A Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Austin Health Clinical Genetics Service, Heidelberg, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Patrick Yap
- Genetic Health Service NZ, Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew Regan
- Monash Genetics, Monash Health, Clayton, VIC, Australia.,Department of Paediatrics, Monash University, Clayton, VIC, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Miriam Fanjul Fernandez
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Justine Marum
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
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46
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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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47
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Won D, Kim SH, Kim B, Lee ST, Kang HC, Choi JR. Reanalysis of Genomic Sequencing Results in a Clinical Laboratory: Advantages and Limitations. Front Neurol 2020; 11:612. [PMID: 32695065 PMCID: PMC7338758 DOI: 10.3389/fneur.2020.00612] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 05/25/2020] [Indexed: 11/13/2022] Open
Abstract
Genetic diagnosis of patients with neurodevelopmental disorders is imperative and a standard clinical practice. Considering the continuous accumulation of data on disease-causing variants, reanalysis of previously established sequencing data is important. Periodic reanalysis of variants with uncertain significance has become mandatory in clinical laboratories. Therefore, to confirm the utility of the reanalysis of targeted gene panel data in clinical laboratories, we re-evaluated the data of two groups of patients who had undergone targeted gene panel testing for neurodevelopmental disorders (n = 116) and epileptic encephalopathy (n = 384). This reanalysis was based on a reannotation process reflecting updated databases. Six (5.2%) and seven (1.8%) new pathogenic or likely pathogenic variants were identified in these two groups, respectively, attributable to the updated guidelines and de novo reports from unrelated patients. Although relatively low, considerable increase in the diagnostic yield was confirmed. We suggest that reanalysis of genetic variants, mainly using changes in databases and updated interpretations, should be implemented as a routine practice in clinical laboratories.
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Affiliation(s)
- Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Se Hee Kim
- Division of Pediatric Neurology, Department of Pediatrics, Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Borahm Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Department of Pediatrics, Epilepsy Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
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48
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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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49
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Granadillo JL, P A Stegmann A, Guo H, Xia K, Angle B, Bontempo K, Ranells JD, Newkirk P, Costin C, Viront J, Stumpel CT, Sinnema M, Panis B, Pfundt R, Krapels IPC, Klaassens M, Nicolai J, Li J, Jiang Y, Marco E, Canton A, Latronico AC, Montenegro L, Leheup B, Bonnet C, M Amudhavalli S, Lawson CE, McWalter K, Telegrafi A, Pearson R, Kvarnung M, Wang X, Bi W, Rosenfeld JA, Shinawi M. Pathogenic variants in TNRC6B cause a genetic disorder characterised by developmental delay/intellectual disability and a spectrum of neurobehavioural phenotypes including autism and ADHD. J Med Genet 2020; 57:717-724. [PMID: 32152250 DOI: 10.1136/jmedgenet-2019-106470] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Rare variants in hundreds of genes have been implicated in developmental delay (DD), intellectual disability (ID) and neurobehavioural phenotypes. TNRC6B encodes a protein important for RNA silencing. Heterozygous truncating variants have been reported in three patients from large cohorts with autism, but no full phenotypic characterisation was described. METHODS Clinical and molecular characterisation was performed on 17 patients with TNRC6B variants. Clinical data were obtained by retrospective chart review, parent interviews, direct patient interaction with providers and formal neuropsychological evaluation. RESULTS Clinical findings included DD/ID (17/17) (speech delay in 94% (16/17), fine motor delay in 82% (14/17) and gross motor delay in 71% (12/17) of subjects), autism or autistic traits (13/17), attention deficit and hyperactivity disorder (ADHD) (11/17), other behavioural problems (7/17) and musculoskeletal findings (12/17). Other congenital malformations or clinical findings were occasionally documented. The majority of patients exhibited some dysmorphic features but no recognisable gestalt was identified. 17 heterozygous TNRC6B variants were identified in 12 male and five female unrelated subjects by exome sequencing (14), a targeted panel (2) and a chromosomal microarray (1). The variants were nonsense (7), frameshift (5), splice site (2), intragenic deletions (2) and missense (1). CONCLUSIONS Variants in TNRC6B cause a novel genetic disorder characterised by recurrent neurocognitive and behavioural phenotypes featuring DD/ID, autism, ADHD and other behavioural abnormalities. Our data highly suggest that haploinsufficiency is the most likely pathogenic mechanism. TNRC6B should be added to the growing list of genes of the RNA-induced silencing complex associated with ID/DD, autism and ADHD.
