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Bousfiha A, Moundir A, Tangye SG, Picard C, Jeddane L, Al-Herz W, Rundles CC, Franco JL, Holland SM, Klein C, Morio T, Oksenhendler E, Puel A, Puck J, Seppänen MRJ, Somech R, Su HC, Sullivan KE, Torgerson TR, Meyts I. The 2022 Update of IUIS Phenotypical Classification for Human Inborn Errors of Immunity. J Clin Immunol 2022. [PMID: 36198931 DOI: 10.1007/s10875-022-01352-z] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/14/2022] [Indexed: 10/10/2022]
Abstract
The International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) reports here the 2022 updated phenotypic classification, which accompanies and complements the most-recent genotypic classification. This phenotypic classification is aimed for clinicians at the bedside and focuses on clinical features and laboratory phenotypes of specific IEI. In this classification, 485 IEI underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity and auto-inflammation are described, including 55 novel monogenic defects and 1 autoimmune phenocopy. Therefore, all 485 diseases of the genetic classification are presented in this paper in the form of colored tables with essential clinical or immunological phenotype entries.
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Bousfiha A, Jeddane L, Picard C, Al-Herz W, Ailal F, Chatila T, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Puck J, Torgerson TR, Casanova JL, Sullivan KE, Tangye SG. Human Inborn Errors of Immunity: 2019 Update of the IUIS Phenotypical Classification. J Clin Immunol 2020; 40:66-81. [PMID: 32048120 DOI: 10.1007/s10875-020-00758-x] [Citation(s) in RCA: 423] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/22/2020] [Indexed: 02/06/2023]
Abstract
Since 2013, the International Union of Immunological Societies (IUIS) expert committee (EC) on Inborn Errors of Immunity (IEI) has published an updated phenotypic classification of IEI, which accompanies and complements their genotypic classification into ten tables. This phenotypic classification is user-friendly and serves as a resource for clinicians at the bedside. There are now 430 single-gene IEI underlying phenotypes as diverse as infection, malignancy, allergy, autoimmunity, and autoinflammation. We herein report the 2019 phenotypic classification, including the 65 new conditions. The diagnostic algorithms are based on clinical and laboratory phenotypes for each of the ten broad categories of IEI.
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Tangye SG, Al-Herz W, Bousfiha A, Chatila T, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Picard C, Puck J, Torgerson TR, Casanova JL, Sullivan KE. Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol 2020; 40:24-64. [PMID: 31953710 PMCID: PMC7082301 DOI: 10.1007/s10875-019-00737-x] [Citation(s) in RCA: 684] [Impact Index Per Article: 171.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/18/2019] [Indexed: 12/26/2022]
Abstract
We report the updated classification of Inborn Errors of Immunity/Primary Immunodeficiencies, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 430 inborn errors of immunity, including 64 gene defects that have either been discovered in the past 2 years since the previous update (published January 2018) or were characterized earlier but have since been confirmed or expanded upon in subsequent studies. The application of next-generation sequencing continues to expedite the rapid identification of novel gene defects, rare or common; broaden the immunological and clinical phenotypes of conditions arising from known gene defects and even known variants; and implement gene-specific therapies. These advances are contributing to greater understanding of the molecular, cellular, and immunological mechanisms of disease, thereby enhancing immunological knowledge while improving the management of patients and their families. This report serves as a valuable resource for the molecular diagnosis of individuals with heritable immunological disorders and also for the scientific dissection of cellular and molecular mechanisms underlying inborn errors of immunity and related human diseases.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
- Faculty of Medicine, St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Aziz Bousfiha
- King Hassan II University, Laboratoire d'Immunologie Clinique, d'Inflammation et d'Allergy LICIA at Faculty of Medicine and Pharmacy, Clinical Immunology Unit, Pediatric Infectiouse Disease Department, Children's Hospital, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Talal Chatila
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | | | - Amos Etzioni
- Ruth's Children's Hospital-Technion, Haifa, Israel
| | - Jose Luis Franco
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Steven M Holland
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Klein
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hans D Ochs
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, APHP, University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, APHP, Paris, France
- Paris University, Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris University, Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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Abstract
One of the mandates of the International Union of Immunological Societies (IUIS) is to promote immunological education to young scientists across the globe, including a large focus on those from low and low-to-middle income countries (LIC and LMIC). It strives to achieve this goal through the Education Committee (EDU), which is one of ten committees of the IUIS. To this end, EDU organizes three to four one-week courses per year in close cooperation with regional immunological societies and local organizers. Initially, the focus has been on Africa, addressing the most relevant topics and health issues facing specific countries or regions in the continent. The idea was then extended to Latin America and now also includes courses in Asia. The faculty of all courses is a blend of international and local/regional experts also known for their teaching expertise. The courses are highly interactive, and include “meet-the-speakers” sessions, poster walks, and sessions on grant or PhD project writing, and on practical aspects of becoming a successful scientist. Importantly, all the IUIS-EDU courses use a combination of pre- and during-course on-line learning followed by consolidation of knowledge in a collegial setting. This “flipped” classroom approach ensures that participants have acquired the basic knowledge needed to optimize their participation in the course. Immunopaedia is the IUIS-endorsed immunology learning site used for this purpose. All faculty members are requested to contribute material related to their specific topic while students must learn the on-line material before coming in person to the course. All course participants have free access to all Immunopaedia material indefinitely. The implementation of regional immunology courses targeted to local health issues in areas of the world where PhD students, post-doctoral, and early career scientists often do not have access to open on-line resources and contact with renowned experts in the field has proven to be highly successful. The long-term impact of this structured educational program is already visible through the large number of young scientists who are now connected via Immunopaedia and who are forming networks in regions where there had been very little contact before and building new Immunological Societies.
