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Coskun A, Ertaylan G, Pusparum M, Van Hoof R, Kaya ZZ, Khosravi A, Zarrabi A. Advancing personalized medicine: Integrating statistical algorithms with omics and nano-omics for enhanced diagnostic accuracy and treatment efficacy. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167339. [PMID: 38986819 DOI: 10.1016/j.bbadis.2024.167339] [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: 04/04/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Medical laboratory services enable precise measurement of thousands of biomolecules and have become an inseparable part of high-quality healthcare services, exerting a profound influence on global health outcomes. The integration of omics technologies into laboratory medicine has transformed healthcare, enabling personalized treatments and interventions based on individuals' distinct genetic and metabolic profiles. Interpreting laboratory data relies on reliable reference values. Presently, population-derived references are used for individuals, risking misinterpretation due to population heterogeneity, and leading to medical errors. Thus, personalized references are crucial for precise interpretation of individual laboratory results, and the interpretation of omics data should be based on individualized reference values. We reviewed recent advancements in personalized laboratory medicine, focusing on personalized omics, and discussed strategies for implementing personalized statistical approaches in omics technologies to improve global health and concluded that personalized statistical algorithms for interpretation of omics data have great potential to enhance global health. Finally, we demonstrated that the convergence of nanotechnology and omics sciences is transforming personalized laboratory medicine by providing unparalleled diagnostic precision and innovative therapeutic strategies.
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Affiliation(s)
- Abdurrahman Coskun
- Acibadem University, School of Medicine, Department of Medical Biochemistry, Istanbul, Turkey.
| | - Gökhan Ertaylan
- Unit Health, Environmental Intelligence, Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
| | - Murih Pusparum
- Unit Health, Environmental Intelligence, Flemish Institute for Technological Research (VITO), Mol 2400, Belgium; I-Biostat, Data Science Institute, Hasselt University, Hasselt 3500, Belgium
| | - Rebekka Van Hoof
- Unit Health, Environmental Intelligence, Flemish Institute for Technological Research (VITO), Mol 2400, Belgium
| | - Zelal Zuhal Kaya
- Nisantasi University, School of Medicine, Department of Medical Biochemistry, Istanbul, Turkey
| | - Arezoo Khosravi
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Istanbul Okan University, Istanbul 34959, Turkey
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Turkey; Graduate School of Biotehnology and Bioengeneering, Yuan Ze University, Taoyuan 320315, Taiwan; Department of Research Analytics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600 077, India
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Chengyan L, Chupeng X, You W, Yinhui C, Binglong H, Dang A, Ling L, Chuan T. Identification of genetic causes in children with unexplained epilepsy based on trio-whole exome sequencing. Clin Genet 2024; 106:140-149. [PMID: 38468460 DOI: 10.1111/cge.14519] [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: 11/03/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Genotype and clinical phenotype analyses of 128 children were performed based on whole exome sequencing (WES), providing a reference for the provision of genetic counseling and the precise diagnosis and treatment of epilepsy. A total of 128 children with unexplained epilepsy were included in this study, and all their clinical data were analyzed. The children's treatments, epilepsy control, and neurodevelopmental levels were regularly followed up every 3 months. The genetic diagnostic yield of the 128 children with epilepsy is 50.8%, with an SNV diagnostic yield of 39.8% and a CNV diagnostic yield of 12.5%. Among the 128 children with epilepsy, 57.0% had onset of epilepsy in infancy, 25.8% have more than two clinical seizure forms, 62.5% require two or more anti-epileptic drug treatments, and 72.7% of the children have varying degrees of psychomotor development retardation. There are significant differences between ages of onset, neurodevelopmental levels and the presence of drug resistance in the genetic diagnostic yield (all p < 0.05). The 52 pathogenic/likely pathogenic SNVs involve 31 genes, with genes encoding ion channels having the largest number of mutations (30.8%). There were 16 cases of pathogenic/possibly pathogenic CNVs, among which the main proportions of CNVs were located in chromosome 15 and chromosome 16. Trio-WES is an essential tool for the genetic diagnosis of unexplained epilepsy, with a genetic diagnostic yield of up to 50.8%. Early genetic testing can provide an initiate appropriate therapies and accurate molecular diagnosis.
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Affiliation(s)
- Li Chengyan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Xue Chupeng
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
- Department of Pediatrics, Shantou Central Hospital, Shantou, People's Republic of China
| | - Wang You
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Chen Yinhui
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Huang Binglong
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Ao Dang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Liu Ling
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Tian Chuan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Damiani G. Bayesian cost-effectiveness analysis of Whole genome sequencing versus Whole exome sequencing in a pediatric population with suspected genetic disorders. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2024; 25:999-1011. [PMID: 37975990 PMCID: PMC11283423 DOI: 10.1007/s10198-023-01644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Genetic diseases are medical conditions caused by sequence or structural changes in an individual's genome. Whole exome sequencing (WES) and whole genome sequencing (WGS) are increasingly used for diagnosing suspected genetic conditions in children to reduce the diagnostic delay and accelerating the implementation of appropriate treatments. While more information is becoming available on clinical efficacy and economic sustainability of WES, the broad implementation of WGS is still hindered by higher complexity and economic issues. The aim of this study is to estimate the cost-effectiveness of WGS versus WES and standard testing for pediatric patients with suspected genetic disorders. A Bayesian decision tree model was set up. Model parameters were retrieved both from hospital administrative datasets and scientific literature. The analysis considered a lifetime time frame and adopted the perspective of the Italian National Health Service (NHS). Bayesian inference was performed using the Markov Chain Monte Carlo simulation method. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI). The present analysis showed that implementing first-line WGS would be a cost-effective strategy, against the majority of the other tested alternatives at a threshold of €30,000-50,000, for diagnosing outpatient pediatric patients with suspected genetic disorders. According to the sensitivity analyses, the findings were robust to most assumption and parameter uncertainty. Lessons learnt from this modeling study reinforces the adoption of first-line WGS, as a cost-effective strategy, depending on actual difficulties for the NHS to properly allocate limited resources.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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Maver A, Lohmann K, Borovečki F, Wolstenholme N, Taylor RL, Spielmann M, Haack TB, Gerberding M, Peterlin B, Graessner H. Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network. Eur J Hum Genet 2024; 32:1014-1021. [PMID: 38839988 PMCID: PMC11292006 DOI: 10.1038/s41431-024-01639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
In the past decade, next-generation sequencing (NGS) has revolutionised genetic diagnostics for rare neurological disorders (RND). However, the lack of standardised technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonisation, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasised the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.
