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Erman B, Aba U, Ipsir C, Pehlivan D, Aytekin C, Cildir G, Cicek B, Bozkurt C, Tekeoglu S, Kaya M, Aydogmus C, Cipe F, Sucak G, Eltan SB, Ozen A, Barıs S, Karakoc-Aydiner E, Kıykım A, Karaatmaca B, Kose H, Uygun DFK, Celmeli F, Arikoglu T, Ozcan D, Keskin O, Arık E, Aytekin ES, Cesur M, Kucukosmanoglu E, Kılıc M, Yuksek M, Bıcakcı Z, Esenboga S, Ayvaz DÇ, Sefer AP, Guner SN, Keles S, Reisli I, Musabak U, Demirbas ND, Haskologlu S, Kilic SS, Metin A, Dogu F, Ikinciogulları A, Tezcan I. Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye. J Clin Immunol 2024; 44:157. [PMID: 38954121 PMCID: PMC11219406 DOI: 10.1007/s10875-024-01759-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients' long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.
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Affiliation(s)
- Baran Erman
- Institute of Child Health, Hacettepe University, Ankara, Turkey.
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey.
| | - Umran Aba
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Canberk Ipsir
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Damla Pehlivan
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Caner Aytekin
- Pediatric Immunology, SBU Ankara Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gökhan Cildir
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia
| | - Begum Cicek
- Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Ceren Bozkurt
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Sidem Tekeoglu
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Melisa Kaya
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Cigdem Aydogmus
- Department of Pediatric Allergy and Clinical Immunology, University of Health Sciences, Istanbul Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Funda Cipe
- Department of Pediatric Allergy and Clinical Immunology, Altinbas University School of Medicine, Istanbul, Turkey
| | - Gulsan Sucak
- Medical Park Bahçeşehir Hospital, Clinic of Hematology and Transplantation, İstanbul, Turkey
| | - Sevgi Bilgic Eltan
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ahmet Ozen
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Safa Barıs
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ayca Kıykım
- Pediatric Allergy and Immunology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Betul Karaatmaca
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Hulya Kose
- Department of Pediatric Immunology, Diyarbakir Children Hospital, Diyarbakır, Turkey
| | - Dilara Fatma Kocacık Uygun
- Division of Allergy Immunology, Department of Pediatrics, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Fatih Celmeli
- Republic of Turkey Ministry of Health Antalya Training and Research Hospital Pediatric Immunology and Allergy Diseases, Antalya, Turkey
| | - Tugba Arikoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Dilek Ozcan
- Division of Pediatric Allergy and Immunology, Faculty of Medicine, Balcali Hospital, Cukurova University, Adana, Turkey
| | - Ozlem Keskin
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Arık
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Soyak Aytekin
- Department of Pediatric Allergy and Immunology, Etlik City Hospital, Ankara, Turkey
| | - Mahmut Cesur
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ercan Kucukosmanoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Mehmet Kılıc
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Firat, Elazığ, Turkey
| | - Mutlu Yuksek
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Zafer Bıcakcı
- Department of Pediatric Hematology, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Saliha Esenboga
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Deniz Çagdaş Ayvaz
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
- Section of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Asena Pınar Sefer
- Department of Pediatric Allergy and Immunology, Şanlıurfa Training and Research Hospital, Şanlıurfa, Turkey
| | - Sukrü Nail Guner
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sevgi Keles
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ismail Reisli
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ugur Musabak
- Department of Immunology and Allergy, Baskent University School of Medicine, Ankara, Turkey
| | - Nazlı Deveci Demirbas
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sara Sebnem Kilic
- Division of Pediatric Immunology-Rheumatology, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
- Translational Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ayse Metin
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Aydan Ikinciogulları
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ilhan Tezcan
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
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Sharma M, Suratannon N, Leung D, Baris S, Takeuchi I, Samra S, Yanagi K, Rosa Duque JS, Benamar M, Del Bel KL, Momenilandi M, Béziat V, Casanova JL, van Hagen PM, Arai K, Nomura I, Kaname T, Chatchatee P, Morita H, Chatila TA, Lau YL, Turvey SE. Human germline gain-of-function in STAT6: from severe allergic disease to lymphoma and beyond. Trends Immunol 2024; 45:138-153. [PMID: 38238227 DOI: 10.1016/j.it.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024]
Abstract
Signal transducer and activator of transcription (STAT)-6 is a transcription factor central to pro-allergic immune responses, although the function of human STAT6 at the whole-organism level has long remained unknown. Germline heterozygous gain-of-function (GOF) rare variants in STAT6 have been recently recognized to cause a broad and severe clinical phenotype of early-onset, multi-system allergic disease. Here, we provide an overview of the clinical presentation of STAT6-GOF disease, discussing how dysregulation of the STAT6 pathway causes severe allergic disease, and identifying possible targeted treatment approaches. Finally, we explore the mechanistic overlap between STAT6-GOF disease and other monogenic atopic disorders, and how this group of inborn errors of immunity (IEIs) powerfully inform our fundamental understanding of common human allergic disease.
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Jabbarpour N, Bonyadi M, Sadeghi L. A novel loss of function mutation in the PHD domain of the RAG2 gene, affecting zinc-binding affinity. Mol Biol Rep 2023; 50:8771-8775. [PMID: 37573280 DOI: 10.1007/s11033-023-08731-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 08/02/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND Severe combined immune deficiencies (SCIDs) are genetically heterogeneous disorders that lead to the absence or malfunction of adaptive immune cells, including T- and B-cells. Pathogenic variants in the RAG2 gene are associated with this disease. METHODS A couple with consanguineous marriage from the Iranian-Azeri-Turkish ethnic group was referred to the genetic lab. Two children of this family died due to SCID disease with symptoms of skin granulomas, lack of developed T- and B-cells, and intact NK cells. To infer their genotypes, DNA samples obtained from the parents were subjected to whole-exome sequencing (WES). RESULTS WES data analysis revealed that both parents were carriers of a pathogenic variant, NC_000011.10 (NM_000536.4):c.1268G > C, in the RAG2 gene. This variant was absent in our cohort of 400 healthy individuals from the same ethnic group. To gain insight into the consequence of the variant on the protein function, further analysis was performed by applying bioinformatics tools. This study revealed that the replacement of cysteine with serine at the zinc-binding domain diminished the domain's affinity to zinc ion, resulting in the loss of the mutant protein's ability to bind to the recombination signal sequence (RSS). The formation of the RAG2-RSS complex is vital for T- and B-cell development. CONCLUSION The identification of a novel pathogenic variant, c.1268G > C, revealed that this variant in the zinc-binding domain diminished the affinity of the zinc ion to the mutant protein and consequently led to the loss of its ability to bind to the RSS.
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Affiliation(s)
- Neda Jabbarpour
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mortaza Bonyadi
- Center of Excellence for Biodiversity, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.
| | - Leila Sadeghi
- Animal Biology Department, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
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4
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Mauracher AA, Henrickson SE. Leveraging Systems Immunology to Optimize Diagnosis and Treatment of Inborn Errors of Immunity. FRONTIERS IN SYSTEMS BIOLOGY 2022; 2:910243. [PMID: 37670772 PMCID: PMC10477056 DOI: 10.3389/fsysb.2022.910243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Inborn errors of immunity (IEI) are monogenic disorders that can cause diverse symptoms, including recurrent infections, autoimmunity and malignancy. While many factors have contributed, the increased availability of next-generation sequencing has been central in the remarkable increase in identification of novel monogenic IEI over the past years. Throughout this phase of disease discovery, it has also become evident that a given gene variant does not always yield a consistent phenotype, while variants in seemingly disparate genes can lead to similar clinical presentations. Thus, it is increasingly clear that the clinical phenotype of an IEI patient is not defined by genetics alone, but is also impacted by a myriad of factors. Accordingly, we need methods to amplify our current diagnostic algorithms to better understand mechanisms underlying the variability in our patients and to optimize treatment. In this review, we will explore how systems immunology can contribute to optimizing both diagnosis and treatment of IEI patients by focusing on identifying and quantifying key dysregulated pathways. To improve mechanistic understanding in IEI we must deeply evaluate our rare IEI patients using multimodal strategies, allowing both the quantification of altered immune cell subsets and their functional evaluation. By studying representative controls and patients, we can identify causative pathways underlying immune cell dysfunction and move towards functional diagnosis. Attaining this deeper understanding of IEI will require a stepwise strategy. First, we need to broadly apply these methods to IEI patients to identify patterns of dysfunction. Next, using multimodal data analysis, we can identify key dysregulated pathways. Then, we must develop a core group of simple, effective functional tests that target those pathways to increase efficiency of initial diagnostic investigations, provide evidence for therapeutic selection and contribute to the mechanistic evaluation of genetic results. This core group of simple, effective functional tests, targeting key pathways, can then be equitably provided to our rare patients. Systems biology is thus poised to reframe IEI diagnosis and therapy, fostering research today that will provide streamlined diagnosis and treatment choices for our rare and complex patients in the future, as well as providing a better understanding of basic immunology.