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Affiliation(s)
- Dieter Kabelitz
- Institute of Immunology, University of Kiel, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Michelle Letarte
- Department of Immunology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
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Bousfiha A, Jeddane L, Picard C, Ailal F, Bobby Gaspar H, Al-Herz W, Chatila T, Crow YJ, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Puck J, Tang MLK, Tangye SG, Torgerson TR, Casanova JL, Sullivan KE. The 2017 IUIS Phenotypic Classification for Primary Immunodeficiencies. J Clin Immunol 2017; 38:129-143. [PMID: 29226301 PMCID: PMC5742599 DOI: 10.1007/s10875-017-0465-8] [Citation(s) in RCA: 366] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/31/2017] [Indexed: 01/13/2023]
Abstract
Since the 1990s, the International Union of Immunological Societies (IUIS) PID expert committee (EC), now called Inborn Errors of Immunity Committee, has published every other year a classification of the inborn errors of immunity. This complete catalog serves as a reference for immunologists and researchers worldwide. However, it was unadapted for clinicians at the bedside. For those, the IUIS PID EC is now publishing a phenotypical classification since 2013, which proved to be more user-friendly. There are now 320 single-gene inborn errors of immunity underlying phenotypes as diverse as infection, malignancy, allergy, auto-immunity, and auto-inflammation. We herein propose the revised 2017 phenotypic classification, based on the accompanying 2017 IUIS Inborn Errors of Immunity Committee classification.
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Affiliation(s)
- Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy LICIA, Faculty of Medicine and Pharmacy, King Hassan II University, Casablanca, Morocco.
| | - Leïla Jeddane
- Laboratory of Clinical Immunology, Inflammation and Allergy LICIA, Faculty of Medicine and Pharmacy, King Hassan II University, Casablanca, Morocco
- Laboratoire National de Référence, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Capucine Picard
- Center for the Study of Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris(APHP), Paris, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris Descartes University, Paris, France
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy LICIA, Faculty of Medicine and Pharmacy, King Hassan II University, Casablanca, Morocco
| | - H Bobby Gaspar
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Talal Chatila
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | - Yanick J Crow
- Laboratory of Neuroinflammation and Neurogenetics, Necker Branch, INSERM UMR1163, Sorbonne-Paris-Cité, Institut Imagine, Paris Descartes University, Paris, France
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | | | - Amos Etzioni
- Ruth's Children's Hospital-Technion, Haifa, Israel
| | - Jose Luis Franco
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Christoph Klein
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hans D Ochs
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Mimi L K Tang
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
- Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, University Paris Descartes, Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children APHP, Paris, France
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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Picard C, Bobby Gaspar H, Al-Herz W, Bousfiha A, Casanova JL, Chatila T, Crow YJ, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Puck J, Tang MLK, Tangye SG, Torgerson TR, Sullivan KE. International Union of Immunological Societies: 2017 Primary Immunodeficiency Diseases Committee Report on Inborn Errors of Immunity. J Clin Immunol 2017; 38:96-128. [PMID: 29226302 PMCID: PMC5742601 DOI: 10.1007/s10875-017-0464-9] [Citation(s) in RCA: 526] [Impact Index Per Article: 75.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022]
Abstract
Beginning in 1970, a committee was constituted under the auspices of the World Health Organization (WHO) to catalog primary immunodeficiencies. Twenty years later, the International Union of Immunological Societies (IUIS) took the remit of this committee. The current report details the categorization and listing of 354 (as of February 2017) inborn errors of immunity. The growth and increasing complexity of the field have been impressive, encompassing an increasing variety of conditions, and the classification described here will serve as a critical reference for immunologists and researchers worldwide.