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Affiliation(s)
- Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| | | | - Rachel L Taylor
- EMQN CIC, Unit 4 Enterprise Hse, Manchester Science Park, Manchester, UK
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Matthias Gerberding
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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5
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Lopacinska-Jørgensen J, Vestergaard LK, Schejbel L, Høgdall CK, Poulsen TS, Høgdall EV. Paired comparison of the analytical performance between the Oncomine™ Comprehensive Assay v3 and whole-exome sequencing of ovarian cancer tissue. Mol Biol Rep 2024; 51:820. [PMID: 39017860 PMCID: PMC11255052 DOI: 10.1007/s11033-024-09715-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: 02/19/2024] [Accepted: 06/09/2024] [Indexed: 07/18/2024]
Abstract
BACKGROUND Next-generation sequencing (NGS) has been implemented in clinical oncology as a personalized medicine tool to identify targetable genetic alterations and to guide treatment decisions. However, the optimal NGS test strategy and target genes for clinical use are still being discussed. The aim was to compare the performance of the Oncomine™ Comprehensive Assay v3 (OCAv3) (targeted gene panel) and whole-exome sequencing (WES) to investigate somatic single and multiple nucleotide variants and small indels in ovarian cancer patients. METHODS AND RESULTS Genomic DNA was isolated from fresh frozen samples of five high-grade serous (HGSC) and three clear cell ovarian (oCCC) cancer patients. Exome sequencing libraries were prepared by using the Ion AmpliSeq Exome RDY kit, whereas libraries for OCAv3 were prepared using by Ion AmpliSeq™ Library Kit Plus. Sequencing was performed using the Ion S5XL System (Thermo Fisher Scientific). When including only variants classified as pathogenic, likely pathogenic or unknown significance based on ClinVar database verdicts and comparing overlapping regions covered both by the OCAv3 assay and WES, 23 variants were detected by both assays. However, OCAv3 detected additionally two variants: ARID1A: p.Gln563Ter and TP53: p.Ser261ValfsTer84 that have not passed WES filtering criteria due to low coverage. CONCLUSIONS With the present treatment possibilities, OCAv3 panel testing provided higher diagnostic yield due to better coverage. Our study emphasizes that WES, although offering the potential to identify novel findings in genes not covered by OCAv3, might overlook variants in genes relevant for OC.
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Affiliation(s)
- Joanna Lopacinska-Jørgensen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Lau K Vestergaard
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Lone Schejbel
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Claus K Høgdall
- Department of Gynaecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tim Svenstrup Poulsen
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 25, Herlev, 2730, Denmark.
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Prawitt D, Eggermann T. Molecular mechanisms of human overgrowth and use of omics in its diagnostics: chances and challenges. Front Genet 2024; 15:1382371. [PMID: 38894719 PMCID: PMC11183334 DOI: 10.3389/fgene.2024.1382371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 05/14/2024] [Indexed: 06/21/2024] Open
Abstract
Overgrowth disorders comprise a group of entities with a variable phenotypic spectrum ranging from tall stature to isolated or lateralized overgrowth of body parts and or organs. Depending on the underlying physiological pathway affected by pathogenic genetic alterations, overgrowth syndromes are associated with a broad spectrum of neoplasia predisposition, (cardio) vascular and neurodevelopmental anomalies, and dysmorphisms. Pathologic overgrowth may be of prenatal or postnatal onset. It either results from an increased number of cells (intrinsic cellular hyperplasia), hypertrophy of the normal number of cells, an increase in interstitial spaces, or from a combination of all of these. The underlying molecular causes comprise a growing number of genetic alterations affecting skeletal growth and Growth-relevant signaling cascades as major effectors, and they can affect the whole body or parts of it (mosaicism). Furthermore, epigenetic modifications play a critical role in the manifestation of some overgrowth diseases. The diagnosis of overgrowth syndromes as the prerequisite of a personalized clinical management can be challenging, due to their clinical and molecular heterogeneity. Physicians should consider molecular genetic testing as a first diagnostic step in overgrowth syndromes. In particular, the urgent need for a precise diagnosis in tumor predisposition syndromes has to be taken into account as the basis for an early monitoring and therapy. With the (future) implementation of next-generation sequencing approaches and further omic technologies, clinical diagnoses can not only be verified, but they also confirm the clinical and molecular spectrum of overgrowth disorders, including unexpected findings and identification of atypical cases. However, the limitations of the applied assays have to be considered, for each of the disorders of interest, the spectrum of possible types of genomic variants has to be considered as they might require different methodological strategies. Additionally, the integration of artificial intelligence (AI) in diagnostic workflows significantly contribute to the phenotype-driven selection and interpretation of molecular and physiological data.
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Affiliation(s)
- Dirk Prawitt
- Center for Pediatrics and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genome Medicine, Medical Faculty, RWTH Aachen, Aachen, Germany
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Marshall DA, Hua N, Buchanan J, Christensen KD, Frederix GWJ, Goranitis I, Ijzerman M, Jansen JP, Lavelle TA, Regier DA, Smith HS, Ungar WJ, Weymann D, Wordsworth S, Phillips KA. Paving the path for implementation of clinical genomic sequencing globally: Are we ready? HEALTH AFFAIRS SCHOLAR 2024; 2:qxae053. [PMID: 38783891 PMCID: PMC11115369 DOI: 10.1093/haschl/qxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicolle Hua
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - James Buchanan
- Health Economics and Policy Research Unit, Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London E1 2AB, United Kingdom
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Geert W J Frederix
- Epidemiology and Health Economics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Australian Genomics, Parkville, Victoria 3052, Australia
| | - Maarten Ijzerman
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria 3000, Australia
- Erasmus School of Health Policy & Management, Eramus University Rotterdam, 3062 PA Rotterdam, The Netherlands
| | - Jeroen P Jansen
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, United States
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hadley S Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario M5T 3M6, Canada
| | - Deirdre Weymann
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health and NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Kathryn A Phillips
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
- Health Affairs Scholar Emerging & Global Health Policy, Health Affairs, Washington, DC 20036, United States
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Lee WW, Lee CG, Ki CS. KCNJ3 is a novel candidate gene for autosomal dominant pure hereditary spastic paraplegia identified using whole genome sequencing. Am J Med Genet B Neuropsychiatr Genet 2024:e32984. [PMID: 38597354 DOI: 10.1002/ajmg.b.32984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/05/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
Hereditary spastic paraplegia (HSP) is a group of familial diseases characterized by progressive corticospinal tract degeneration. Clinically, patients present with lower-limb spasticity and weakness. To date, more than 80 genetic HSP types have been identified. Despite advances in molecular genetics, novel HSP gene discoveries are ongoing, with a low genetic diagnostic yield. In this study, we aimed to determine pathogenic variants in a family with HSP, which was not diagnosed through conventional genetic testing. We clinically characterized a large family and conducted whole genome sequencing (WGS) analysis of four affected and three unaffected individuals in the family to identify the genetic cause of HSP. This family had autosomal dominant pure (uncomplicated) late childhood-onset HSP. The patients' symptoms accelerated between the ages of 20 and 30. Brain magnetic resonance images typically showed white matter changes, a thin corpus callosum, and cerebellar atrophy. We identified a heterozygous missense variant, KCNJ3 c.1297T>G (p.Leu433Val), through WGS and family genetic analysis, confirmed by Sanger sequencing. We suggest that the identification of KCNJ3 c.1297T>G (p.Leu433Val) constitutes the discovery of a potential novel gene responsible for HSP in this family. This is the first study to report the possible role of a KCNJ3 variant in HSP pathogenesis. Our findings further expand the phenotypic and genotypic spectrum of HSP.
