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Kraemer D, Terumalai D, Famiglietti ML, Filges I, Joset P, Koller S, Maurer F, Meier S, Nouspikel T, Sanz J, Zweier C, Abramowicz M, Berger W, Cichon S, Schaller A, Superti-Furga A, Barbié V, Rauch A. SwissGenVar: A Platform for Clinical-Grade Interpretation of Genetic Variants to Foster Personalized Healthcare in Switzerland. J Pers Med 2024; 14:648. [PMID: 38929869 PMCID: PMC11204794 DOI: 10.3390/jpm14060648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Large-scale next-generation sequencing (NGS) germline testing is technically feasible today, but variant interpretation represents a major bottleneck in analysis workflows. This includes extensive variant prioritization, annotation, and time-consuming evidence curation. The scale of the interpretation problem is massive, and variants of uncertain significance (VUSs) are a challenge to personalized medicine. This challenge is further compounded by the complexity and heterogeneity of the standards used to describe genetic variants and the associated phenotypes when searching for relevant information to support clinical decision making. To address this, all five Swiss academic institutions for Medical Genetics joined forces with the Swiss Institute of Bioinformatics (SIB) to create SwissGenVar as a user-friendly nationwide repository and sharing platform for genetic variant data generated during routine diagnostic procedures and research sequencing projects. Its aim is to provide a protected environment for expert evidence sharing about individual variants to harmonize and upscale their significance interpretation at the clinical grade according to international standards. To corroborate the clinical assessment, the variant-related data will be combined with consented high-quality clinical information. Broader visibility will be achieved by interfacing with international databases, thus supporting global initiatives in personalized healthcare.
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Affiliation(s)
- Dennis Kraemer
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
| | - Dillenn Terumalai
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | | | - Isabel Filges
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Pascal Joset
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
| | - Fabienne Maurer
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Stéphanie Meier
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - Thierry Nouspikel
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Javier Sanz
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Marc Abramowicz
- Genetic Medicine Division, Diagnostics Department/Center for Genomic Medicine, Geneva University Hospitals (HUG), 1206 Geneva, Switzerland; (T.N.); (M.A.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics (IMMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland; (S.K.); (W.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, CH-8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, CH-8057 Zurich, Switzerland
| | - Sven Cichon
- Medical Genetics, Institute of Medical Genetics and Pathology, University Hospital Basel and University of Basel, CH-4031 Basel, Switzerland; (I.F.); (P.J.); (S.M.); (S.C.)
| | - André Schaller
- Department of Human Genetics, Inselspital, Bern University Hospital, CH-3010 Bern, Switzerland; (J.S.); (C.Z.); (A.S.)
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), CH-1011 Lausanne, Switzerland; (F.M.); (A.S.-F.)
| | - Valérie Barbié
- Swiss Institute of Bioinformatics (SIB), Clinical Bioinformatics, CH-1202 Geneva, Switzerland; (D.T.); (V.B.)
| | - Anita Rauch
- Institute of Medical Genetics (IMG), University of Zurich (UZH), Wagistrasse 12, CH-8952 Zurich, Switzerland;
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Lankhuijzen LM, Ridler T. Opioids, microglia, and temporal lobe epilepsy. Front Neurol 2024; 14:1298489. [PMID: 38249734 PMCID: PMC10796828 DOI: 10.3389/fneur.2023.1298489] [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: 09/21/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
A lack of treatment options for temporal lobe epilepsy (TLE) demands an urgent quest for new therapies to recover neuronal damage and reduce seizures, potentially interrupting the neurotoxic cascades that fuel hyper-excitability. Endogenous opioids, along with their respective receptors, particularly dynorphin and kappa-opioid-receptor, present as attractive candidates for controlling neuronal excitability and therapeutics in epilepsy. We perform a critical review of the literature to evaluate the role of opioids in modulating microglial function and morphology in epilepsy. We find that, in accordance with anticonvulsant effects, acute opioid receptor activation has unique abilities to modulate microglial activation through toll-like 4 receptors, regulating downstream secretion of cytokines. Abnormal activation of microglia is a dominant feature of neuroinflammation, and inflammatory cytokines are found to aggravate TLE, inspiring the challenge to alter microglial activation by opioids to suppress seizures. We further evaluate how opioids can modulate microglial activation in epilepsy to enhance neuroprotection and reduce seizures. With controlled application, opioids may interrupt inflammatory cycles in epilepsy, to protect neuronal function and reduce seizures. Research on opioid-microglia interactions has important implications for epilepsy and healthcare approaches. However, preclinical research on opioid modulation of microglia supports a new therapeutic pathway for TLE.
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Affiliation(s)
| | - Thomas Ridler
- Hatherly Laboratories, Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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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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