Whole-genome sequencing of a sporadic primary immunodeficiency cohort.

Autor: Thaventhiran JED; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK. jedt2@cam.ac.uk.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK. jedt2@cam.ac.uk.; Medical Research Council Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge, UK. jedt2@cam.ac.uk., Lango Allen H; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.; Medical Research Council Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK., Burren OS; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK., Rae W; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK., Greene D; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.; Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK., Staples E; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK., Zhang Z; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; Molecular Development of the Immune System Section, Laboratory of Immune System Biology and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA., Farmery JHR; Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK., Simeoni I; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Rivers E; UCL Great Ormond Street Institute of Child Health, London, UK.; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK., Maimaris J; UCL Great Ormond Street Institute of Child Health, London, UK.; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK., Penkett CJ; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Stephens J; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Deevi SVV; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Sanchis-Juan A; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Gleadall NS; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK., Thomas MJ; Department of Immunology, Queen Elizabeth University Hospital, Glasgow, UK.; Gartnavel General Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK., Sargur RB; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.; Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK., Gordins P; East Yorkshire Regional Adult Immunology and Allergy Unit, Hull Royal Infirmary, Hull and East Yorkshire Hospitals NHS Trust, Hull, UK., Baxendale HE; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK., Brown M; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Tuijnenburg P; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam, The Netherlands.; Department of Experimental Immunology, Amsterdam University Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands., Worth A; UCL Great Ormond Street Institute of Child Health, London, UK.; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK., Hanson S; Institute of Immunity and Transplantation, University College London, London, UK.; Department of Immunology, Royal Free London NHS Foundation Trust, London, UK., Linger RJ; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK., Buckland MS; Institute of Immunity and Transplantation, University College London, London, UK.; Department of Immunology, Royal Free London NHS Foundation Trust, London, UK., Rayner-Matthews PJ; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Gilmour KC; UCL Great Ormond Street Institute of Child Health, London, UK.; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK., Samarghitean C; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Seneviratne SL; Institute of Immunity and Transplantation, University College London, London, UK.; Department of Immunology, Royal Free London NHS Foundation Trust, London, UK., Sansom DM; Institute of Immunity and Transplantation, University College London, London, UK.; Department of Immunology, Royal Free London NHS Foundation Trust, London, UK., Lynch AG; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.; School of Mathematics and Statistics, University of St Andrews, St Andrews, UK.; School of Medicine, University of St Andrews, St Andrews, UK., Megy K; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Ellinghaus E; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway., Ellinghaus D; Department of Transplantation, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway.; Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany., Jorgensen SF; Section of Clinical Immunology and Infectious Diseases, Department of Rheumatology, Dermatology and Infectious Diseases, Oslo University Hospital, Oslo, Norway.; Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway., Karlsen TH; K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Oslo, Norway., Stirrups KE; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Cutler AJ; JDRF/Wellcome Diabetes and Inflammation Laboratory, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK., Kumararatne DS; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Chandra A; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK., Edgar JDM; St James's Hospital, Dublin, Ireland.; Trinity College Dublin, Dublin, Ireland., Herwadkar A; Salford Royal NHS Foundation Trust, Salford, UK., Cooper N; Department of Medicine, Imperial College London, London, UK., Grigoriadou S; Barts Health NHS Foundation Trust, London, UK., Huissoon AP; West Midlands Immunodeficiency Centre, University Hospitals Birmingham, Birmingham, UK.; Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK., Goddard S; University Hospitals of North Midlands NHS Trust, Stoke-on-Trent, UK., Jolles S; Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, UK., Schuetz C; Department of Pediatric Immunology, University Hospital Carl Gustav Carus, Dresden, Germany., Boschann F; Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany., Lyons PA; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK., Hurles ME; Department of Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Savic S; Department of Clinical Immunology and Allergy, St James's University Hospital, Leeds, UK.; The NIHR Leeds Biomedical Research Centre, Leeds, UK.; Leeds Institute of Rheumatic and Musculoskeletal Medicine, Leeds, UK., Burns SO; Institute of Immunity and Transplantation, University College London, London, UK.; Department of Immunology, Royal Free London NHS Foundation Trust, London, UK., Kuijpers TW; Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam, The Netherlands.; Department of Experimental Immunology, Amsterdam University Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands.; Department of Blood Cell Research, Sanquin, Amsterdam, The Netherlands., Turro E; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.; Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK., Ouwehand WH; Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.; NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK.; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK., Thrasher AJ; UCL Great Ormond Street Institute of Child Health, London, UK.; Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK., Smith KGC; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK. kgcs2@cam.ac.uk.; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK. kgcs2@cam.ac.uk.
Jazyk: angličtina
Zdroj: Nature [Nature] 2020 Jul; Vol. 583 (7814), pp. 90-95. Date of Electronic Publication: 2020 May 06.
DOI: 10.1038/s41586-020-2265-1
Abstrakt: Primary immunodeficiency (PID) is characterized by recurrent and often life-threatening infections, autoimmunity and cancer, and it poses major diagnostic and therapeutic challenges. Although the most severe forms of PID are identified in early childhood, most patients present in adulthood, typically with no apparent family history and a variable clinical phenotype of widespread immune dysregulation: about 25% of patients have autoimmune disease, allergy is prevalent and up to 10% develop lymphoid malignancies 1-3 . Consequently, in sporadic (or non-familial) PID genetic diagnosis is difficult and the role of genetics is not well defined. Here we address these challenges by performing whole-genome sequencing in a large PID cohort of 1,318 participants. An analysis of the coding regions of the genome in 886 index cases of PID found that disease-causing mutations in known genes that are implicated in monogenic PID occurred in 10.3% of these patients, and a Bayesian approach (BeviMed 4 ) identified multiple new candidate PID-associated genes, including IVNS1ABP. We also examined the noncoding genome, and found deletions in regulatory regions that contribute to disease causation. In addition, we used a genome-wide association study to identify loci that are associated with PID, and found evidence for the colocalization of-and interplay between-novel high-penetrance monogenic variants and common variants (at the PTPN2 and SOCS1 loci). This begins to explain the contribution of common variants to the variable penetrance and phenotypic complexity that are observed in PID. Thus, using a cohort-based whole-genome-sequencing approach in the diagnosis of PID can increase diagnostic yield and further our understanding of the key pathways that influence immune responsiveness in humans.
Databáze: MEDLINE