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Affiliation(s)
- Woong-Woo Lee
- Department of Neurology, Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul, Republic of Korea
| | - Cha Gon Lee
- Department of Pediatrics, Nowon Eulji Medical Center, Eulji University School of Medicine, Seoul, Republic of Korea
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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10
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Wigby KM, Brockman D, Costain G, Hale C, Taylor SL, Belmont J, Bick D, Dimmock D, Fernbach S, Greally J, Jobanputra V, Kulkarni S, Spiteri E, Taft RJ. Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders. NPJ Genom Med 2024; 9:15. [PMID: 38409289 PMCID: PMC10897481 DOI: 10.1038/s41525-024-00396-x] [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: 06/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.
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Affiliation(s)
- Kristen M Wigby
- University of California, Davis, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | | | | | | | | | - John Belmont
- Genetics & Genomics Services Inc, Houston, TX, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - John Greally
- Albert Einstein College of Medicine, Bronx, NY, USA
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Kvapilova K, Misenko P, Radvanszky J, Brzon O, Budis J, Gazdarica J, Pos O, Korabecna M, Kasny M, Szemes T, Kvapil P, Paces J, Kozmik Z. Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses. BMC Genomics 2024; 25:187. [PMID: 38365587 PMCID: PMC10873937 DOI: 10.1186/s12864-024-10080-0] [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: 09/05/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
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Affiliation(s)
- Katerina Kvapilova
- Faculty of Science, Charles University, Albertov 6, Prague, 128 00, Czech Republic.
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic.
| | - Pavol Misenko
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
| | - Jan Radvanszky
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, Bratislava, 845 05, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Ondrej Brzon
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jaroslav Budis
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Juraj Gazdarica
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
- Slovak Centre for Scientific and Technical Information, Staré Mesto, Lamačská Cesta 8A, Bratislava, 811 04, Slovakia
| | - Ondrej Pos
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Marie Korabecna
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague, 128 00, Czech Republic
| | - Martin Kasny
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 611 37, Czech Republic
| | - Tomas Szemes
- Geneton s.r.o, Ilkovičova 8, Bratislava, 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovičova 3278/6, Karlova Ves, Bratislava, 841 04, Slovakia
- Comenius University Science Park, Comenius University, Ilkovičova 8, Karlova Ves, Bratislava, 841 04, Slovakia
| | - Petr Kvapil
- Institute of Applied Biotechnologies a.s, Služeb 4, Prague, 108 00, Czech Republic
| | - Jan Paces
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague, 142 20, Czech Republic
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12
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Barbitoff YA, Ushakov MO, Lazareva TE, Nasykhova YA, Glotov AS, Predeus AV. Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges. Brief Bioinform 2024; 25:bbad508. [PMID: 38271481 PMCID: PMC10810331 DOI: 10.1093/bib/bbad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/18/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.
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Affiliation(s)
- Yury A Barbitoff
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
| | - Mikhail O Ushakov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Tatyana E Lazareva
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Yulia A Nasykhova
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Andrey S Glotov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
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13
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Fortunato F, Tonelli L, Farnè M, Selvatici R, Ferlini A. DMD deletions underlining mild dystrophinopathies: literature review highlights phenotype-related mutation clusters and provides insights about genetic mechanisms and prognosis. Front Neurol 2024; 14:1288721. [PMID: 38288333 PMCID: PMC10823016 DOI: 10.3389/fneur.2023.1288721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/27/2023] [Indexed: 01/31/2024] Open
Abstract
DMD gene pathogenic variations cause a spectrum of phenotypes, ranging from severe Duchenne muscular dystrophy, the Becker milder cases, the intermediate or very mild muscle phenotypes invariably characterized by high CK, and the ultrarare fully-asymptomatic cases. Besides these phenotypes, X-linked dilated cardiomyopathy is also caused by DMD mutations. Males carrying DMD deletions with absent or very mild phenotypes have been sparsely described. We performed a horizon scan on public datasets to enroll males with the above phenotypes and carrying DMD deletions to delineate myopathic genotype-phenotype relationships. We inventoried 81 males, who were divided into the following clinical categorization: fully-asymptomatic males aged >43 years (A, N = 22); isolated hyperCKemia (CK, N = 35); and mild weakness (any age) with or without high CK (WCK, N = 24). In all cases, deleted intervals were exons 2 to 55, and no downstream exons were ever involved, apart from an exon 78 deletion in a WCK patient. All deletions were in-frame apart from the known exception to the rule of exon 2 and exon 78. We correlated the mild phenotypes (A and CK) to deleted exons, intronic breakpoints, exon-exon junctions, 3' isoforms rule, and protein epitopes, and we found that some genetic profiles are exclusively/mainly occurring in A/CK phenotypes, suggesting they are compatible with a quasi-normal muscular performance. We discussed diverse pathogenic mechanisms that may contribute to mild dystrophinopathic phenotypes, and we tried to address some "critical" genetic configurations or exon content needed to preserve a semi-functional DMD gene.
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Affiliation(s)
| | | | | | | | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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14
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Shreeve N, Sproule C, Choy KW, Dong Z, Gajewska-Knapik K, Kilby MD, Mone F. Incremental yield of whole-genome sequencing over chromosomal microarray analysis and exome sequencing for congenital anomalies in prenatal period and infancy: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:15-23. [PMID: 37725747 DOI: 10.1002/uog.27491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/08/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023]
Abstract
OBJECTIVES First, to determine the incremental yield of whole-genome sequencing (WGS) over quantitative fluorescence polymerase chain reaction (QF-PCR)/chromosomal microarray analysis (CMA) with and without exome sequencing (ES) in fetuses, neonates and infants with a congenital anomaly that was or could have been detected on prenatal ultrasound. Second, to evaluate the turnaround time (TAT) and quantity of DNA required for testing using these pathways. METHODS This review was registered prospectively in December 2022. Ovid MEDLINE, EMBASE, MEDLINE (Web of Science), The Cochrane Library and ClinicalTrials.gov databases were searched electronically (January 2010 to December 2022). Inclusion criteria were cohort studies including three or more fetuses, neonates or infants with (i) one or more congenital anomalies; (ii) an anomaly which was or would have been detectable on prenatal ultrasound; and (iii) negative QF-PCR and CMA. In instances in which the CMA result was unavailable, all cases of causative pathogenic copy number variants > 50 kb were excluded, as these would have been detectable on standard prenatal CMA. Pooled incremental yield was determined using a random-effects model and heterogeneity was assessed using Higgins' I2 test. Subanalyses were performed based on pre- or postnatal cohorts, cases with multisystem anomalies and those meeting the NHS England prenatal ES inclusion criteria. RESULTS A total of 18 studies incorporating 902 eligible cases were included, of which eight (44.4%) studies focused on prenatal cohorts, incorporating 755 cases, and the remaining studies focused on fetuses undergoing postmortem testing or neonates/infants with congenital structural anomalies, constituting the postnatal cohort. The incremental yield of WGS over QF-PCR/CMA was 26% (95% CI, 18-36%) (I2 = 86%), 16% (95% CI, 9-24%) (I2 = 85%) and 39% (95% CI, 27-51%) (I2 = 53%) for all, prenatal and postnatal cases, respectively. The incremental yield increased in cases in which sequencing was performed in line with the NHS England prenatal ES criteria (32% (95% CI, 22-42%); I2 = 70%) and in those with multisystem anomalies (30% (95% CI, 19-43%); I2 = 65%). The incremental yield of WGS for variants of uncertain significance (VUS) was 18% (95% CI, 7-33%) (I2 = 74%). The incremental yield of WGS over QF-PCR/CMA and ES was 1% (95% CI, 0-4%) (I2 = 47%). The pooled median TAT of WGS was 18 (range, 1-912) days, and the quantity of DNA required was 100 ± 0 ng for WGS and 350 ± 50 ng for QF-PCR/CMA and ES (P = 0.03). CONCLUSION While WGS in cases with congenital anomaly holds great promise, its incremental yield over ES is yet to be demonstrated. However, the laboratory pathway for WGS requires less DNA with a potentially faster TAT compared with sequential QF-PCR/CMA and ES. There was a relatively high rate of VUS using WGS. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- N Shreeve