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Affiliation(s)
- Jorge Luis Granadillo
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine in Saint Louis, Saint Louis, Missouri, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Brad Angle
- Advocate Lutheran General Hospital, Park Ridge, Illinois, USA
| | - Kelly Bontempo
- Advocate Lutheran General Hospital, Park Ridge, Illinois, USA
| | - Judith D Ranells
- Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Patricia Newkirk
- Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | | | | | - Constanze T Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Bianca Panis
- Zuyderland Medical Centre Heerlen, Heerlen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre, Nijmgen, The Netherlands
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University, Maastricht, The Netherlands
| | - Merel Klaassens
- Department of Pediatrics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joost Nicolai
- Department of Neurology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jinliang Li
- Peking University First Hospital, Beijing, Beijing, China
| | - Yuwu Jiang
- Peking University First Hospital, Beijing, Beijing, China
| | - Elysa Marco
- UCSF Pediatric Brain Center, UCSF, San Francisco, California, USA
| | - Ana Canton
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ana Claudia Latronico
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Montenegro
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Bruno Leheup
- Service de Génétique clinique, Höpital Brabois, Centre Hospitalier Universitaire de Nancy, Nancy, Lorraine, France
| | - Celine Bonnet
- Centre Hospitalier Universitaire de Nancy, Nancy, Lorraine, France
| | | | | | | | | | | | - Malin Kvarnung
- Department of Clinical Genetics & Department of Molecular Medicine and Surgery, Karolinska University Hospital & Karolinska Institute, Stockholm, Sweden
| | - Xia Wang
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Weimin Bi
- Baylor College of Medicine Department of Molecular and Human Genetics, Houston, Texas, USA
| | - Jill Anne Rosenfeld
- Baylor Genetics Laboratories, Houston, Texas, USA.,Baylor College of Medicine Department of Molecular and Human Genetics, Houston, Texas, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine in Saint Louis, Saint Louis, Missouri, USA
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Matthews E, Balestrini S, Sisodiya SM, Hanna MG. Muscle and brain sodium channelopathies: genetic causes, clinical phenotypes, and management approaches. THE LANCET CHILD & ADOLESCENT HEALTH 2020; 4:536-547. [PMID: 32142633 DOI: 10.1016/s2352-4642(19)30425-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/29/2019] [Accepted: 12/12/2019] [Indexed: 01/26/2023]
Abstract
Voltage-gated sodium channels are essential for excitability of skeletal muscle fibres and neurons. An increasing number of disabling or fatal paediatric neurological disorders linked to mutations of voltage-gated sodium channel genes are recognised. Muscle phenotypes include episodic paralysis, myotonia, neonatal hypotonia, respiratory compromise, laryngospasm or stridor, congenital myasthenia, and myopathy. Evidence suggests a possible link between sodium channel dysfunction and sudden infant death. Increasingly recognised phenotypes of brain sodium channelopathies include several epilepsy disorders and complex encephalopathies. Together, these early-onset muscle and brain phenotypes have a substantial morbidity and a considerable mortality. Important advances in understanding the pathophysiological mechanisms underlying these channelopathies have helped to identify effective targeted therapies. The availability of effective treatments underlines the importance of increasing clinical awareness and the need to achieve a precise genetic diagnosis. In this Review, we describe the expanded range of phenotypes of muscle and brain sodium channelopathies and the underlying knowledge regarding mechanisms of sodium channel dysfunction. We also outline a diagnostic approach and review the available treatment options.
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Affiliation(s)
- Emma Matthews
- Department of Neuromuscular Diseases, Medical Research Council Centre for Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK.
| | - Simona Balestrini
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Buckinghamshire, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Buckinghamshire, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, Medical Research Council Centre for Neuromuscular Diseases, University College London Queen Square Institute of Neurology, London, UK; National Hospital for Neurology and Neurosurgery, University College London Hospitals National Health Service Foundation Trust, London, UK
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