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Affiliation(s)
- Andrea A. Mauracher
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah E. Henrickson
- Division of Allergy and Immunology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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5
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Tangye SG, Al-Herz W, Bousfiha A, Cunningham-Rundles C, Franco JL, Holland SM, Klein C, Morio T, Oksenhendler E, Picard C, Puel A, Puck J, Seppänen MRJ, Somech R, Su HC, Sullivan KE, Torgerson TR, Meyts I. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol 2022; 42:1473-1507. [PMID: 35748970 PMCID: PMC9244088 DOI: 10.1007/s10875-022-01289-3] [Citation(s) in RCA: 449] [Impact Index Per Article: 224.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/02/2022] [Indexed: 12/19/2022]
Abstract
We report the updated classification of inborn errors of immunity, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 55 novel monogenic gene defects, and 1 phenocopy due to autoantibodies, that have either been discovered since the previous update (published January 2020) or were characterized earlier but have since been confirmed or expanded in subsequent studies. While variants in additional genes associated with immune diseases have been reported in the literature, this update includes only those that the committee assessed that reached the necessary threshold to represent novel inborn errors of immunity. There are now a total of 485 inborn errors of immunity. These advances in discovering the genetic causes of human immune diseases continue to significantly further our understanding of molecular, cellular, and immunological mechanisms of disease pathogenesis, thereby simultaneously enhancing immunological knowledge and improving patient diagnosis and management. This report is designed to serve as a resource for immunologists and geneticists pursuing the molecular diagnosis of individuals with heritable immunological disorders and for the scientific dissection of cellular and molecular mechanisms underlying monogenic and related human immune diseases.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine & Health, UNSW Sydney, Darlinghurst, NSW, Australia.
| | - 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
| | | | - 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, Tokyo, Japan
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, APHP, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, APHP, Paris, France
- Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Université Paris Cité, Paris, France
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, INSERM U1163, Necker Hospital, 75015, Paris, France
- Université Paris Cité, Imagine Institute, 75015, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Mikko R J Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center and Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Raz Somech
- Pediatric Department and Immunology Unit, Sheba Medical Center, Tel Aviv, Israel
| | - Helen C Su
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Isabelle Meyts
- Department of Immunology and Microbiology, Laboratory for Inborn Errors of Immunity, Department of Pediatrics, University Hospitals Leuven and KU Leuven, 3000, Leuven, Belgium
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Kermode W, De Santis D, Truong L, Della Mina E, Salman S, Thompson G, Nolan D, Loh R, Mallon D, Mclean-Tooke A, John M, Tangye SG, O'Sullivan M, D'Orsogna LJ. A Novel Targeted Amplicon Next-Generation Sequencing Gene Panel for the Diagnosis of Common Variable Immunodeficiency Has a High Diagnostic Yield: Results from the Perth CVID Cohort Study. J Mol Diagn 2022; 24:586-599. [PMID: 35570134 DOI: 10.1016/j.jmoldx.2022.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 12/23/2021] [Accepted: 02/09/2022] [Indexed: 11/18/2022] Open
Abstract
With the advent of next-generation sequencing (NGS), monogenic forms of common variable immunodeficiency (CVID) have been increasingly described. Our study aimed to identify disease-causing variants in a Western Australian CVID cohort using a novel targeted NGS panel. Targeted amplicon NGS was performed on 22 unrelated subjects who met the formal European Society for Immunodeficiencies-Pan-American Group for Immunodeficiency diagnostic criteria for CVID and had at least one of the following additional criteria: disease onset at age <18 years, autoimmunity, low memory B lymphocytes, family history, and/or history of lymphoproliferation. Candidate variants were assessed by in silico predictions of deleteriousness, comparison to the literature, and classified according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology criteria. All detected genetic variants were verified independently by an external laboratory, and additional functional studies were performed if required. Pathogenic or likely pathogenic variants were detected in 6 of 22 (27%) patients. Monoallelic variants of uncertain significance were also identified in a further 4 of 22 patients (18%). Pathogenic variants, likely pathogenic variants, or variants of uncertain significance were found in TNFRSF13B, TNFRSF13C, ICOS, AICDA, IL21R, NFKB2, and CD40LG, including novel variants and variants with unexpected inheritance pattern. Targeted amplicon NGS is an effective tool to identify monogenic disease-causing variants in CVID, and is comparable or superior to other NGS methods. Moreover, targeted amplicon NGS identified patients who may benefit from targeted therapeutic strategies and had important implications for family members.
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Affiliation(s)
- William Kermode
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Dianne De Santis
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Linh Truong
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Erika Della Mina
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Sam Salman
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Grace Thompson
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - David Nolan
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Richard Loh
- Department of Immunology, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Dominic Mallon
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia
| | - Andrew Mclean-Tooke
- Department of Clinical Immunology and PathWest, Queen Elizabeth II Medical Centre, Perth, Western Australia, Australia
| | - Mina John
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Stuart G Tangye
- Immunology and Immunodeficiency Laboratory, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Kensington, New South Wales, Australia
| | - Michael O'Sullivan
- Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia; Department of Immunology, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Lloyd J D'Orsogna
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia; Department of Clinical Immunology and PathWest, Fiona Stanley Hospital, Perth, Western Australia, Australia.
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7
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Eddens T, Mack M, McCormick M, Chong H, Kalpatthi R. Trends in Pediatric Primary Immunodeficiency: Incidence, Utilization, Transplantation, and Mortality. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:286-296.e3. [PMID: 34718217 PMCID: PMC8961698 DOI: 10.1016/j.jaip.2021.10.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Primary immunodeficiency disorders (PIDDs) describe a myriad of diseases caused by inherited defects within the immune system. As the number of identified genetic defects associated with PIDDs increases, understanding the incidence and outcomes of PIDD patients becomes imperative. OBJECTIVE To characterize the frequency of new diagnoses, patterns of health care utilization, rates of hematopoietic stem cell transplantation (HSCT), and mortality in pediatric patients with PIDDs. METHODS A retrospective cohort analysis of the Pediatric Health Information System database from 2004 to 2018 for pediatric inpatients with an International Classification of Diseases, Ninth and 10th Revisions (ICD-9/ICD-10). code associated with PIDD. RESULTS A total of 17,234 patients with a PIDD were hospitalized from 2004 to 2018. There were 2.8 new PIDD diagnoses and 6.3 PIDD hospitalizations per 1,000 discharges; these metrics were unchanged during the study period. The number of new diagnoses for B-cell and antibody defects significantly increased over time. The number of new PIDD diagnoses significantly increased in adolescents or adults and decreased in infants. T-cell disorders had the highest number of intensive care unit admissions. There were 747 PIDD patients who underwent HSCT; complications of HSCT significantly decreased over time. Mortality rates significantly decreased in all PIDD patients and in patients receiving HSCT. CONCLUSIONS The total hospitalizations and incidence of PIDDs within the hospitalized pediatric population were unchanged. There were significant changes in the class of PIDD diagnosed, the age at diagnosis, and health care utilization metrics. Mortality significantly decreased over time within the PIDD cohort.
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Affiliation(s)
- Taylor Eddens
- Pediatric Scientist Development Program, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pa,Department of Allergy and Immunology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pa
| | - Molly Mack
- Pediatric Residency Program, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pa
| | - Meghan McCormick
- Department of Hematology and Oncology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pa
| | - Hey Chong
- Department of Allergy and Immunology, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pa
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8
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Khalturina EO, Degtyareva ND, Bairashevskaia AV, Mulenkova AV, Degtyareva AV. Modern diagnostic capabilities of neonatal screening for primary immunodeficiencies in newborns. Clin Exp Pediatr 2021; 64:504-510. [PMID: 33781055 PMCID: PMC8498015 DOI: 10.3345/cep.2020.01270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 02/05/2021] [Indexed: 11/27/2022] Open
Abstract
Population screening of newborns is an extremely important and informative diagnostic approach that allows early identification of babies who are predisposed to the development of a number of serious diseases. Some of these diseases are known and have effective treatment methods. Neonatal screening enables the early diagnosis and subsequent timely initiation of therapy. This helps to prevent serious complications and reduce the percentage of disability and deaths among newborns and young children. Primary immunodeficiency diseases and primary immunodeficiency syndrome (PIDS) are a heterogeneous group of diseases and conditions based on impaired immune system function associated with developmental defects and characterized by various combinations of recurrent infections, development of autoimmune and lymphoproliferative syndromes (genetic defects in apoptosis, gene mutation Fas receptor or ligand), granulomatous process, and malignant neoplasms. Most of these diseases manifest in infancy and lead to serious illness, disability, and high mortality rates. Until recently, it was impossible to identify children with PIDS before the onset of the first clinical symptoms, which are usually accompanied by complications in the form of severe coinfections of a viral-bacterial-fungal etiology. Modern advances in medical laboratory technology have allowed the identification of children with severe PIDS, manifested by T- and/or B-cell lymphopenia and other disorders of the immune system. This review discusses the main existing strategies and directions used in PIDS screening programs for newborns, including approaches to screening based on excision of T-cell receptors and kappa-recombination excision circles, as well as the potential role and place of next-generation sequencing technology to increase the diagnostic accuracy of these diseases.
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Affiliation(s)
- Evgenia Olegovna Khalturina
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology, and Perinatology named after Academician V.I. Kulakov of the Ministry of Health of the Russian Federation; Department of Pediatrics and Neonatology, Moscow, Russia
| | - Natalia Dmitrievna Degtyareva
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Anastasiia Vasi'evna Bairashevskaia
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Alena Valerievna Mulenkova
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | - Anna Vladimirovna Degtyareva
- Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia.,National Medical Research Center for Obstetrics, Gynecology, and Perinatology named after Academician V.I. Kulakov of the Ministry of Health of the Russian Federation; Department of Pediatrics and Neonatology, Moscow, Russia
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9
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Karimi E, Mahmoudian F, Reyes SOL, Bargir UA, Madkaikar M, Artac H, Sabzevari A, Lu N, Azizi G, Abolhassani H. Approach to genetic diagnosis of inborn errors of immunity through next-generation sequencing. Mol Immunol 2021; 137:57-66. [PMID: 34216999 DOI: 10.1016/j.molimm.2021.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023]
Abstract
Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.