- Department of Obstetrics & Gynaecology, University of Cambridge, Cambridge, UK
| | - C Sproule
- Department of Obstetrics & Gynaecology, South Eastern Health and Social Care Trust, Belfast, UK
| | - K W Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Z Dong
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - K Gajewska-Knapik
- Department of Obstetrics & Gynaecology, Cambridge University Hospitals, Cambridge, UK
| | - M D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - F Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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15
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Park J, Cho YG, Kim JK, Kim HH. STS and PUDP Deletion Identified by Targeted Panel Sequencing with CNV Analysis in X-Linked Ichthyosis: A Case Report and Literature Review. Genes (Basel) 2023; 14:1925. [PMID: 37895274 PMCID: PMC10606178 DOI: 10.3390/genes14101925] [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: 09/12/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
X-linked recessive ichthyosis (XLI) is clinically characterized by dark brown, widespread dryness with polygonal scales. We describe the identification of STS and PUDP deletions using targeted panel sequencing combined with copy-number variation (CNV) analysis in XLI. A 9-month-old infant was admitted for genetic counseling. Since the second day after birth, the infant's skin tended to be dry and polygonal scales had accumulated over the abdomen and upper extremities. The infant's maternal uncle and brother (who had also exhibited similar skin symptoms from birth) presented with polygonal scales on their trunks. CNV analysis revealed a hemizygous deletion spanning 719.3 Kb on chromosome Xp22 (chrX:7,108,996-7,828,312), which included a segment of the STS gene and exhibited a Z ratio of -2 in the proband. Multiplex ligation-dependent probe amplification (MLPA) confirmed this interstitial Xp22.31 deletion. Our report underscores the importance of implementing CNV screening techniques, including sequencing data analysis and gene dosage assays such as MLPA, to detect substantial deletions that encompass the STS gene region of Xq22 in individuals suspected of having XLI.
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Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea; (J.P.); (Y.G.C.)
| | - Jin Kyu Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
| | - Hyun Ho Kim
- Department of Pediatrics, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea;
- Research Institute of Clinical Medicine, Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
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16
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Ferlini A, Gross ES, Garnier N. Rare diseases' genetic newborn screening as the gateway to future genomic medicine: the Screen4Care EU-IMI project. Orphanet J Rare Dis 2023; 18:310. [PMID: 37794437 PMCID: PMC10548672 DOI: 10.1186/s13023-023-02916-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
Following the reverse genetics strategy developed in the 1980s to pioneer the identification of disease genes, genome(s) sequencing has opened the era of genomics medicine. The human genome project has led to an innumerable series of applications of omics sciences on global health, from which rare diseases (RDs) have greatly benefited. This has propelled the scientific community towards major breakthroughs in disease genes discovery, in technical innovations in bioinformatics, and in the development of patients' data registries and omics repositories where sequencing data are stored. Rare diseases were the first diseases where nucleic acid-based therapies have been applied. Gene therapy, molecular therapy using RNA constructs, and medicines modulating transcription or translation mechanisms have been developed for RD patients and started a new era of medical science breakthroughs. These achievements together with optimization of highly scalable next generation sequencing strategies now allow movement towards genetic newborn screening. Its applications in human health will be challenging, while expected to positively impact the RD diagnostic journey. Genetic newborn screening brings many complexities to be solved, technical, strategic, ethical, and legal, which the RD community is committed to address. Genetic newborn screening initiatives are therefore blossoming worldwide, and the EU-IMI framework has funded the project Screen4Care. This large Consortium will apply a dual genetic and digital strategy to design a comprehensive genetic newborn screening framework to be possibly translated into the future health care.
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Affiliation(s)
- Alessandra Ferlini
- Medical Genetics Unit, Department of Medical Sciences, University of Ferrara, 44121, Ferrara, Italy.
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17
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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18
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Di Resta C, D'Argenio V. Editorial: Whole Genome Sequencing for rare diseases. Front Med (Lausanne) 2023; 10:1267930. [PMID: 37795418 PMCID: PMC10546400 DOI: 10.3389/fmed.2023.1267930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/05/2023] [Indexed: 10/06/2023] Open
Affiliation(s)
- Chiara Di Resta
- Faculty of Medicine, Vita-Salute San Raffaele University, Milan, Italy
- Genomic Unit for the Diagnosis of Human Pathologies, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Naples, Italy
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19
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Khera HK, Mishra R. Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health. Mol Biotechnol 2023:10.1007/s12033-023-00870-4. [PMID: 37695473 DOI: 10.1007/s12033-023-00870-4] [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: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.
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Affiliation(s)
- Harvinder Kour Khera
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
| | - Rakesh Mishra
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, Telangana, 500007, India.
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20
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Chung CCY, Hue SPY, Ng NYT, Doong PHL, Chu ATW, Chung BHY. Meta-analysis of the diagnostic and clinical utility of exome and genome sequencing in pediatric and adult patients with rare diseases across diverse populations. Genet Med 2023; 25:100896. [PMID: 37191093 DOI: 10.1016/j.gim.2023.100896] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE This meta-analysis aims to compare the diagnostic and clinical utility of exome sequencing (ES) vs genome sequencing (GS) in pediatric and adult patients with rare diseases across diverse populations. METHODS A meta-analysis was conducted to identify studies from 2011 to 2021. RESULTS One hundred sixty-one studies across 31 countries/regions were eligible, featuring 50,417 probands of diverse populations. Diagnostic rates of ES (0.38, 95% CI 0.36-0.40) and GS (0.34, 95% CI 0.30-0.38) were similar (P = .1). Within-cohort comparison illustrated 1.2-times odds of diagnosis by GS over ES (95% CI 0.79-1.83, P = .38). GS studies discovered a higher range of novel genes than ES studies; yet, the rate of variant of unknown significance did not differ (P = .78). Among high-quality studies, clinical utility of GS (0.77, 95% CI 0.64-0.90) was higher than that of ES (0.44, 95% CI 0.30-0.58) (P < .01). CONCLUSION This meta-analysis provides an important update to demonstrate the similar diagnostic rates between ES and GS and the higher clinical utility of GS over ES. With the newly published recommendations for clinical interpretation of variants found in noncoding regions of the genome and the trend of decreasing variant of unknown significance and GS cost, it is expected that GS will be more widely used in clinical settings.