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Affiliation(s)
- Capucine Picard
- Center for the Study of Immunodeficiencies, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France.,Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris Descartes University, Paris, France
| | - H Bobby Gaspar
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Aziz Bousfiha
- Laboratoire d'Immunologie Clinique, d'Inflammation et d'Allergy LICIA Clinical Immunology Unit, Casablanca Children's Hospital, Ibn Rochd Medical School, King Hassan II University, Casablanca, Morocco
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, University Paris Descartes, Paris, France.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children APHP, Paris, France
| | - Talal Chatila
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | - Yanick J Crow
- Laboratory of Neuroinflammation and Neurogenetics, Necker Branch, INSERM UMR1163, Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Amos Etzioni
- Ruth's Children's Hospital-Technion, Haifa, Israel
| | - Jose Luis Franco
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Christoph Klein
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hans D Ochs
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Mimi L K Tang
- Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia.,Department of Allergy and Immunology, Royal Children's Hospital, Melbourne, Australia
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, ARC 1216-I 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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7
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Al-Herz W, Bousfiha A, Casanova JL, Chatila T, Conley ME, Cunningham-Rundles C, Etzioni A, Franco JL, Gaspar HB, Holland SM, Klein C, Nonoyama S, Ochs HD, Oksenhendler E, Picard C, Puck JM, Sullivan K, Tang MLK. Primary immunodeficiency diseases: an update on the classification from the international union of immunological societies expert committee for primary immunodeficiency. Front Immunol 2014; 5:162. [PMID: 24795713 PMCID: PMC4001072 DOI: 10.3389/fimmu.2014.00162] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
We report the updated classification of primary immunodeficiencies (PIDs) compiled by the Expert Committee of the International Union of Immunological Societies. In comparison to the previous version, more than 30 new gene defects are reported in this updated version. In addition, we have added a table of acquired defects that are phenocopies of PIDs. For each disorder, the key clinical and laboratory features are provided. This classification is the most up-to-date catalog of all known PIDs and acts as a current reference of the knowledge of these conditions and is an important aid for the molecular diagnosis of patients with these rare diseases.
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Affiliation(s)
- Waleed Al-Herz
- Department of Pediatrics, Kuwait University , Kuwait City , Kuwait ; Allergy and Clinical Immunology Unit, Department of Pediatrics, Al-Sabah Hospital , Kuwait City , Kuwait
| | - Aziz Bousfiha
- Clinical Immunology Unit, Casablanca Children's Hospital, Ibn Rochd Medical School, King Hassan II University , Casablanca , Morocco
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University , New York, NY , USA ; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institut, Necker Medical School, University Paris Descartes , Paris , France
| | - Talal Chatila
- Division of Immunology, Children's Hospital Boston , Boston, MA , USA
| | - Mary Ellen Conley
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University , New York, NY , USA
| | | | - Amos Etzioni
- Meyer Children's Hospital-Technion , Haifa , Israel
| | - Jose Luis Franco
- Group of Primary Immunodeficiencies, University of Antioquia , Medellin , Colombia
| | | | - Steven M Holland
- Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases , Bethesda, MD , USA
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University Munich , Munich , Germany
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College , Saitama , Japan
| | - Hans D Ochs
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington , Seattle, WA , USA
| | - Erik Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris , Paris , France ; Sorbonne Paris Cité, Université Paris Diderot , Paris , France
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institut, Necker Medical School, University Paris Descartes , Paris , France ; Centre d'Étude des Déficits Immunitaires (CEDI), Hôpital Necker-Enfants Malades, AP-HP , Paris , France
| | - Jennifer M Puck
- Department of Pediatrics, UCSF Benioff Children's Hospital, University of California San Francisco , San Francisco, CA , USA
| | - Kate Sullivan
- Department of Pediatrics, Division of Allergy Immunology, The Children's Hospital of Philadelphia , Philadelphia, PA , USA
| | - Mimi L K Tang
- Murdoch Childrens Research Institute , Melbourne, VIC , Australia ; Department of Paediatrics, University of Melbourne , Melbourne, VIC , Australia ; Department of Allergy and Immunology, Royal Children's Hospital , Melbourne, VIC , Australia
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Nijman IJ, van Montfrans JM, Hoogstraat M, Boes ML, van de Corput L, Renner ED, van Zon P, van Lieshout S, Elferink MG, van der Burg M, Vermont CL, van der Zwaag B, Janson E, Cuppen E, Ploos van Amstel JK, van Gijn ME. Targeted next-generation sequencing: a novel diagnostic tool for primary immunodeficiencies. J Allergy Clin Immunol 2013; 133:529-34. [PMID: 24139496 DOI: 10.1016/j.jaci.2013.08.032] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/04/2013] [Accepted: 08/26/2013] [Indexed: 12/18/2022]