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Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, 85721, USA; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saul O Lugo Reyes
- Immune Deficiencies Lab, National Institute of Pediatrics, Mexico City, Mexico
| | - Umair Ahmed Bargir
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Manisha Madkaikar
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Selcuk University, Konya, Turkey
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden.
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10
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Strubbe S, De Bruyne M, Pannicke U, Beyls E, Vandekerckhove B, Leclercq G, De Baere E, Bordon V, Vral A, Schwarz K, Haerynck F, Taghon T. A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair. Front Immunol 2021; 12:674226. [PMID: 34220820 PMCID: PMC8248492 DOI: 10.3389/fimmu.2021.674226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the DCLRE1C gene in a T-B-NK+ SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the DCLRE1C transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all DCLRE1C splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the DCLRE1C gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.
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Affiliation(s)
- Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Ulrich Pannicke
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Elien Beyls
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Victoria Bordon
- Department of Internal Medicine and Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Klaus Schwarz
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, Germa Red Cross Blood Service Baden-Württemberg – Hessen, Ulm, Germany
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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11
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Edwards ESJ, Bosco JJ, Ojaimi S, O'Hehir RE, van Zelm MC. Beyond monogenetic rare variants: tackling the low rate of genetic diagnoses in predominantly antibody deficiency. Cell Mol Immunol 2021; 18:588-603. [PMID: 32801365 PMCID: PMC8027216 DOI: 10.1038/s41423-020-00520-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Predominantly antibody deficiency (PAD) is the most prevalent form of primary immunodeficiency, and is characterized by broad clinical, immunological and genetic heterogeneity. Utilizing the current gold standard of whole exome sequencing for diagnosis, pathogenic gene variants are only identified in less than 20% of patients. While elucidation of the causal genes underlying PAD has provided many insights into the cellular and molecular mechanisms underpinning disease pathogenesis, many other genes may remain as yet undefined to enable definitive diagnosis, prognostic monitoring and targeted therapy of patients. Considering that many patients display a relatively late onset of disease presentation in their 2nd or 3rd decade of life, it is questionable whether a single genetic lesion underlies disease in all patients. Potentially, combined effects of other gene variants and/or non-genetic factors, including specific infections can drive disease presentation. In this review, we define (1) the clinical and immunological variability of PAD, (2) consider how genetic defects identified in PAD have given insight into B-cell immunobiology, (3) address recent technological advances in genomics and the challenges associated with identifying causal variants, and (4) discuss how functional validation of variants of unknown significance could potentially be translated into increased diagnostic rates, improved prognostic monitoring and personalized medicine for PAD patients. A multidisciplinary approach will be the key to curtailing the early mortality and high morbidity rates in this immune disorder.
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Affiliation(s)
- Emily S J Edwards
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
| | - Julian J Bosco
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
| | - Samar Ojaimi
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Infectious Diseases, Monash Health, Clayton, VIC, Australia
- Centre for Inflammatory Diseases, Monash Health, Clayton, VIC, Australia
- Department of Allergy and Immunology, Monash Health, Clayton, VIC, Australia
| | - Robyn E O'Hehir
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
| | - Menno C van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia.
- The Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiencies, Melbourne, VIC, Australia.
- Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Monash University and Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia.
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12
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Fusaro M, Rosain J, Grandin V, Lambert N, Hanein S, Fourrage C, Renaud N, Gil M, Chevalier S, Chahla WA, Bader-Meunier B, Barlogis V, Blanche S, Boutboul D, Castelle M, Comont T, Diana JS, Fieschi C, Galicier L, Hermine O, Lefèvre-Utile A, Malphettes M, Merlin E, Oksenhendler E, Pasquet M, Suarez F, André I, Béziat V, De Saint Basile G, De Villartay JP, Kracker S, Lagresle-Peyrou C, Latour S, Rieux-Laucat F, Mahlaoui N, Bole C, Nitschke P, Hulier-Ammar E, Fischer A, Moshous D, Neven B, Alcais A, Vogt G, Bustamante J, Picard C. Improving the diagnostic efficiency of primary immunodeficiencies with targeted next-generation sequencing. J Allergy Clin Immunol 2021; 147:734-737. [DOI: 10.1016/j.jaci.2020.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 01/09/2023]
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13
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Suspitsin EN, Guseva MN, Kostik MM, Sokolenko AP, Skripchenko NV, Levina AS, Goleva OV, Dubko MF, Tumakova AV, Makhova MA, Lyazina LV, Bizin IV, Sokolova NE, Gabrusskaya TV, Ditkovskaya LV, Kozlova OP, Vahliarskaya SS, Kondratenko IV, Imyanitov EN. Next generation sequencing analysis of consecutive Russian patients with clinical suspicion of inborn errors of immunity. Clin Genet 2020; 98:231-239. [PMID: 32441320 DOI: 10.1111/cge.13789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
Primary immune deficiencies are usually attributed to genetic defects and, therefore, frequently referred to as inborn errors of immunity (IEI). We subjected the genomic DNA of 333 patients with clinical signs of IEI to next generation sequencing (NGS) analysis of 344 immunity-related genes and, in some instances, additional genetic techniques. Genetic causes of the disease were identified in 69/333 (21%) of subjects, including 11/18 (61%) of children with syndrome-associated IEIs, 45/202 (22%) of nonsyndromic patients with Jeffrey Modell Foundation (JMF) warning signs, 9/56 (16%) of subjects with periodic fever, 3/30 (10%) of cases of autoimmune cytopenia, 1/21 (5%) of patients with unusually severe infections and 0/6 (0%) of individuals with isolated elevation of IgE level. There were unusual clinical observations: twins with severe immunodeficiency carried a de novo CHARGE syndrome-associated SEMA3E c.2108C>T (p.S703L) allele; however, they lacked clinical features of CHARGE syndrome. Additionally, there were genetically proven instances of Netherton syndrome, Х-linked agammaglobulinemia, severe combined immune deficiency (SCID), IPEX and APECED syndromes, among others. Some patients carried recurrent pathogenic alleles, such as AIRE c.769C>T (p.R257*), NBN c.657del5, DCLRE1C c.103C>G (p.H35D), NLRP12 c.1054C>T (p.R352C) and c.910C>T (p.H304Y). NGS is a powerful tool for high-throughput examination of patients with malfunction of immunity.
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Affiliation(s)
- Evgeny N Suspitsin
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Marina N Guseva
- Outpatient Department, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Department of Immunology, First Pavlov State Medical University, St. Petersburg, Russia
| | - Mikhail M Kostik
- Department of Hospital Pediatrics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Anna P Sokolenko
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Nataliya V Skripchenko
- Department of Infectious Diseases in Children, Faculty of Postgraduate Education, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Department of Neuroinfections and Nervous System Pathology, Pediatric Research and Clinical Center for Infectious Diseases, St. Petersburg, Russia
| | - Anastasia S Levina
- Department of Infectious Diseases in Children, Faculty of Postgraduate Education, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Olga V Goleva
- Department of Virusology and Molecular Biology, Pediatric Research and Clinical Center for Infectious Diseases, St. Petersburg, Russia
| | - Margarita F Dubko
- Department of Hospital Pediatrics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Anastasia V Tumakova
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Maria A Makhova
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | | | - Ilya V Bizin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
| | - Natalia E Sokolova
- Department of Hematology, First City Children Hospital, St. Petersburg, Russia
| | - Tatiana V Gabrusskaya
- Department of Gastroenterology, Faculty of Postgraduate Education, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Liliya V Ditkovskaya
- I.M. Vorontsov Department of Pediatrics, Faculty of Postgraduate Education, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
| | - Olga P Kozlova
- Department of Clinical Mycology, Allergology and Immunology, I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia
| | - Svetlana S Vahliarskaya
- Department of Clinical Immunology, Russian Children Clinical Hospital, N.N. Pirogov National Research Medical University, Moscow, Russia
| | - Irina V Kondratenko
- Department of Clinical Immunology, Russian Children Clinical Hospital, N.N. Pirogov National Research Medical University, Moscow, Russia
| | - Evgeny N Imyanitov
- Department of Medical Genetics, St. Petersburg State Pediatric Medical University, St. Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St. Petersburg, Russia
- Department of Oncology, I.I. Mechnikov North-Western Medical University, St. Petersburg, Russia
- Department of Oncology, Saint Petersburg State University, St. Petersburg, Russia
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14
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Simon AJ, Golan AC, Lev A, Stauber T, Barel O, Somekh I, Klein C, AbuZaitun O, Eyal E, Kol N, Unal E, Amariglio N, Rechavi G, Somech R. Whole exome sequencing (WES) approach for diagnosing primary immunodeficiencies (PIDs) in a highly consanguineous community. Clin Immunol 2020; 214:108376. [PMID: 32135276 DOI: 10.1016/j.clim.2020.108376] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/06/2020] [Accepted: 03/01/2020] [Indexed: 12/15/2022]
Abstract
Primary immunodeficiencies (PIDs) are a heterogeneous group of monogenic inborn errors of immunity. The genetic causes of these diseases can be identified using whole exome sequencing (WES). Here, DNA samples from 106 patients with a clinical suspicion of PID were subjected to WES in order to test the diagnostic yield of this test in a highly consanguineous community. A likely genetic diagnosis was achieved in 70% of patients. Several factors were considered to possibly influence the diagnostic rate of WES among our cohort including early age, presence of consanguinity, family history suggestive of PID, the number of family members who underwent WES and the clinical phenotype of the patient. The highest diagnostic rate was in patients with combined immunodeficiency or with a syndrome. Notably, WES findings altered the clinical management in 39% (41/106) of patients in our cohort. Our findings support the use of WES as an important diagnostic tool in patients with suspected PID, especially in highly consanguineous communities.