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Affiliation(s)
| | - Shirley P Y Hue
- Hong Kong Genome Institute, Hong Kong Special Administrative Region
| | - Nicole Y T Ng
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Annie T W Chu
- Hong Kong Genome Institute, Hong Kong Special Administrative Region.
| | - Brian H Y Chung
- Hong Kong Genome Institute, Hong Kong Special Administrative Region; Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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21
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Chumakova OS, Baulina NM. Advanced searching for hypertrophic cardiomyopathy heritability in real practice tomorrow. Front Cardiovasc Med 2023; 10:1236539. [PMID: 37583586 PMCID: PMC10425241 DOI: 10.3389/fcvm.2023.1236539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease associated with morbidity and mortality at any age. As studies in recent decades have shown, the genetic architecture of HCM is quite complex both in the entire population and in each patient. In the rapidly advancing era of gene therapy, we have to provide a detailed molecular diagnosis to our patients to give them the chance for better and more personalized treatment. In addition to emphasizing the importance of genetic testing in routine practice, this review aims to discuss the possibility to go a step further and create an expanded genetic panel that contains not only variants in core genes but also new candidate genes, including those located in deep intron regions, as well as structural variations. It also highlights the benefits of calculating polygenic risk scores based on a combination of rare and common genetic variants for each patient and of using non-genetic HCM markers, such as microRNAs that can enhance stratification of risk for HCM in unselected populations alongside rare genetic variants and clinical factors. While this review is focusing on HCM, the discussed issues are relevant to other cardiomyopathies.
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Affiliation(s)
- Olga S. Chumakova
- Laboratory of Functional Genomics of Cardiovascular Diseases, National Medical Research Centre of Cardiology Named After E.I. Chazov, Moscow, Russia
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22
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Papadopoulou E, Bouzarelou D, Tsaousis G, Papathanasiou A, Vogiatzi G, Vlachopoulos C, Miliou A, Papachristou P, Prappa E, Servos G, Ritsatos K, Seretis A, Frogoudaki A, Nasioulas G. Application of next generation sequencing in cardiology: current and future precision medicine implications. Front Cardiovasc Med 2023; 10:1202381. [PMID: 37424920 PMCID: PMC10327645 DOI: 10.3389/fcvm.2023.1202381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Inherited cardiovascular diseases are highly heterogeneous conditions with multiple genetic loci involved. The application of advanced molecular tools, such as Next Generation Sequencing, has facilitated the genetic analysis of these disorders. Accurate analysis and variant identification are required to maximize the quality of the sequencing data. Therefore, the application of NGS for clinical purposes should be limited to laboratories with a high level of technological expertise and resources. In addition, appropriate gene selection and variant interpretation can result in the highest possible diagnostic yield. Implementation of genetics in cardiology is imperative for the accurate diagnosis, prognosis and management of several inherited disorders and could eventually lead to the realization of precision medicine in this field. However, genetic testing should also be accompanied by an appropriate genetic counseling procedure that clarifies the significance of the genetic analysis results for the proband and his family. In this regard, a multidisciplinary collaboration among physicians, geneticists, and bioinformaticians is imperative. In the present review, we address the current state of knowledge regarding genetic analysis strategies employed in the field of cardiogenetics. Variant interpretation and reporting guidelines are explored. Additionally, gene selection procedures are accessed, with a particular emphasis on information concerning gene-disease associations collected from international alliances such as the Gene Curation Coalition (GenCC). In this context, a novel approach to gene categorization is proposed. Moreover, a sub-analysis is conducted on the 1,502,769 variation records with submitted interpretations in the Clinical Variation (ClinVar) database, focusing on cardiology-related genes. Finally, the most recent information on genetic analysis's clinical utility is reviewed.
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Affiliation(s)
| | | | | | | | - Georgia Vogiatzi
- Third Department of Cardiology, Sotiria Hospital, Athens, Greece
| | - Charalambos Vlachopoulos
- Unit of Inherited Cardiac Conditions and Sports Cardiology, First Department of Cardiology, National and Kapodistrian University of Athens, Athens, Greece
| | - Antigoni Miliou
- Unit of Inherited Cardiac Conditions and Sports Cardiology, First Department of Cardiology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Efstathia Prappa
- Second Department of Cardiology, Arrhythmia Unit, Evangelismos General Hospital of Athens, Athens, Greece
| | - Georgios Servos
- Pediatric Cardiology Unit, “P. & A. Kyriakou” Children’s Hospital, Athens, Greece
| | - Konstantinos Ritsatos
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Center, Athens, Greece
| | - Aristeidis Seretis
- Unit of Inherited and Rare Cardiovascular Diseases, Onassis Cardiac Surgery Center, Athens, Greece
| | - Alexandra Frogoudaki
- Second Department of Cardiology, Attikon University Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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23
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Roman-Naranjo P, Parra-Perez AM, Lopez-Escamez JA. A systematic review on machine learning approaches in the diagnosis and prognosis of rare genetic diseases. J Biomed Inform 2023:104429. [PMID: 37352901 DOI: 10.1016/j.jbi.2023.104429] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/05/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
BACKGROUND The diagnosis of rare genetic diseases is often challenging due to the complexity of the genetic underpinnings of these conditions and the limited availability of diagnostic tools. Machine learning (ML) algorithms have the potential to improve the accuracy and speed of diagnosis by analyzing large amounts of genomic data and identifying complex multiallelic patterns that may be associated with specific diseases. In this systematic review, we aimed to identify the methodological trends and the ML application areas in rare genetic diseases. METHODS We performed a systematic review of the literature following the PRISMA guidelines to search studies that used ML approaches to enhance the diagnosis of rare genetic diseases. Studies that used DNA-based sequencing data and a variety of ML algorithms were included, summarized, and analyzed using bibliometric methods, visualization tools, and a feature co-occurrence analysis. FINDINGS Our search identified 22 studies that met the inclusion criteria. We found that exome sequencing was the most frequently used sequencing technology (59%), and rare neoplastic diseases were the most prevalent disease scenario (59%). In rare neoplasms, the most frequent applications of ML models were the differential diagnosis or stratification of patients (38.5%) and the identification of somatic mutations (30.8%). In other rare diseases, the most frequent goals were the prioritization of rare variants or genes (55.5%) and the identification of biallelic or digenic inheritance (33.3%). The most employed method was the random forest algorithm (54.5%). In addition, the features of the datasets needed for training these algorithms were distinctive depending on the goal pursued, including the mutational load in each gene for the differential diagnosis of patients, or the combination of genotype features and sequence-derived features (such as GC-content) for the identification of somatic mutations. CONCLUSIONS ML algorithms based on sequencing data are mainly used for the diagnosis of rare neoplastic diseases, with random forest being the most common approach. We identified key features in the datasets used for training these ML models according to the objective pursued. These features can support the development of future ML models in the diagnosis of rare genetic diseases.
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Affiliation(s)
- P Roman-Naranjo
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain.
| | - A M Parra-Perez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
| | - J A Lopez-Escamez
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain; Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO - Centre for Genomics and Oncological Research - Pfizer, University of Granada, Junta de Andalucía, PTS, Granada, Spain; Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain; Meniere's Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, New South Wales, Australia
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24
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Florian K, Benet-Pagès A, Berner D, Teubert A, Eck S, Arnold N, Bauer P, Begemann M, Sturm M, Kleinle S, B. Haack T, Eggermann T. Quality assurance within the context of genome diagnostics (a german perspective). MED GENET-BERLIN 2023; 35:91-104. [PMID: 38840862 PMCID: PMC10842579 DOI: 10.1515/medgen-2023-2028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The rapid and dynamic implementation of Next-Generation Sequencing (NGS)-based assays has revolutionized genetic testing, and in the near future, nearly all molecular alterations of the human genome will be diagnosable via massive parallel sequencing. While this progress will further corroborate the central role of human genetics in the multidisciplinary management of patients with genetic disorders, it must be accompanied by quality assurance measures in order to allow the safe and optimal use of knowledge ascertained from genome diagnostics. To achieve this, several valuable tools and guidelines have been developed to support the quality of genome diagnostics. In this paper, authors with experience in diverse aspects of genomic analysis summarize the current status of quality assurance in genome diagnostics, with the aim of facilitating further standardization and quality improvement in one of the core competencies of the field.
