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Vorsteveld EE, Van der Made CI, Smeekens SP, Schuurs-Hoeijmakers JH, Astuti G, Diepstra H, Gilissen C, Hoenselaar E, Janssen A, van Roozendaal K, Engelen JSV, Steyaert W, Weiss MM, Yntema HG, Mantere T, AlZahrani MS, van Aerde K, Derfalvi B, Faqeih EA, Henriet SSV, van Hoof E, Idressi E, Issekutz TB, Jongmans MCJ, Keski-Filppula R, Krapels I, Te Loo M, Mulders-Manders CM, Ten Oever J, Potjewijd J, Sarhan NT, Slot MC, Terhal PA, Thijs H, Vandersteen A, Vanhoutte EK, van de Veerdonk F, van Well G, Netea MG, Simons A, Hoischen A, Arts RJW, Bijker EM, Bruno M, Hobo W, Hoppenreijs E, de Jonge MI, van Laarhoven A, van der Molen R, Oud M, Schatorje EJH, Smeets R, Sprenkeler EGG, Stol K, Verhagen LM, Zonneveld-Huijssoon E. Clinical exome sequencing data from patients with inborn errors of immunity: Cohort level diagnostic yield and the benefit of systematic reanalysis. Clin Immunol 2024:110375. [PMID: 39369972 DOI: 10.1016/j.clim.2024.110375] [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: 06/11/2024] [Revised: 09/25/2024] [Accepted: 09/27/2024] [Indexed: 10/08/2024]
Abstract
While next generation sequencing has expanded the scientific understanding of Inborn Errors of Immunity (IEI), the clinical use and re-use of exome sequencing is still emerging. We revisited clinical exome data from 1300 IEI patients using an updated in silico IEI gene panel. Variants were classified and curated through expert review. The molecular diagnostic yield after standard exome analysis was 11.8 %. Through systematic reanalysis, we identified variants of interest in 5.2 % of undiagnosed patients, with 76.7 % being (candidate) disease-causing, providing a (candidate) diagnosis in 15.2 % of our cohort. We find a 1.7 percentage point increase in conclusive molecular diagnoses. We find a high degree of actionability in patients with a genetic diagnosis (76.4 %). Despite the modest absolute diagnostic gain, these data support the benefit of iterative exome reanalysis in IEI patients, conveying the notion that our current understanding of genes and variants involved in IEI is by far not saturated.
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Affiliation(s)
- Emil E Vorsteveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caspar I Van der Made
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heleen Diepstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Hoenselaar
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alice Janssen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kees van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | | | - Wouter Steyaert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marjan M Weiss
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mofareh S AlZahrani
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Koen van Aerde
- Department of Paediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Beata Derfalvi
- Division of Immunology, Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Eissa Ali Faqeih
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Stefanie S V Henriet
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Pediatric Infectious Diseases and Immunology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elise van Hoof
- Department of Rheumatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eman Idressi
- Department of Pediatrics, Children's specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Marjolijn C J Jongmans
- Princess Máxima Center for Pediatric Oncology and Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Riikka Keski-Filppula
- PEDEGO Research Unit, University of Oulu, Oulu, Finland; Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland; Medical Research Center Oulu, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Ingrid Krapels
- Department of Clinical Genetics, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Maroeska Te Loo
- Department of Pediatric Hematology, Amalia children's hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Catharina M Mulders-Manders
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Ten Oever
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Judith Potjewijd
- Department of Internal Medicine, Division of Experimental and Clinical Immunology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Nora Tarig Sarhan
- Section of Medical Genetics, Children's Specialist Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Marjan C Slot
- Department of Allergology and Clinical Immunology, Maastricht UMC+, Maastricht, The Netherlands
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Herman Thijs
- Department of Pediatrics, Gelre Ziekenhuizen Zutphen, The Netherlands
| | - Anthony Vandersteen
- Division of Medical Genetics, Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada; Maritime Medical Genetics Service, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Els K Vanhoutte
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Frank van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Gijs van Well
- Department of Paediatrics, Maastricht University Medical Center, MosaKids Children's Hospital, Maastricht, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Annet Simons
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Rob J W Arts
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Else M Bijker
- Department of Paediatrics, Maastricht University Medical Center, MosaKids Children's Hospital, Maastricht, The Netherlands; Department of Paediatrics, Oxford Vaccine Group, University of Oxford, Oxford, UK
| | - Mariolina Bruno
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willemijn Hobo
- RadboudUMC Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Esther Hoppenreijs
- Department of Pediatric Rheumatology and Immunology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marien I de Jonge
- Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands; Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Renate van der Molen
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Manon Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen J H Schatorje
- Department of Pediatric Rheumatology and Immunology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ruben Smeets
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien G G Sprenkeler
- Department of Laboratory Medicine, Laboratory of Medical Immunology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kim Stol
- Department of Paediatrics, Amalia Children's Hospital, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Lilly M Verhagen
- Radboud Centre for Infectious Diseases (RCI), Radboud University Medical Centre, Nijmegen, The Netherlands; Department of Pediatric Infectious Diseases and Immunology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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