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Affiliation(s)
- Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel; Division of Haematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel; Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Adi Cohen Golan
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Tali Stauber
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Ido Somekh
- Dr. von Hauner Children's Hospital, University Hospital, Ludwig Maximilian University, Munich, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, University Hospital, Ludwig Maximilian University, Munich, Germany
| | | | - Eran Eyal
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Nitzan Kol
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Ekrem Unal
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, 2-Molecular Biology and Genetic Department, Gevher Nesibe Genom and Stem Cell Institution, GENKOK Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey
| | - Ninette Amariglio
- Division of Haematology and Bone Marrow Transplantation, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel; Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel; The Everard and Mina Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Gideon Rechavi
- Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel; The Everard and Mina Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Israel.
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15
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Abstract
Severe combined immunodeficiency (SCID) encompasses a group of genetic defects. T cell development is universally affected and has alteration of B and/or NK cells. We present the case of a 5-day-old boy with combined heterozygous frame shift (c.256_257del, p.(Lys86Valfs*33)) and missense (c.1186C>T, p.(Arg396Cys)) variations in the RAG1 gene. He was admitted to our institution because of 0 TREC on Newborn Screen and worsening rash. Initially thought to have Omenn syndrome versus maternal engraftment with graft versus host disease, DNA analysis identified the noted mutations and he subsequently received a bone marrow transplant from a matched sibling.
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Affiliation(s)
- Matthew Tallar
- Pediatrics, Medical College of Wisconsin, 9000 West Wisconsin Avenue Suite 440, Milwaukee, WI 53226, USA.
| | - John Routes
- Pediatrics, Medical College of Wisconsin, 9000 West Wisconsin Avenue Suite 440, Milwaukee, WI 53226, USA
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16
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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: 713] [Impact Index Per Article: 178.3] [Reference Citation Analysis] [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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17
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Yska HAF, Elsink K, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Diagnostic Yield of Next Generation Sequencing in Genetically Undiagnosed Patients with Primary Immunodeficiencies: a Systematic Review. J Clin Immunol 2019; 39:577-591. [PMID: 31250335 PMCID: PMC6697711 DOI: 10.1007/s10875-019-00656-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND As the application of next generation sequencing (NGS) is moving to earlier stages in the diagnostic pipeline for primary immunodeficiencies (PIDs), re-evaluation of its effectiveness is required. The aim of this study is to systematically review the diagnostic yield of NGS in PIDs. METHODS PubMed and Embase databases were searched for relevant studies. Studies were eligible when describing the use of NGS in patients that had previously been diagnosed with PID on clinical and/or laboratory findings. Relevant data on study characteristics, technological performance and diagnostic yield were extracted. RESULTS Fourteen studies were eligible for data extraction. Six studies described patient populations from specific PID subcategories. The remaining studies included patients with unsorted PIDs. The studies were based on populations from Italy, Iran, Turkey, Thailand, the Netherlands, Norway, Saudi Arabia, Sweden, the UK, and the USA. Eight studies used an array-based targeted gene panel, four used WES in combination with a PID filter, and two used both techniques. The mean reported reading depth ranged from 98 to 1337 times. Five studies described the sensitivity of the applied techniques, ranging from 83 to 100%, whereas specificity ranged from 45 to 99.9%. The percentage of patients who were genetically diagnosed ranged from 15 to 79%. Several studies described clinical implications of the genetic findings. DISCUSSION NGS has the ability to contribute significantly to the identification of molecular mechanisms in PID patients. The diagnostic yield highly depends on population and on the technical circumstances under which NGS is employed. Further research is needed to determine the exact diagnostic yield and clinical implications of NGS in patients with PID.
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Affiliation(s)
- Hemmo A F Yska
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mariëlle E van Gijn
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands.
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18
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Shillitoe B, Bangs C, Guzman D, Gennery AR, Longhurst HJ, Slatter M, Edgar DM, Thomas M, Worth A, Huissoon A, Arkwright PD, Jolles S, Bourne H, Alachkar H, Savic S, Kumararatne DS, Patel S, Baxendale H, Noorani S, Yong PFK, Waruiru C, Pavaladurai V, Kelleher P, Herriot R, Bernatonienne J, Bhole M, Steele C, Hayman G, Richter A, Gompels M, Chopra C, Garcez T, Buckland M. The United Kingdom Primary Immune Deficiency (UKPID) registry 2012 to 2017. Clin Exp Immunol 2019; 192:284-291. [PMID: 29878323 DOI: 10.1111/cei.13125] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2018] [Indexed: 01/25/2023] Open
Abstract
This is the second report of the United Kingdom Primary Immunodeficiency (UKPID) registry. The registry will be a decade old in 2018 and, as of August 2017, had recruited 4758 patients encompassing 97% of immunology centres within the United Kingdom. This represents a doubling of recruitment into the registry since we reported on 2229 patients included in our first report of 2013. Minimum PID prevalence in the United Kingdom is currently 5·90/100 000 and an average incidence of PID between 1980 and 2000 of 7·6 cases per 100 000 UK live births. Data are presented on the frequency of diseases recorded, disease prevalence, diagnostic delay and treatment modality, including haematopoietic stem cell transplantation (HSCT) and gene therapy. The registry provides valuable information to clinicians, researchers, service commissioners and industry alike on PID within the United Kingdom, which may not otherwise be available without the existence of a well-established registry.
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Affiliation(s)
- B Shillitoe
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,Great North Children's Hospital, Newcastle upon Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - C Bangs
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,Manchester University NHS Foundation Trust, Manchester, UK
| | - D Guzman
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,UCL Centre for Immunodeficiency, Royal Free Hospital, London, UK
| | - A R Gennery
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,Great North Children's Hospital, Newcastle upon Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - H J Longhurst
- Addenbrooke's Hospital, Cambridge Universities NHS Foundation Trust, Cambridge, UK
| | - M Slatter
- Great North Children's Hospital, Newcastle upon Tyne, UK.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - M Thomas
- NHS Greater Glasgow and Clyde, Glasgow, UK
| | - A Worth
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,Great Ormond Street Hospital and Institute of Child Health, London, UK
| | - A Huissoon
- Heart of England NHS Foundation Trust, Birmingham, Birmingham, UK
| | - P D Arkwright
- Manchester University NHS Foundation Trust, Manchester, UK
| | - S Jolles
- University Hospital of Wales, Cardiff, UK
| | - H Bourne
- The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - H Alachkar
- Salford Royal NHS Foundation Trust, Salford, UK
| | - S Savic
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - D S Kumararatne
- Addenbrooke's Hospital, Cambridge Universities NHS Foundation Trust, Cambridge, UK
| | - S Patel
- John Radcliffe Hospital, Headington, Oxford, UK
| | - H Baxendale
- Papworth NHS Foundation Trust, Cambridge, UK
| | - S Noorani
- Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, UK
| | - P F K Yong
- Frimley Health NHS Foundation Trust, Frimley, UK
| | - C Waruiru
- Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - V Pavaladurai
- Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - P Kelleher
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | | | - J Bernatonienne
- University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - M Bhole
- The Dudley Group NHS Foundation Trust, Dudley, UK
| | | | - G Hayman
- Epsom and St Helier University Hospitals NHS Trust, St Helier, UK
| | - A Richter
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - M Gompels
- North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | | | - T Garcez
- Manchester University NHS Foundation Trust, Manchester, UK
| | - M Buckland
- On behalf of the UKPIN Registry Committee, UKPIN, London, UK.,UCL Centre for Immunodeficiency, Royal Free Hospital, London, UK.,Great Ormond Street Hospital and Institute of Child Health, London, UK
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19
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, Houston, TX.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
| | - Jordan S Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY.,New York Presbyterian Morgan Stanley Children's Hospital, New York, NY
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20
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Cifaldi C, Brigida I, Barzaghi F, Zoccolillo M, Ferradini V, Petricone D, Cicalese MP, Lazarevic D, Cittaro D, Omrani M, Attardi E, Conti F, Scarselli A, Chiriaco M, Di Cesare S, Licciardi F, Davide M, Ferrua F, Canessa C, Pignata C, Giliani S, Ferrari S, Fousteri G, Barera G, Merli P, Palma P, Cesaro S, Gattorno M, Trizzino A, Moschese V, Chini L, Villa A, Azzari C, Finocchi A, Locatelli F, Rossi P, Sangiuolo F, Aiuti A, Cancrini C, Di Matteo G. Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies. Front Immunol 2019; 10:316. [PMID: 31031743 PMCID: PMC6470723 DOI: 10.3389/fimmu.2019.00316] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders. Objective: To evaluate the strength and weakness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes. Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology. Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage. Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
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Affiliation(s)
- Cristina Cifaldi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Immacolata Brigida
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Ferradini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Davide Petricone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Attardi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesca Conti
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Alessia Scarselli
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Maria Chiriaco
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Silvia Di Cesare
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesco Licciardi
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Montin Davide
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Clementina Canessa
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Giliani
- Department of Molecular and Translational Medicine, A. Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia, Italy
| | - Simona Ferrari
- Unit of Medical Genetics, St. Orsola-Malpighi University Hospital, University of Bologna, Bologna, Italy
| | - Georgia Fousteri
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Graziano Barera
- Pediatric Department, San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- Department of Onco-Hematology and Cell and Gene Therapy, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Paolo Palma
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Simone Cesaro
- Paediatric Hematology-Oncology, “Ospedale della Donna e del Bambino”, Verona, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Giannina Gaslini, Genoa, Italy
| | - Antonio Trizzino
- Department of Pediatric Hematology and Oncology, “ARNAS Civico Di Cristina Benfratelli” Hospital, Palermo, Italy
| | - Viviana Moschese
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Loredana Chini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Anna Villa
- Milan Unit, National Research Council (CNR) Institute for Genetic and Biomedical Research (IRGB), Milan, Italy
- Humanitas Clinical and Research Institute, Rozzano, Italy
| | - Chiara Azzari
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Andrea Finocchi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, University of Rome La Sapienza, Rome, Italy
| | - Paolo Rossi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Gigliola Di Matteo
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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21
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Genetic diagnosis of primary immunodeficiencies: A survey of the French national registry. J Allergy Clin Immunol 2019; 143:1646-1649.e10. [PMID: 30639347 DOI: 10.1016/j.jaci.2018.12.994] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 11/21/2022]
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22
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Belmont JW. Molecular Methods. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Chi ZH, Wei W, Bu DF, Li HH, Ding F, Zhu P. Targeted high-throughput sequencing technique for the molecular diagnosis of primary immunodeficiency disorders. Medicine (Baltimore) 2018; 97:e12695. [PMID: 30290665 PMCID: PMC6200533 DOI: 10.1097/md.0000000000012695] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The aim of this study was to investigate the usefulness of targeted high-throughput sequencing (HTS) for the molecular diagnosis of primary immunodeficiency diseases (PID).A total of 56 clinically diagnosed or suspected PID patients were divided into 4 groups according to the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency 2015 and their chief clinical presentations. Patients and their biological family members were examined by targeted HTS, which sequenced the exons and ±10 bp flanking introns of 171 PID-related genes panel. All significant variants were confirmed by PCR-Sanger sequencing. Pathogenicity of the variants was evaluated by using bioinformatics.A total of 117 variants in 73 genes were found in 56 patients. Accurate molecular diagnosis of PID was made in 13 (23.2%) patients, and 12 novel mutations were detected in these patients. Twenty-seven patients carried heterozygous variants that are probably pathogenic in ≥2 genes; 16 patients had only 1 missense variant, or had several variants but not >1 variant was deleterious as evaluated by bioinformatics. The meaning of the targeted HTS results of these patients remains to be studied.Targeted HTS can make a precise molecular diagnosis of PID and detect more novel pathogenic mutations. More and more variations with ambiguous significance are discovered and explanation of these variations is a challenge to the clinicians.