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Affiliation(s)
- Kraft Florian
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinAachenDeutschland
| | - Anna Benet-Pagès
- Institut für NeurogenomikHelmholtz Zentrum MünchenNeuherbergDeutschland
| | | | | | | | - Norbert Arnold
- Universitätsklinikum Schleswig-HolsteinZentrum für familiären Brust- und Eierstockkrebs; Klinik für Gynäkologie und GeburtshilfeKielDeutschland
| | | | - Matthias Begemann
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinAachenDeutschland
| | - Marc Sturm
- Universität TübingenInstitut für Medizinische Genetik und Angewandte GenomikTübingenDeutschland
| | | | - Tobias B. Haack
- Universität TübingenInstitut für Medizinische Genetik und Angewandte GenomikTübingenDeutschland
| | - Thomas Eggermann
- Medizinische Fakultät der RWTH AachenInstitut für Humangenetik und GenommedizinPauwelsstr. 3052074AachenDeutschland
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25
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Schuermans N, Verdin H, Ghijsels J, Hellemans M, Debackere E, Bogaert E, Symoens S, Naesens L, Lecomte E, Crosiers D, Bergmans B, Verhoeven K, Poppe B, Laureys G, Herdewyn S, Van Langenhove T, Santens P, De Bleecker JL, Hemelsoet D, Dermaut B. Exome Sequencing and Multigene Panel Testing in 1,411 Patients With Adult-Onset Neurologic Disorders. Neurol Genet 2023; 9:e200071. [PMID: 37152446 PMCID: PMC10160959 DOI: 10.1212/nxg.0000000000200071] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/21/2023] [Indexed: 05/09/2023]
Abstract
Background and Objectives Owing to their extensive clinical and molecular heterogeneity, hereditary neurologic diseases in adults are difficult to diagnose. The current knowledge about the diagnostic yield and clinical utility of exome sequencing (ES) for neurologic diseases in adults is limited. This observational study assesses the diagnostic value of ES and multigene panel analysis in adult-onset neurologic disorders. Methods From January 2019 through April 2022, ES-based multigene panel testing was conducted in 1,411 patients with molecularly unexplained neurologic phenotypes at the Ghent University Hospital. Gene panels were developed for ataxia and spasticity, leukoencephalopathy, movement disorders, paroxysmal episodic disorders, neurodegeneration with brain iron accumulation, progressive myoclonic epilepsy, and amyotrophic lateral sclerosis. Single nucleotide variants, small indels, and copy number variants were analyzed. Across all panels, our analysis covered a total of 725 genes associated with Mendelian inheritance. Results A molecular diagnosis was established in 10% of the cases (144 of 1,411) representing 71 different monogenic disorders. The diagnostic yield depended significantly on the presenting phenotype with the highest yield seen in patients with ataxia or spastic paraparesis (19%). Most of the established diagnoses comprised disorders with an autosomal dominant inheritance (62%), and the most frequently mutated genes were NOTCH3 (13 patients), SPG7 (11 patients), and RFC1 (8 patients). 34% of the disease-causing variants were novel, including a unique likely pathogenic variant in APP (Ghent mutation, p.[Asn698Asp]) in a family presenting with stroke and severe cerebral white matter disease. 7% of the pathogenic variants comprised copy number variants detected in the ES data and confirmed by an independent technique. Discussion ES and multigene panel testing is a powerful and efficient tool to diagnose patients with unexplained, adult-onset neurologic disorders.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Hannah Verdin
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Jody Ghijsels
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Madeleine Hellemans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elke Debackere
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elke Bogaert
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Sofie Symoens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Leslie Naesens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Elien Lecomte
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - David Crosiers
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bruno Bergmans
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Kristof Verhoeven
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bruce Poppe
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Guy Laureys
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Sarah Herdewyn
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Tim Van Langenhove
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Patrick Santens
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Jan L De Bleecker
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Dimitri Hemelsoet
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
| | - Bart Dermaut
- Center for Medical Genetics (N.S., H.V., J.G., E.D., E.B., S.S., B.P., B.D.), Ghent University Hospital; Department of Biomolecular Medicine (N.S., H.V., J.G., M.H., E.D., E.B., S.S., B.P., B.D.), Faculty of Medicine and Health Sciences, Ghent University; Department of Internal Medicine and Pediatrics (L.N.), Ghent University; Primary Immunodeficiency Research Lab (L.N.), Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital; Department of Neurology (E.L.), O.L.V. Lourdes Hospital, Waregem; Department of Neurology (D.C.), Antwerp University Hospital UZA; Translational Neurosciences (D.C.), Faculty of Medicine and Health Sciences, University of Antwerp; Department of Neurology (B.B., K.V.), AZ Sint-Jan, Bruges; and Department of Neurology (B.B., G.L., S.H., T.V.L., P.S., J.L.D.B., D.H.), Ghent University Hospital, Belgium
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26
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Lecoquierre F, Quenez O, Fourneaux S, Coutant S, Vezain M, Rolain M, Drouot N, Boland A, Olaso R, Meyer V, Deleuze JF, Dabbagh D, Gilles I, Gayet C, Saugier-Veber P, Goldenberg A, Guerrot AM, Nicolas G. High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders. Hum Genet 2023; 142:773-783. [PMID: 37076692 DOI: 10.1007/s00439-023-02553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Dana Dabbagh
- Department of Pediatrics, Elbeuf Hospital, Elbeuf, France
| | | | - Claire Gayet
- Department of Pediatrics, CHU Rouen, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
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Chang YT, Hong SY, Lin WD, Lin CH, Lin SS, Tsai FJ, Chou IC. Genetic Testing in Children with Developmental and Epileptic Encephalopathies: A Review of Advances in Epilepsy Genomics. CHILDREN 2023; 10:children10030556. [PMID: 36980114 PMCID: PMC10047509 DOI: 10.3390/children10030556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Advances in disease-related gene discovery have led to tremendous innovations in the field of epilepsy genetics. Identification of genetic mutations that cause epileptic encephalopathies has opened new avenues for the development of targeted therapies. Clinical testing using extensive gene panels, exomes, and genomes is currently accessible and has resulted in higher rates of diagnosis and better comprehension of the disease mechanisms underlying the condition. Children with developmental disabilities have a higher risk of developing epilepsy. As our understanding of the mechanisms underlying encephalopathies and epilepsies improves, there may be greater potential to develop innovative therapies tailored to an individual’s genotype. This article provides an overview of the significant progress in epilepsy genomics in recent years, with a focus on developmental and epileptic encephalopathies in children. The aim of this review is to enhance comprehension of the clinical utilization of genetic testing in this particular patient population. The development of effective and precise therapeutic strategies for epileptic encephalopathies may be facilitated by a comprehensive understanding of their molecular pathogenesis.