Abstract
BACKGROUND Primary immunodeficiency (PID) disorders are a heterogeneous group of inherited disorders caused by a variety of monogenetic immune defects. Thus far, mutations in more than 170 different genes causing PIDs have been described. A clear genotype-phenotype correlation is often not available, which makes a genetic diagnosis in patients with PIDs complex and laborious. OBJECTIVE We sought to develop a robust, time-effective, and cost-effective diagnostic method to facilitate a genetic diagnosis in any of 170 known PID-related genes by using next-generation sequencing (NGS). METHODS We used both targeted array-based and in-solution enrichment combined with a SOLiD sequencing platform and a bioinformatic pipeline developed in house to analyze genetic changes in the DNA of 41 patients with PIDs with known mutations and 26 patients with undiagnosed PIDs. RESULTS This novel NGS-based method accurately detected point mutations (sensitivity and specificity >99% in covered regions) and exonic deletions (100% sensitivity and specificity). For the 170 genes of interest, the DNA coverage was greater than 20× in 90% to 95%. Nine PID-related genes proved not eligible for evaluation by using this NGS-based method because of inadequate coverage. The NGS method allowed us to make a genetic diagnosis in 4 of 26 patients who lacked a genetic diagnosis despite routine functional and genetic testing. Three of these patients proved to have an atypical presentation of previously described PIDs. CONCLUSION This novel NGS tool facilitates accurate simultaneous detection of mutations in 161 of 170 known PID-related genes. In addition, these analyses will generate more insight into genotype-phenotype correlations for the different PID disorders.
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Affiliation(s)
- Isaac J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marlous Hoogstraat
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marianne L Boes
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lisette van de Corput
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen D Renner
- Department of Immunology, University Children's Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Patrick van Zon
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stef van Lieshout
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martin G Elferink
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Clementien L Vermont
- Department of Pediatric Infectious Diseases, Immunology and Stem Cell Transplantation, Leiden University Medical Center, Leiden, The Netherlands
| | - Bert van der Zwaag
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Esther Janson
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Edwin Cuppen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Marielle E van Gijn
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands.
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Kulkarni A, Ananthanarayan L, Raman K. Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. Comput Biol Chem 2013; 47:149-55. [PMID: 24099701 DOI: 10.1016/j.compbiolchem.2013.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Revised: 07/11/2013] [Accepted: 08/12/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND Allergy has become a key cause of morbidity worldwide. Although many legumes (plants in the Fabaceae family) are healthy foods, they may have a number of allergenic proteins. A number of allergens have been identified and characterized in Fabaceae family, such as soybean and peanut, on the basis of biochemical and molecular biological approaches. However, our understanding of the allergens from chickpea (Cicer arietinum L.), belonging to this family, is very limited. OBJECTIVE In this study, we aimed to identify putative and cross-reactive allergens from Chickpea (C. arietinum) by means of in silico analysis of the chickpea protein sequences and allergens sequences from Fabaceae family. METHODS We retrieved known allergen sequences in Fabaceae family from the IUIS Allergen Nomenclature Database. We performed a protein BLAST (BLASTp) on these sequences to retrieve the similar sequences from chickpea. We further analyzed the retrieved chickpea sequences using a combination of in silico tools, to assess them for their allergenicity potential. Following this, we built structure models using FUGUE: Sequence-structure homology; these models generated by the recognition tool were viewed in Swiss-PDB viewer. RESULTS Through this in silico approach, we identified seven novel putative allergens from chickpea proteome sequences on the basis of similarity of sequence, structure and physicochemical properties with the known reported legume allergens. Four out of seven putative allergens may also show cross reactivity with reported allergens since potential allergens had common sequence and structural features with the reported allergens. CONCLUSION The in silico proteomic identification of the allergen proteins in chickpea provides a basis for future research on developing hypoallergenic foods containing chickpea. Such bioinformatics approaches, combined with experimental methodology, will help delineate an efficient and comprehensive approach to assess allergenicity and pave the way for a better understanding of the biological and medical basis of the same.
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Affiliation(s)
- Anuja Kulkarni
- Food Engineering & Technology Department, Institute of Chemical Technology, Mumbai, India(1)
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