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Affiliation(s)
- Zuo Hua Chi
- The First Affiliated Hospital/School of Clinical Medicine, Guang Dong Pharmaceutical University, Guangzhou
| | | | - Ding Fang Bu
- Hematology Research Laboratory, Peking University First Hospital, Beijing
| | - Huan Huan Li
- Department of Pediatrics, Zhengzhou University First Hospital, Zhengzhou
| | - Fei Ding
- Hematology & Oncology Institute, Beijing Aerospace General Hospital, Beijing, China
| | - Ping Zhu
- Hematology Research Laboratory, Peking University First Hospital, Beijing
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24
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Charbit-Henrion F, Parlato M, Hanein S, Duclaux-Loras R, Nowak J, Begue B, Rakotobe S, Bruneau J, Fourrage C, Alibeu O, Rieux-Laucat F, Lévy E, Stolzenberg MC, Mazerolles F, Latour S, Lenoir C, Fischer A, Picard C, Aloi M, Dias JA, Hariz MB, Bourrier A, Breuer C, Breton A, Bronsky J, Buderus S, Cananzi M, Coopman S, Crémilleux C, Dabadie A, Dumant-Forest C, Gurkan OE, Fabre A, Fischer A, Diaz MG, Gonzalez-Lama Y, Goulet O, Guariso G, Gurcan N, Homan M, Hugot JP, Jeziorski E, Karanika E, Lachaux A, Lewindon P, Lima R, Magro F, Major J, Malamut G, Mas E, Mattyus I, Mearin LM, Melek J, Navas-Lopez VM, Paerregaard A, Pelatan C, Pigneur B, Pais IP, Rebeuh J, Romano C, Siala N, Strisciuglio C, Tempia-Caliera M, Tounian P, Turner D, Urbonas V, Willot S, Ruemmele FM, Cerf-Bensussan N. Diagnostic Yield of Next-generation Sequencing in Very Early-onset Inflammatory Bowel Diseases: A Multicentre Study. J Crohns Colitis 2018; 12:1104-1112. [PMID: 29788237 PMCID: PMC6113703 DOI: 10.1093/ecco-jcc/jjy068] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/14/2018] [Accepted: 05/16/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS An expanding number of monogenic defects have been identified as causative of severe forms of very early-onset inflammatory bowel diseases [VEO-IBD]. The present study aimed at defining how next-generation sequencing [NGS] methods can be used to improve identification of known molecular diagnosis and to adapt treatment. METHODS A total of 207 children were recruited in 45 paediatric centres through an international collaborative network [ESPGHAN GENIUS working group] with a clinical presentation of severe VEO-IBD [n = 185] or an anamnesis suggestive of a monogenic disorder [n = 22]. Patients were divided at inclusion into three phenotypic subsets: predominantly small bowel inflammation, colitis with perianal lesions, and colitis only. Methods to obtain molecular diagnosis included functional tests followed by specific Sanger sequencing, custom-made targeted NGS, and in selected cases whole exome sequencing [WES] of parents-child trios. Genetic findings were validated clinically and/or functionally. RESULTS Molecular diagnosis was achieved in 66/207 children [32%]: 61% with small bowel inflammation, 39% with colitis and perianal lesions, and 18% with colitis only. Targeted NGS pinpointed gene mutations causative of atypical presentations, and identified large exonic copy number variations previously missed by WES. CONCLUSIONS Our results lead us to propose an optimised diagnostic strategy to identify known monogenic causes of severe IBD.
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Affiliation(s)
- Fabienne Charbit-Henrion
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Paediatric Gastroenterology, Hepatology and Nutrition Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Marianna Parlato
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Sylvain Hanein
- INSERM, UMR 1163 Translational Genetic, and Imagine Institute, Paris, France
| | - Rémi Duclaux-Loras
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Jan Nowak
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Bernadette Begue
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Sabine Rakotobe
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Julie Bruneau
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Pathology Department, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cécile Fourrage
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Bioinformatics Platform, Imagine Institute Paris, France
| | - Olivier Alibeu
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Genomic Platform, Imagine Institute, Paris, France
| | - Frédéric Rieux-Laucat
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Immunogenetics of Paediatric Autoimmunity, and Imagine Institute, Paris, France
| | - Eva Lévy
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Immunogenetics of Paediatric Autoimmunity, and Imagine Institute, Paris, France
| | - Marie-Claude Stolzenberg
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Immunogenetics of Paediatric Autoimmunity, and Imagine Institute, Paris, France
| | - Fabienne Mazerolles
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Immunogenetics of Paediatric Autoimmunity, and Imagine Institute, Paris, France
| | - Sylvain Latour
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Lymphocyte activation and EBV susceptibility, and Imagine Institute, Paris, France
| | - Christelle Lenoir
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Lymphocyte activation and EBV susceptibility, and Imagine Institute, Paris, France
| | - Alain Fischer
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Collège de France, Médecine expérimentale, Paris, France,INSERM UMR 1163 and Imagine Institute, Paris, France
| | - Capucine Picard
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,INSERM, UMR1163, Lymphocyte activation and EBV susceptibility, and Imagine Institute, Paris, France,Investigation Centre for Immunodeficiency, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris and Imagine Institute, Paris, France
| | - Marina Aloi
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Sapienza University of Rome, Paediatric Gastroenterology and Liver Unit, Department of Pediatrics, Rome, Italy
| | - Jorge Amil Dias
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centro Hospitalar São João, Porto, Portugal
| | - Mongi Ben Hariz
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Hopital La Marsa, Tunisia
| | - Anne Bourrier
- Department of Gastroenterology, Hôpital St Antoine, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Christian Breuer
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Universitätsklinikum Hamburg, Hamburg, Germany
| | - Anne Breton
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Gastroenterology, Hepatology, Nutrition, and Diabetes, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Jiri Bronsky
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],University Hospital Motol, Prague, Czech Republic
| | - Stephan Buderus
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],St. Marien Hospital, Bonn, Germany
| | - Mara Cananzi
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Unit of Paediatric Hepatology, Department of Woman and Child Health, University Hospital of Padova, Padova, Italy
| | - Stéphanie Coopman
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Division of Gastroenterology, Hepatology and Nutrition, Department of Paediatrics, Jeanne De Flandre Children’s Hospital, Lille University Faculty of Medicine, Lille, France
| | - Clara Crémilleux
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre Hospitalo-Universitaire de St-Etienne, St-Etienne, France
| | - Alain Dabadie
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Service de médecine de l’enfant et de l’adolescent, Hôpital Sud – Centre Hospitalo-Universitaire de Rennes, Rennes, France
| | - Clémentine Dumant-Forest
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre Hospitalo-Universitaire Charles Nicolle, Rouen, France
| | - Odul Egritas Gurkan
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Paediatric Gastroenterology, Hepatology and Nutrition, Gazi University, Ankara, Turkey
| | - Alexandre Fabre
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Assistance publique Hôpitaux de Marseille, Hôpital de la Timone, Marseille, France
| | - Aude Fischer
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre Hospitalo-Universitaire Sud Réunion, St Pierre, France
| | - Marta German Diaz
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Unit of Paediatric Nutrition, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Yago Gonzalez-Lama
- Inflammatory Bowel Disease Unit, Hospital Universitario Puerta de Hierro–Majadahonda, Madrid, Spain
| | - Olivier Goulet
- Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Paediatric Gastroenterology, Hepatology and Nutrition Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Graziella Guariso
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],University of Padua, Italy
| | - Neslihan Gurcan
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Paediatric Gastroenterology, Hepatology and Nutrition, Gazi University, Ankara, Turkey
| | - Matjaz Homan
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Gastroenterology, Hepatology and Nutrition, University Children’s Hospital, Ljubljana, Slovenia
| | - Jean-Pierre Hugot
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Departments of Paediatric Digestive and Respiratory Diseases, Hôpital Robert-Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Jeziorski
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Infectious diseases and Immunology, Centre Hospitalo-Universitaire de Montpellier, Montpellier, France
| | - Evi Karanika
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, University General Hospital of Thessaloniki, Thessaloniki, Greece
| | - Alain Lachaux
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatric Gastroenterology, Hepatology and Nutrition, Centre de Nutrition parentérale à domicile, Hôpital Femme–Mère–Enfant CHU de Lyon HCL - GH Est, Bron, France