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Affiliation(s)
- Yu-Tzu Chang
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung 40447, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40447, Taiwan
| | - Wei-De Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medial University, Taichung 40447, Taiwan
| | - Sheng-Shing Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Division of Genetics and Metabolism, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 40447, Taiwan
| | - I-Ching Chou
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40447, Taiwan
- Correspondence: ; Tel.: +886-4-22052121
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28
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WGS Data Collections: How Do Genomic Databases Transform Medicine? Int J Mol Sci 2023; 24:ijms24033031. [PMID: 36769353 PMCID: PMC9917848 DOI: 10.3390/ijms24033031] [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: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
As a scientific community we assumed that exome sequencing will elucidate the basis of most heritable diseases. However, it turned out it was not the case; therefore, attention has been increasingly focused on the non-coding sequences that encompass 98% of the genome and may play an important regulatory function. The first WGS-based datasets have already been released including underrepresented populations. Although many databases contain pooled data from several cohorts, recently the importance of local databases has been highlighted. Genomic databases are not only collecting data but may also contribute to better diagnostics and therapies. They may find applications in population studies, rare diseases, oncology, pharmacogenetics, and infectious and inflammatory diseases. Further data may be analysed with Al technologies and in the context of other omics data. To exemplify their utility, we put a highlight on the Polish genome database and its practical application.
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McNeill A. 2022: the year that was in the European Journal of Human Genetics. Eur J Hum Genet 2023; 31:131-133. [PMID: 36750730 PMCID: PMC9905485 DOI: 10.1038/s41431-023-01283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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30
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Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. Eur J Hum Genet 2023; 31:148-163. [PMID: 36513735 PMCID: PMC9905091 DOI: 10.1038/s41431-022-01249-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Primary mitochondrial disease describes a diverse group of neuro-metabolic disorders characterised by impaired oxidative phosphorylation. Diagnosis is challenging; >350 genes, both nuclear and mitochondrial DNA (mtDNA) encoded, are known to cause mitochondrial disease, leading to all possible inheritance patterns and further complicated by heteroplasmy of the multicopy mitochondrial genome. Technological advances, particularly next-generation sequencing, have driven a shift in diagnostic practice from 'biopsy first' to genome-wide analyses of blood and/or urine DNA. This has led to the need for a reference framework for laboratories involved in mitochondrial genetic testing to facilitate a consistent high-quality service. In the United Kingdom, consensus guidelines have been prepared by a working group of Clinical Scientists from the NHS Highly Specialised Service followed by national laboratory consultation. These guidelines summarise current recommended technologies and methodologies for the analysis of mtDNA and nuclear-encoded genes in patients with suspected mitochondrial disease. Genetic testing strategies for diagnosis, family testing and reproductive options including prenatal diagnosis are outlined. Importantly, recommendations for the minimum levels of mtDNA testing for the most common referral reasons are included, as well as guidance on appropriate referrals and information on the minimal appropriate gene content of panels when analysing nuclear mitochondrial genes. Finally, variant interpretation and recommendations for reporting of results are discussed, focussing particularly on the challenges of interpreting and reporting mtDNA variants.
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31
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Hui EKY, Yam JCS, Rahman F, Pang CP, Kumaramanickavel G. Ophthalmic genetic counselling: emerging trends in practice perspectives in Asia. J Community Genet 2023; 14:81-89. [PMID: 36322374 PMCID: PMC9947206 DOI: 10.1007/s12687-022-00616-w] [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: 05/04/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022] Open
Abstract
Genetic counselling (GC) provides information to the patient and the family to make informed choices. Among the advanced Western countries and a few Asian countries, there are certified or trained professionals who perform GC. The Human Genome Project and next-generation sequencing diagnostics have provided an opportunity for increased genetic testing in the field of ophthalmology. The recent interventional therapeutic research strategies have also generated additional interest to seek GC globally, including in Asia. However, GC has several barriers to practise in the developing countries in Asia, namely, (a) shortage of qualified or trained genetic counsellors, (b) poor knowledge and reluctance in clinical adoption of genomics among the physicians in clinical practice, (c) overstretched public health services, and (d) negligible ophthalmic GC-related research and publications. The GC inadequacy in Asia is glaring in the most populous countries like China and India. Cultural differences, religious beliefs, misogyny, genetic discrimination, and a multitude of languages in Asia create unique challenges that counsellors in the West may only encounter with the immigrant minorities. Since there are currently 500 or more specific Mendelian genetic eye disorders, it is important for genetic counsellors to translate the genetic results at a level that the patient and family understand. There is therefore a need for governmental and healthcare organisations to train genetic counsellors in Asia and especially this practice must be included in the routine comprehensive ophthalmic care practice.
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Affiliation(s)
- Esther K. Y. Hui
- Department of Ophthalmology, University College London, London, UK
| | - Jason C. S. Yam
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong
| | - Farhana Rahman
- Department of Pharmacology, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education and Research (BIHER), Chennai, India.
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Kowloon, Hong Kong
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32
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Reactive gene curation to support interpretation and reporting of a clinical genome test for rare disease: Experience from over 1,000 cases. CELL GENOMICS 2023; 3:100258. [PMID: 36819666 PMCID: PMC9932986 DOI: 10.1016/j.xgen.2023.100258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/13/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023]
Abstract
Current standards in clinical genetics recognize the need to establish the validity of gene-disease relationships as a first step in the interpretation of sequence variants. We describe our experience incorporating the ClinGen Gene-Disease Clinical Validity framework in our interpretation and reporting workflow for a clinical genome sequencing (cGS) test for individuals with rare and undiagnosed genetic diseases. This "reactive" gene curation is completed upon identification of candidate variants during active case analysis and within the test turn-around time by focusing on the most impactful evidence and taking advantage of the broad applicability of the framework to cover a wide range of disease areas. We demonstrate that reactive gene curation can be successfully implemented in support of cGS in a clinical laboratory environment, enabling robust clinical decision making and allowing all variants to be fully and appropriately considered and their clinical significance confidently interpreted.
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33
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Tudini E, Haas MA, Mattiske T, Spurdle AB. Reporting clinically relevant genetic variants unrelated to genomic test requests: a survey of Australian clinical laboratory policies and practices. J Med Genet 2023; 60:609-614. [PMID: 36604177 DOI: 10.1136/jmg-2022-108808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/02/2022] [Indexed: 01/07/2023]
Abstract
Approaches to reporting clinically important genetic findings unrelated to the initial test request vary internationally. We sought to investigate practices regarding the management and return of these findings in Australia. Australian clinically accredited genetic testing laboratories were surveyed in 2017 and 2020 regarding their opinions on issues relating to the return of clinically important genetic findings unrelated to the initial test request. Responses were collated and analysed for 15 laboratories in 2017, and 17 laboratories in 2020. Content analysis was also performed on seven laboratory policies in 2020. Analysis showed that overall there was a lack of consensus about the terminology used to describe such findings and reporting practices across different testing contexts. A clear exception was that no laboratories were actively searching for a list of medically actionable genes (eg, American College of Medical Genetics and Genomics secondary findings gene list). Laboratory policies showed little consistency in the documentation of issues related to the handling of these findings. These findings indicate a need for Australian-specific policy guidance that covers all aspects of clinically important genetic findings unrelated to the initial test request. We present recommendations for consideration when developing laboratory policies.
