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Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea
Britt-Sabina Petersen1, Dietrich August, Renate Abt
11Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany; 2Center for Chronic Immunodeficiency (CCI), DZIF Satellite Center, Medical Center, Faculty of Medicine, Germany; 3Paediatric Gastroenterology, Klinikum Nürnberg, Nuremberg, Germany; 4Laboratory of Applied Molecular Biology and Immunology, University of Abou-Bekr Belkaïd, Tlemcen, Algeria; 5Department of Pediatrics, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; 6Clinic of Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey; 7Department of Gastroenterology and Clinical Nutrition, Birmingham Children's Hospital, Birmingham, United Kingdom; 8Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; 9Department of Immunology, Royal Free Hospital, London, United Kingdom; 10Primary Immunodeficiencies Unit, Hospital Dona Estefania, Pediatric University Hospital, and CEDOC, Chronic Diseases Research Center, NOVA Medical School, Lisbon, Portugal; 11Department of Pediatric Gasteroentrology and Hepatology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 12Helios Kliniken, Childrens Hospital, Krefeld, Germany; 13Pediatrics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; 14Paediatric Gastroenterology/Hepatology, University of Freiburg, Freiburg, Germany; 15Institute of Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany; 16Department of Pediatrics, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 17Department of Medicine II, University Hospital and Medical Faculty, University Freiburg, Freiburg, Germany; 18Department of Paediatrics, Centre for Diagnosis and Treatment of Primary Immunodeficiencies, Jessenius Faculty of Medicine, Commenius University in Bratislava, Martin, Slovakia; 19Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey; 20Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 21Pediatric Immunology Division, Uludag University Medical Faculty, Department of Pediatrics, Bursa, Turkey; 22Dr. von Hauner Children's Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität Munich, Munich, Germany; 23Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 24Center for Pediatrics, Department of Pediatric Hematology and Oncology, University Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 25Department of Paediatric Immunology and Infectious Diseases, Our Lady's Children's Hospital, Dublin, Ireland; 26Department of Immunology, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 27Department of Paediatric Gastroenterology, St. George's Healthcare NHS Trust and University of London, London, United Kingdom; 28Department of Gastroenterology and Clinical Nutrition, Marmara University Medical Faculty, Istanbul, Turkey; 29Service of Clinical Laboratory, Division of Immunology, San Pedro De Alcántara Hospital, Cáceres, Spain; 30Bone Marrow Failure Group, Division of Pediatric Hematology and Oncology, University of Freiburg, Germany; 31Children's Hospital, University of Bonn, Germany; 32University College London Institute of Immunity and Transplantation, Royal Free Campus, London, United Kingdom; 33Department of Paediatrics, St. George's Hospital, University of London, London, United Kingdom; 34Department of Pediatrics, Universitair Ziekenhuis Brussel, Brussels, Belgium; 35Pediatric Pneumology and Immunology, Department of Immunology, Charité University Medicine Labor Berlin Charité Vivantes GmbH, Berlin, Germany; 36Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 37Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany; and 38Institute of Laboratory Medicine, Brandenburg Hospital, Brandenburg Medical School, Brandenburg/Havel, Germany.
Background:
In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients.
Methods:
We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients.
Results:
Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients.
Conclusions:
Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.
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