| | - Peter Lewindon
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Gastroenterology and Hepatology, Lady Cilento Children’s Hospital and the Faculty of Medicine and Biomedical Sciences, TUniversity of Queensland, Brisbane, Australia
| | - Rosa Lima
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centro Hospitalar São João, Porto, Portugal
| | - Fernando Magro
- Gastroenterology Department, Hospital de São João, Institute of Pharmacology and Therapeutics Faculty of Medicine and MedInUP - Centre for Drug Discovery and Innovative Medicines, University of Porto, Porto, Portugal
| | - Janos Major
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],MRE Bethesda Gyermekkórháza; Department of Pediatrics, Budapest, Hungary
| | - Georgia Malamut
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Department of Gastroenterology, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Mas
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Gastroenterology, Hepatology, Nutrition, and Diabetes, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - Istvan Mattyus
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Semmelweis University; Department of Paediatrics, Budapest, Hungary
| | - Luisa M Mearin
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Leiden University Medical Centre, Department of Paediatrics, Leiden, The Netherlands
| | - Jan Melek
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],University Hospital, Hradec Kralove, Czech Republic
| | - Victor Manuel Navas-Lopez
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Hospital Regional Universitario de Málaga, Departamento de Pediatría, Malaga, Spain
| | - Anders Paerregaard
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Hvidovre University Hospital, Department of Paediatrics, Copenhagen, Denmark
| | - Cecile Pelatan
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre Hospitalier du Mans, Le Mans, France
| | - Bénédicte Pigneur
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Paediatric Gastroenterology, Hepatology and Nutrition Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Isabel Pinto Pais
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Centro Hospitalar Gaia Espinho, Department of Paediatrics, Vila Nova de Gaia, Portugal
| | - Julie Rebeuh
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre Hospitalo-Universitaire de Strasbourg, Strasbourg, France
| | - Claudio Romano
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Hospital of Messina, University of Messina, Messina, Italy
| | - Nadia Siala
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Hôpital Mongi Slim, La Marsa, Tunisia
| | - Caterina Strisciuglio
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Woman, Child and General and Specialized Surgery, Second University of Naples, Naples, Italy
| | - Michela Tempia-Caliera
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, FMH Pédiatrie et FA Gastroentérologie et hépatologie, Clinique des Grangettes, Geneva, Switzerland
| | - Patrick Tounian
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatric Nutrition and Gastroenterology, Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Dan Turner
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Shaare Zedek Medical Centre, Jerusalem, Israel
| | - Vaidotas Urbonas
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatric Gastroenterology, Vilnius University Clinic for Children’s Diseases, Vilnius, Lithuania
| | - Stéphanie Willot
- GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Department of Paediatrics, Centre hospitalier régional universitaire, Hôpital Clocheville, Tours, France
| | - Frank M Ruemmele
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,Paediatric Gastroenterology, Hepatology and Nutrition Unit, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN]
| | - Nadine Cerf-Bensussan
- INSERM, UMR1163, Laboratory of Intestinal Immunity, and Imagine Institute, Paris, France,Université Paris Descartes-Sorbonne Paris Cité, Paris, France,GENIUS Group [GENetically ImmUne–mediated enteropathieS] from the European Society for Paediatric Gastroenterology, Hepatology and Nutrition [ESPGHAN],Corresponding author: Nadine Cerf-Bensussan, Laboratory of Intestinal Immunity, Institut IMAGINE-INSERM 1163, Université Paris Descartes-Sorbonne Paris Cité. 24, boulevard du Montparnasse. 75015 Paris, France. Tel: 33-[0]1-42-75-42-88;
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25
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Carey B, Lambourne J, Porter S, Hodgson T. Chronic mucocutaneous candidiasis due to gain-of-function mutation in STAT1. Oral Dis 2018; 25:684-692. [PMID: 29702748 DOI: 10.1111/odi.12881] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/06/2018] [Accepted: 02/20/2018] [Indexed: 12/26/2022]
Abstract
Chronic mucocutaneous candidiasis (CMC) is a heterogenous group of primary immunodeficiency diseases characterised by susceptibility to chronic or recurrent superficial Candida infection of skin, nails and mucous membranes. Gain-of-function mutations in the STAT1 gene (STAT1-GOF) are the most common genetic aetiology for CMC, and mutation analysis should be considered. These mutations lead to defective responses in Type 1 and Type 17 helper T cells (Th1 and Th17), which, depending on the mutation, also predispose to infection with Staphylococci, Mycobacteria and Herpesviridae. We describe the clinical and genetic findings for three patients with CMC due to gain-of-function mutations in the STAT1 gene.
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Affiliation(s)
- Barbara Carey
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
| | - Jonathan Lambourne
- Department of Microbiology and Infectious Diseases, Barts Health NHS Trust, London, UK
| | - Stephen Porter
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
| | - Tim Hodgson
- Oral Medicine Unit, UCLH NHS Foundation Trust, Eastman Dental Hospital, UCL Eastman Dental Institute, London, UK
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26
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Frans G, Meert W, Van der Werff Ten Bosch J, Meyts I, Bossuyt X, Vermeesch JR, Hestand MS. Conventional and Single-Molecule Targeted Sequencing Method for Specific Variant Detection in IKBKG while Bypassing the IKBKGP1 Pseudogene. J Mol Diagn 2018; 20:195-202. [DOI: 10.1016/j.jmoldx.2017.10.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/09/2017] [Accepted: 10/25/2017] [Indexed: 12/30/2022] Open
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27
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Frequently used bioinformatics tools overestimate the damaging effect of allelic variants. Genes Immun 2017; 20:10-22. [PMID: 29217828 DOI: 10.1038/s41435-017-0002-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 09/05/2017] [Accepted: 09/18/2017] [Indexed: 11/08/2022]
Abstract
We selected two sets of naturally occurring human missense allelic variants within innate immune genes. The first set represented eleven non-synonymous variants in six different genes involved in interferon (IFN) induction, present in a cohort of patients suffering from herpes simplex encephalitis (HSE) and the second set represented sixteen allelic variants of the IFNLR1 gene. We recreated the variants in vitro and tested their effect on protein function in a HEK293T cell based assay. We then used an array of 14 available bioinformatics tools to predict the effect of these variants upon protein function. To our surprise two of the most commonly used tools, CADD and SIFT, produced a high rate of false positives, whereas SNPs&GO exhibited the lowest rate of false positives in our test. As the problem in our test in general was false positive variants, inclusion of mutation significance cutoff (MSC) did not improve accuracy.
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28
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A novel pathogenic frameshift variant of CD3E gene in two T-B+ NK+ SCID patients from Turkey. Immunogenetics 2017; 69:653-659. [PMID: 28597365 DOI: 10.1007/s00251-017-1005-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/27/2017] [Indexed: 10/19/2022]
Abstract
Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiency, which is characterized by the dysfunction and/or absence of T lymphocytes. Early diagnosis of SCID is crucial for overall survival, and if it remains untreated, SCID is often fatal. Next-generation sequencing (NGS) has become a rapid, high-throughput technology, and has already been proven to be beneficial in medical diagnostics. In this study, a targeted NGS panel was developed to identify the genetic variations of SCID by using SmartChip-TE technology, and a novel pathogenic frameshift variant was found in the CD3E gene. Sanger sequencing has confirmed the segregation of the variant among patients. We found a novel deletion in the CD3E gene (NM000733.3:p.L58Hfs*9) in two T-B+ NK+ patients. The variant was not found in the databases of dbSNP, ExAC, and 1000G. One sibling in family I was homozygous and the rest of the family members were heterozygous for this variant. T cell receptor excision circle (TREC) and kappa-deleting recombination excision circle (KREC) analyses were performed for T and B cell maturation. TRECs were not detected in both patients and the KREC copy numbers were similar to the other family members. In addition, heterozygous family members showed decreased TREC levels when compared with the wild-type sibling, indicating that carrying this variant in one allele does not cause immunodeficiency, but does effect T cell proliferation. Here, we report a novel pathogenic frameshift variant in CD3E gene by using targeted NGS panel.