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Affiliation(s)
- Emma Tudini
- Australian Genomics Health Alliance, Parkville, Victoria, Australia.,Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Matilda A Haas
- Australian Genomics Health Alliance, Parkville, Victoria, Australia .,Genetics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Tessa Mattiske
- Australian Genomics Health Alliance, Parkville, Victoria, Australia.,Genetics, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Amanda B Spurdle
- Population Health, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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34
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Hernandez-Pacheco N, Melén E. Unraveling the genetic architecture of asthma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1257. [PMID: 36618807 PMCID: PMC9816849 DOI: 10.21037/atm-22-5375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Natalia Hernandez-Pacheco
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden;,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden;,Sachs’ Children’s Hospital, South General Hospital, Stockholm, Sweden
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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. Response to Grosse and Gudgeon. Genet Med 2022; 24:2597-2598. [PMID: 36166002 DOI: 10.1016/j.gim.2022.08.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA.
| | - Xue Feng
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Marlena Keisler
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Joshua T Cohen
- Center for the Evaluation of Value and Risk in Health, Tufts Medical Center, Boston, MA
| | - Peter J Neumann
- Center for the Evaluation of Value and Risk in Health, 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, Tufts Medical Center, Boston, MA
| | - Jill L Maron
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI
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36
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Rendtorff ND, Karstensen HG, Lodahl M, Tolmie J, McWilliam C, Bak M, Tommerup N, Nazaryan-Petersen L, Kunst H, Wong M, Joss S, Carelli V, Tranebjærg L. Identification and analysis of deletion breakpoints in four Mohr-Tranebjærg syndrome (MTS) patients. Sci Rep 2022; 12:14959. [PMID: 36056138 PMCID: PMC9440042 DOI: 10.1038/s41598-022-18040-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
Mohr-Tranebjærg syndrome is an X-linked syndrome characterized by sensorineural hearing impairment in childhood, followed by progressive neurodegeneration leading to a broad phenotypic spectrum. Genetically MTS is caused by pathogenic variants in the TIMM8A gene, including gene deletions and larger contiguous gene deletions. Some of the latter involve the neighboring gene BTK, resulting in agammaglobulinemia. By next-generation mate-pair sequencing we have mapped the chromosomal deletion breakpoints of one MTS case and three XLA-MTS cases and used breakpoint-spanning PCR to fine map the breakpoints by Sanger sequencing. Two of the XLA-MTS cases presented with large deletions (63.5 and 27.2 kb), and the junctional regions were characterized by long stretches of microhomology, indicating that the events have emerged through homologous recombination. Conversely, the MTS case exhibited a small 2 bp region of microhomology, and the regions were not characterized by extensive microhomology. The third XLA-MTS case had a more complex breakpoint, including a 59 bp inverted insertion, thus at least four breakpoints were involved in this event. In conclusion, mate-pair library generation combined with next-generation sequencing is an efficient method for breakpoint identification, also in regions characterized by repetitive elements.
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Affiliation(s)
- Nanna Dahl Rendtorff
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Helena Gásdal Karstensen
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Lodahl
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - John Tolmie
- Clinical Genetics Service, Laboratory Medicine Building, Southern General Hospital, Glasgow, Scotland
| | - Catherine McWilliam
- Clinical Genetics, Human Genetics Unit, Ninewells Hospital, Dundee, Scotland
| | - Mads Bak
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Tommerup
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Wilhelm Johannsen Center for Functional Genome Research, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Henricus Kunst
- Department of Otorhinolaryngology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Melanie Wong
- Department of Allergy and Immunology, The Children's Hospital at Westmead, Sydney, Australia
| | - Shelagh Joss
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Lisbeth Tranebjærg
- Department of Clinical Genetics, Center of Diagnostics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
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McNeill A. Guidelines, guidelines everywhere-and still I'm not sure what to do. Eur J Hum Genet 2022; 30:989-990. [PMID: 36050495 PMCID: PMC9437043 DOI: 10.1038/s41431-022-01167-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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38
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Making Sure That Orphan Incentives Tip the Right Way in Europe. Healthcare (Basel) 2022; 10:healthcare10091600. [PMID: 36141212 PMCID: PMC9498781 DOI: 10.3390/healthcare10091600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 12/03/2022] Open
Abstract
The delicate balance of funding research and development of treatments for rare disease is only imperfectly achieved in Europe, and even the current provisional equilibrium is under a new threat from well-intentioned policy changes now in prospect that could—in addition to the intrinsic complexities of research—reduce the incentives on which commercial activity in this area is dependent. The European Union review of its pharmaceutical legislation, for which proposals are scheduled to appear before the end of 2022, envisages adjusting the decade-old incentives to meet objectives that are more precisely targeted. However, researchers, physicians, patients and industry have expressed concerns that ill-considered modifications could have unintended consequences in disrupting the current balance and could reduce rather than increase the flow of innovative treatments for rare diseases.
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Characterization of Novel Pathogenic Variants Leading to Caspase-8 Cleavage-Resistant RIPK1-Induced Autoinflammatory Syndrome. J Clin Immunol 2022; 42:1421-1432. [PMID: 35716229 PMCID: PMC9674708 DOI: 10.1007/s10875-022-01298-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Pathogenic RIPK1 variants have been described as the cause of two different inborn errors of immunity. Biallelic loss-of-function variants cause the recessively inherited RIPK1 deficiency, while monoallelic variants impairing the caspase-8-mediated RIPK1 cleavage provoke a novel autoinflammatory disease (AID) called cleavage-resistant RIPK1-induced autoinflammatory (CRIA) syndrome. The aim of this study was to characterize the pathogenicity of two novel RIPK1 variants located at the cleavage site of caspase-8 detected in patients with dominantly-inherited, early-onset undefined AID. RIPK1 genotyping was performed by Sanger and next-generation sequencing. Clinical and analytical data were collected from medical charts, and in silico and in vitro assays were performed to evaluate the functional consequences. Genetic analyses identified two novel heterozygous RIPK1 variants at the caspase-8 cleavage site (p.Leu321Arg and p.Asp324Gly), which displayed a perfect intrafamilial phenotype-genotype segregation following a dominant inheritance pattern. Structural analyses suggested that these variants disrupt the normal RIPK1 structure, probably making it less accessible to and/or less cleavable by caspase-8. In vitro experiments confirmed that the p.Leu321Arg and p.Asp324Gly RIPK1 variants were resistant to caspase-8-mediated cleavage and induced a constitutive activation of necroptotic pathway in a similar manner that previously characterized RIPK1 variants causing CRIA syndrome. All these results strongly supported the pathogenicity of the two novel RIPK1 variants and the diagnosis of CRIA syndrome in all enrolled patients. Moreover, the evidences here collected expand the phenotypic and genetic diversity of this recently described AID, and provide interesting data about effectiveness of treatments that may benefit future patients.
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40
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McNeill A. What's new in genetics in June 2022? Eur J Hum Genet 2022; 30:633-634. [PMID: 35676534 DOI: 10.1038/s41431-022-01122-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK. .,Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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