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29
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Mahlaoui N, Warnatz K, Jones A, Workman S, Cant A. Advances in the Care of Primary Immunodeficiencies (PIDs): from Birth to Adulthood. J Clin Immunol 2017; 37:452-460. [PMID: 28523402 PMCID: PMC5489581 DOI: 10.1007/s10875-017-0401-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/08/2017] [Indexed: 12/14/2022]
Abstract
Primary immunodeficiencies (PIDs) are a widely heterogeneous group of inherited defects of the immune system consisting of many clinical phenotypes with at least 300 underlying genetic deficits currently known. Patients with PIDs can present with, or develop during the course of their life, a susceptibility to recurrent and chronic infection along with autoimmune, allergic, inflammatory, and/or proliferative disorders, all potentially leading to end-organ damage. In recent years, a combination of basic and clinical research has greatly improved understanding of the underlying immunological and genetic defects in PIDs, leading to improved diagnosis, classification, and treatment approaches. In this review, we consider some of the key understandings that should direct diagnostic and treatment approaches in PID and offer insights into current and emerging management approaches and the lifelong care of patients from childhood through to adulthood.
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Affiliation(s)
- Nizar Mahlaoui
- French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France. .,Pediatric Immuno-Haematology and Rheumatology Unit, Necker Enfants Malades University Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France. .,INSERM UMR 1163, Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris, France. .,Sorbonne Paris Cité, Imagine Institute, Paris Descartes University, Paris, France.
| | - Klaus Warnatz
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alison Jones
- Immunology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sarita Workman
- Department of Immunology, Royal Free London NHS Foundation Trust, 2nd Floor, Pond Street, Hampstead, London, NW3 2QG, UK
| | - Andrew Cant
- Great North Children's Hospital, & Institute for Cellular Medicine University of Newcastle, Newcastle upon Tyne, NE4 1LP, UK
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30
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Langlais D, Fodil N, Gros P. Genetics of Infectious and Inflammatory Diseases: Overlapping Discoveries from Association and Exome-Sequencing Studies. Annu Rev Immunol 2017; 35:1-30. [DOI: 10.1146/annurev-immunol-051116-052442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Philippe Gros
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec H3G 0B1, Canada;, ,
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 0B1, Canada
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31
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Erman B, Bilic I, Hirschmugl T, Salzer E, Boztug H, Sanal Ö, Çağdaş Ayvaz D, Tezcan I, Boztug K. Investigation of Genetic Defects in Severe Combined Immunodeficiency Patients from Turkey by Targeted Sequencing. Scand J Immunol 2017; 85:227-234. [PMID: 28109013 DOI: 10.1111/sji.12523] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/13/2017] [Indexed: 12/30/2022]
Abstract
Primary immunodeficiencies (PIDs) represent a large group of disorders with an increased susceptibility to infections. Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiencies (PIDs) with marked T-cell lymphopenia. Investigation of the genetic aetiology using classical Sanger sequencing is associated with considerable diagnostic delay. We here established a custom-designed, next-generation sequencing (NGS)-based panel to efficiently identify disease-causing genetic defects in PID patients and applied this method in SCID patients of Turkish origin with previously undefined genetic aetiology. We used HaloPlex enrichment technology, a targeted, NGS-based method which was designed to diagnose patients with SCID and other PIDs. Our HaloPlex panel included a total of 356 PID-related genes, and we searched disease-causing mutations in 19 Turkish SCID patients without a genetic diagnosis. The coverage of targeted regions ranged from 97.47% to 99.62% with an average of 98.31% for all patients. All known SCID genes were covered with a percentage of at least 97.3%. We made a genetic diagnosis in six of 19 (33%) patients, including four novel disease-causing mutations identified in RAG1, JAK3 and IL2RG, respectively. We showed that this NGS-based method can provide rapid genetic diagnosis for patients suffering from SCID, potentially facilitating clinical treatment decisions.
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Affiliation(s)
- B Erman
- Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - I Bilic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - T Hirschmugl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - E Salzer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - H Boztug
- Department of Paediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria
| | - Ö Sanal
- Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey
| | - D Çağdaş Ayvaz
- Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey
| | - I Tezcan
- Department of Immunology, Ihsan Dogramaci Children's Hospital, Hacettepe University, Ankara, Turkey
| | - K Boztug
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Paediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
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Stray-Pedersen A, Sorte HS, Samarakoon P, Gambin T, Chinn IK, Coban Akdemir ZH, Erichsen HC, Forbes LR, Gu S, Yuan B, Jhangiani SN, Muzny DM, Rødningen OK, Sheng Y, Nicholas SK, Noroski LM, Seeborg FO, Davis CM, Canter DL, Mace EM, Vece TJ, Allen CE, Abhyankar HA, Boone PM, Beck CR, Wiszniewski W, Fevang B, Aukrust P, Tjønnfjord GE, Gedde-Dahl T, Hjorth-Hansen H, Dybedal I, Nordøy I, Jørgensen SF, Abrahamsen TG, Øverland T, Bechensteen AG, Skogen V, Osnes LTN, Kulseth MA, Prescott TE, Rustad CF, Heimdal KR, Belmont JW, Rider NL, Chinen J, Cao TN, Smith EA, Caldirola MS, Bezrodnik L, Lugo Reyes SO, Espinosa Rosales FJ, Guerrero-Cursaru ND, Pedroza LA, Poli CM, Franco JL, Trujillo Vargas CM, Aldave Becerra JC, Wright N, Issekutz TB, Issekutz AC, Abbott J, Caldwell JW, Bayer DK, Chan AY, Aiuti A, Cancrini C, Holmberg E, West C, Burstedt M, Karaca E, Yesil G, Artac H, Bayram Y, Atik MM, Eldomery MK, Ehlayel MS, Jolles S, Flatø B, Bertuch AA, Hanson IC, Zhang VW, Wong LJ, Hu J, Walkiewicz M, Yang Y, Eng CM, Boerwinkle E, Gibbs RA, Shearer WT, Lyle R, Orange JS, Lupski JR. Primary immunodeficiency diseases: Genomic approaches delineate heterogeneous Mendelian disorders. J Allergy Clin Immunol 2017; 139:232-245. [PMID: 27577878 PMCID: PMC5222743 DOI: 10.1016/j.jaci.2016.05.042] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/10/2016] [Accepted: 05/13/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.
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Affiliation(s)
- Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway; Department of Pediatrics, Oslo University Hospital, Oslo, Norway.
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pubudu Samarakoon
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tomasz Gambin
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Ivan K Chinn
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Zeynep H Coban Akdemir
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | | | - Lisa R Forbes
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Shen Gu
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Bo Yuan
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Shalini N Jhangiani
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Donna M Muzny
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Sarah K Nicholas
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Lenora M Noroski
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Filiz O Seeborg
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carla M Davis
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Debra L Canter
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Emily M Mace
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Timothy J Vece
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Carl E Allen
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Harshal A Abhyankar
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex; Texas Children's Cancer and Hematology Center, Department of Pediatrics, Center for Cell and Gene Therapy, Texas Children's Hospital and Baylor College of Medicine, Houston, Tex
| | - Philip M Boone
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine R Beck
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Wojciech Wiszniewski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Børre Fevang
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir E Tjønnfjord
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Henrik Hjorth-Hansen
- Department of Hematology, St Olavs Hospital, Trondheim, Norway; Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingunn Dybedal
- Department of Hematology, Oslo University Hospital, Oslo, Norway
| | - Ingvild Nordøy
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Silje F Jørgensen
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tore G Abrahamsen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Vegard Skogen
- Department of Infectious Diseases, Medical Clinic, University Hospital of North-Norway, Tromsø, Norway
| | - Liv T N Osnes
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Mari Ann Kulseth
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine E Prescott
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil R Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Nicholas L Rider
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Javier Chinen
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Tram N Cao
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Eric A Smith
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Tex
| | - Maria Soledad Caldirola
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Liliana Bezrodnik
- Immunology Service, Ricardo Gutierrez Children's Hospital, Ciudad Autonoma de Buenos Aires, Buenos Aires, Argentina
| | - Saul Oswaldo Lugo Reyes
- Immunodeficiencies Research Unit, National Institute of Pediatrics, Coyoacan, Mexico City, Mexico
| | | | | | | | - Cecilia M Poli
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Hospital Roberto del Rio, Universidad de Chile, Santiago, Chile
| | - Jose L Franco
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Claudia M Trujillo Vargas
- Grupo de Inmunodeficiencias Primarias, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | | | - Nicola Wright
- Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Thomas B Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Andrew C Issekutz
- Department of Pediatrics, Dalhousie University, Izaak Walton Killam Health Centre, Halifax, Nova Scotia, Canada
| | - Jordan Abbott
- Department of Pediatrics, National Jewish Health, Denver, Colo
| | - Jason W Caldwell
- Section of Pulmonary, Critical Care, Allergic and Immunological Diseases, Wake Forest Baptist Medical Center, Medical Center Boulevard, Winston-Salem, NC
| | - Diana K Bayer
- Department of Pediatrics, Division of Pediatric Allergy/Immunology and Pulmonology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Alice Y Chan
- Department of Pediatrics, University of California, San Francisco, Calif
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), and Vita-Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- University Department of Pediatrics, DPUO, Bambino Gesù Children's Hospital, and Tor Vergata University, Rome, Italy
| | - Eva Holmberg
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Christina West
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Magnus Burstedt
- Department of Clinical Genetics, University Hospital of Umeå, Umeå, Sweden
| | - Ender Karaca
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Gözde Yesil
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Medical Genetics, Bezmi Alem Vakif University Faculty of Medicine, Istanbul, Turkey
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Selcuk University Medical Faculty, Alaeddin Keykubat Kampusu, Konya, Turkey
| | - Yavuz Bayram
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mehmed Musa Atik
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad K Eldomery
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Mohammad S Ehlayel
- Department of Pediatrics, Section of Pediatric Allergy and Immunology, Hamad Medical Corporation, Doha, Department of Paediatrics, Weill Cornell Medical College, Ar-Rayyan, Qatar
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Alison A Bertuch
- Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Tex
| | - I Celine Hanson
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Victor W Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Jianhong Hu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex
| | - Eric Boerwinkle
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex; Human Genetics Center, University of Texas School of Public Health, Houston, Tex
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex
| | - William T Shearer
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Jordan S Orange
- Center for Human Immunobiology of Texas Children's Hospital/Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex.
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Department of Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, Tex; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Tex; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Tex.
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Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, Pedergnana V, Moens L, Picard C, Cobat A, Bossuyt X, Abel L, Casanova JL. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol 2016; 138:957-969. [PMID: 27720020 PMCID: PMC5074686 DOI: 10.1016/j.jaci.2016.08.003] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023]
Abstract
The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology and Microbiology, Childhood Immunology, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Alexandre Bolze
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Helix, San Carlos, Calif
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Leen Moens
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Paris Descartes University-Sorbonne Paris Cité, Paris, France; Study Center for Immunodeficiency, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Xavier Bossuyt
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
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Déficits immunitaires héréditaires de l’immunité innée et infections. Arch Pediatr 2016; 23:760-8. [DOI: 10.1016/j.arcped.2016.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/12/2016] [Accepted: 04/21/2016] [Indexed: 11/16/2022]
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Fodil N, Langlais D, Gros P. Primary Immunodeficiencies and Inflammatory Disease: A Growing Genetic Intersection. Trends Immunol 2016; 37:126-140. [PMID: 26791050 DOI: 10.1016/j.it.2015.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/10/2015] [Accepted: 12/13/2015] [Indexed: 02/08/2023]
Abstract
Recent advances in genome analysis have provided important insights into the genetic architecture of infectious and inflammatory diseases. The combined analysis of loci detected by genome-wide association studies (GWAS) in 22 inflammatory diseases has revealed a shared genetic core and associated biochemical pathways that play a central role in pathological inflammation. Parallel whole-exome sequencing studies have identified 265 genes mutated in primary immunodeficiencies (PID). Here, we examine the overlap between these two data sets, and find that it consists of genes essential for protection against infections and in which persistent activation causes pathological inflammation. Based on this intersection, we propose that, although strong or inactivating mutations (rare variants) in these genes may cause severe disease (PIDs), their more subtle modulation potentially by common regulatory/coding variants may contribute to chronic inflammation.
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Affiliation(s)
- Nassima Fodil
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - David Langlais
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Complex Traits Group, McGill University, Montreal, QC, Canada.
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Stranneheim H, Wedell A. Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders. J Intern Med 2016; 279:3-15. [PMID: 26250718 DOI: 10.1111/joim.12399] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Massively parallel DNA sequencing has revolutionized analyses of human genetic variation. From having been out of reach for individual research groups and even more so for clinical diagnostic laboratories until recently, it is now possible to analyse complete human genomes within reasonable time frames and at a reasonable cost using technologies that are becoming increasingly available. This represents a huge advance in our ability to provide correct diagnoses for patients with rare inherited disorders and their families. This paradigm shift is especially dramatic within the area of monogenic disorders. Not only can rapid and safe diagnostics of virtually all known single-gene defects now be established, but novel causes of disease in previously unsolved cases can also be identified, illuminating novel pathways important for normal physiology. This greatly increases the capability not only to improve management of rare disorders, but also to improve understanding of pathogenetic mechanisms relevant for common, complex diseases.
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Affiliation(s)
- H Stranneheim
- Department of Molecular Medicine and Surgery, Science for Life Laboratory, Center for Molecular Medicine, Karolinska Institutet and the Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - A Wedell
- Department of Molecular Medicine and Surgery, Science for Life Laboratory, Center for Molecular Medicine, Karolinska Institutet and the Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
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Abstract
Genomic DNA sequencing technologies have been one of the great advances of the 21st century, having decreased in cost by seven orders of magnitude and opening up new fields of investigation throughout research and clinical medicine. Genomics coupled with biochemical investigation has allowed the molecular definition of a growing number of new genetic diseases that reveal new concepts of immune regulation. Also, defining the genetic pathogenesis of these diseases has led to improved diagnosis, prognosis, genetic counseling, and, most importantly, new therapies. We highlight the investigational journey from patient phenotype to treatment using the newly defined XMEN disease, caused by the genetic loss of the MAGT1 magnesium transporter, as an example. This disease illustrates how genomics yields new fundamental immunoregulatory insights as well as how research genomics is integrated into clinical immunology. At the end, we discuss two other recently described diseases, CHAI/LATAIE (CTLA-4 deficiency) and PASLI (PI3K dysregulation), as additional examples of the journey from unknown immunological diseases to new precision medicine treatments using genomics.
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Affiliation(s)
- Michael Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
| | - Bernice Lo
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
| | - Carrie L Lucas
- Molecular Development of the Immune System Section, Laboratory of Immunology, and Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;
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Recent advances in understanding the pathophysiology of primary T cell immunodeficiencies. Trends Mol Med 2015; 21:408-16. [DOI: 10.1016/j.molmed.2015.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/31/2015] [Accepted: 04/07/2015] [Indexed: 02/06/2023]
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IJspeert H, Wentink M, van Zessen D, Driessen GJ, Dalm VASH, van Hagen MP, Pico-Knijnenburg I, Simons EJ, van Dongen JJM, Stubbs AP, van der Burg M. Strategies for B-cell receptor repertoire analysis in primary immunodeficiencies: from severe combined immunodeficiency to common variable immunodeficiency. Front Immunol 2015; 6:157. [PMID: 25904919 PMCID: PMC4389565 DOI: 10.3389/fimmu.2015.00157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/23/2015] [Indexed: 01/08/2023] Open
Abstract
The antigen receptor repertoires of B- and T-cells form the basis of the adaptive immune response. The repertoires should be sufficiently diverse to recognize all possible pathogens. However, careful selection is needed to prevent responses to self or harmless antigens. Limited antigen receptor repertoire diversity leads to immunodeficiency, whereas unselected or misdirected repertoires can result in autoimmunity. The antigen receptor repertoire harbors information about abnormalities in many immunological disorders. Recent developments in next generation sequencing allow the analysis of the antigen receptor repertoire in much greater detail than ever before. Analyzing the antigen receptor repertoire in patients with mutations in genes responsible for the generation of the antigen receptor repertoire will give new insights into repertoire formation and selection. In this perspective, we describe strategies and considerations for analysis of the naive and antigen-selected B-cell repertoires in primary immunodeficiency patients with a focus on severe combined immunodeficiency and common variable immunodeficiency.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Marjolein Wentink
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands ; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Martin P van Hagen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Erik J Simons
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Jacques J M van Dongen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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Ebadi M, Aghamohammadi A, Rezaei N. Primary immunodeficiencies: a decade of shifting paradigms, the current status and the emergence of cutting-edge therapies and diagnostics. Expert Rev Clin Immunol 2014; 11:117-39. [DOI: 10.1586/1744666x.2015.995096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Stoddard JL, Niemela JE, Fleisher TA, Rosenzweig SD. Targeted NGS: A Cost-Effective Approach to Molecular Diagnosis of PIDs. Front Immunol 2014; 5:531. [PMID: 25404929 PMCID: PMC4217515 DOI: 10.3389/fimmu.2014.00531] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 10/08/2014] [Indexed: 12/27/2022] Open
Abstract
Background: Primary immunodeficiencies (PIDs) are a diverse group of disorders caused by multiple genetic defects. Obtaining a molecular diagnosis for PID patients using a phenotype-based approach is often complex, expensive, and not always successful. Next-generation sequencing (NGS) methods offer an unbiased genotype-based approach, which can facilitate molecular diagnostics. Objective: To develop an efficient NGS method to identify variants in PID-related genes. Methods: We performed HaloPlex custom target enrichment and NGS using the Ion Torrent PGM to screen 173 genes in 11 healthy controls, 13 PID patients previously evaluated with either an identified mutation or SNP, and 120 patients with undiagnosed PIDs. Sensitivity and specificity were determined by comparing NGS and Sanger sequencing results for 33 patients. Run metrics and coverage analyses were done to identify systematic deficiencies. Results: A molecular diagnosis was identified for 18 of 120 patients who previously lacked a genetic diagnosis, including 9 who had atypical presentations and extensive previous genetic and functional studies. Our NGS method detected variants with 98.1% sensitivity and >99.9% specificity. Uniformity was variable (72–89%), and we were not able to reliably sequence 45 regions (45/2455 or 1.8% of total regions) due to low (<20) average read depth or <90% region coverage; thus, we optimized probe hybridization conditions to improve read-depth and coverage for future analyses, and established criteria to help identify true positives. Conclusion: While NGS methods are not as sensitive as Sanger sequencing for individual genes, targeted NGS is a cost-effective, first-line genetic test for the evaluation of patients with PIDs. This approach decreases time to diagnosis, increases diagnostic rate, and provides insight into the genotype–phenotype correlation of PIDs in a cost-effective way.
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Affiliation(s)
- Jennifer L Stoddard
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Julie E Niemela
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Thomas A Fleisher
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health , Bethesda, MD , USA
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health , Bethesda, MD , USA
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