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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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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [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: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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Al-Mousa H, Barbouche MR. Genetics of Inborn Errors of Immunity in highly consanguineous Middle Eastern and North African populations. Semin Immunol 2023; 67:101763. [PMID: 37075586 DOI: 10.1016/j.smim.2023.101763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Consanguineous marriages in Middle Eastern and North African (MENA) countries are deeply-rooted tradition and highly prevalent resulting into increased prevalence of autosomal recessive diseases including Inborn Errors of Immunity (IEIs). Molecular genetic testing is an important diagnostic tool for IEIs since it provides a definite diagnosis, genotype-phenotype correlation, and guide therapy. In this review, we will discuss the current state and challenges of genomic and variome studies in MENA region populations, as well as the importance of funding advanced genome projects. In addition, we will review the MENA underlying molecular genetic defects of over 2457 patients published with the common IEIs, where autosomal recessive mode of inheritance accounts for 76% of cases with increased prevalence of combined immunodeficiency diseases (50%). The efforts made in the last three decades in terms of international collaboration and of in situ capacity building in MENA region countries led to the discovery of more than 150 novel genes involved in IEIs. Expanding sequencing studies within the MENA will undoubtedly be a unique asset for the IEI genetics which can advance research, and support precise genomic diagnostics and therapeutics.
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Affiliation(s)
- Hamoud Al-Mousa
- Section of Allergy and Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Mohamed-Ridha Barbouche
- Department of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain.
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Quinn J, Modell V, Johnson B, Poll S, Aradhya S, Orange JS, Modell F. Global Expansion of Jeffrey's Insights: Jeffrey Modell Foundation's Genetic Sequencing Program for Primary Immunodeficiency. Front Immunol 2022; 13:906540. [PMID: 35757720 PMCID: PMC9226364 DOI: 10.3389/fimmu.2022.906540] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic disorders that impair the immune system, known as Primary Immunodeficiencies (PI), include over 450 single-gene inborn errors of immunity. Timely and appropriate diagnosis and treatment is vital to quality of life (QOL) and sometimes survival, as patients are susceptible to frequent, persistent, severe, and sometimes life-threatening infections or autoimmunity. Suspected PI patients that do not have a genetic diagnosis often endure a prolonged, onerous, inefficient, and expensive experience, known as a diagnostic odyssey. The resulting diagnostic delay prohibits proper disease management and treatment, causing unnecessary distress and diminished QOL. Next-generation sequencing (NGS) offers relief from the distress of the diagnostic odyssey, but because of cost and barriers to access, it is regularly unobtainable. The Jeffrey Modell Foundation (JMF) introduced "Jeffrey's Insights", a no-charge genetic sequencing pilot program, in January 2019 for patients within the Jeffrey Modell Centers Network (JMCN) with an underlying PI, but no genetic diagnosis. Building on the success of the pilot program, JMF expanded it globally to more than 400 Centers in the JMCN in early 2020. The most current version of Invitae's PI Panel available was used for this program. All participating clinicians were invited to complete a brief questionnaire assessing prior impediments to access and post-sequencing alterations in disease management and treatment. A total of 1,398 patients were tested, with 20.3% receiving a molecular diagnosis and many more receiving helpful diagnostic leads. Results obtained from genetic sequencing led to an alteration of clinical diagnosis, disease management, treatment, and genetic counseling in 39%, 38%, 35%, and 53% of patients, respectively. The global expansion of this program further underscores the crucial need for NGS for PI, along with its efficiency and potential cost savings. The results of this program to date further define rationale for the availability of comprehensive diagnostic NGS for patients with PI when requisitioned by an expert immunologist.
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Affiliation(s)
- Jessica Quinn
- Jeffrey Modell Foundation, New York, NY, United States
| | - Vicki Modell
- Jeffrey Modell Foundation, New York, NY, United States
| | | | - Sarah Poll
- Invitae, San Francisco, CA, United States
| | | | | | - Fred Modell
- Jeffrey Modell Foundation, New York, NY, United States
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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: 0] [Impact Index Per Article: 0] [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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Primary antibody deficiencies in Turkey: molecular and clinical aspects. Immunol Res 2021; 70:44-55. [PMID: 34618307 DOI: 10.1007/s12026-021-09242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Primary antibody deficiencies (PAD) are the most common subtype of primary immunodeficiencies, characterized by increased susceptibility to infections and autoimmunity, allergy, or malignancy predisposition. PAD syndromes comprise of immune system genes highlighted the key role of B cell activation, proliferation, migration, somatic hypermutation, or isotype switching have a wide spectrum from agammaglobulinemia to selective Ig deficiency. In this study, we describe the molecular and the clinical aspects of fifty-two PAD patients. The most common symptoms of our cohort were upper and lower respiratory infections, bronchiectasis, diarrhea, and recurrent fever. Almost all patients (98%) had at least one of the symptoms like autoimmunity, lymphoproliferation, allergy, or gastrointestinal disease. A custom-made next-generation sequencing (NGS) panel, which contains 24 genes, was designed to identify well-known disease-causing variants in our cohort. We identified eight variants (15.4%) among 52 PAD patients. The variants mapped to BTK (n = 4), CD40L (n = 1), ICOS (n = 1), IGHM (n = 1), and TCF3 (n = 1) genes. Three novel variants were described in the BTK (p.G414W), ICOS (p.G60*), and IGHM (p.S19*) genes. We performed Sanger sequencing to validate pathogenic variants and check for allelic segregation in the family. Targeted NGS panel sequencing can be beneficial as a suitable diagnostic modality for diagnosing well-known monogenic PAD diseases (only 2-10% of PADs); however, screening only the coding regions of the genome may not be adequately powered to solve the pathogenesis of PAD in all cases. Deciphering the regulatory regions of the genome and better understanding the epigenetic modifications will elucidate the molecular basis of complex PADs.
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Vorsteveld EE, Hoischen A, van der Made CI. Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. Clin Rev Allergy Immunol 2021; 61:212-225. [PMID: 33666867 PMCID: PMC7934351 DOI: 10.1007/s12016-021-08838-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/18/2022]
Abstract
Primary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of the genetic and molecular basis of genetic diseases, thereby also leading to a sharp increase in the discovery of new genes associated with primary immunodeficiencies. In this review, we discuss the current diagnostic yield of this generic diagnostic approach by evaluating the studies that have employed next-generation sequencing techniques in cohorts of patients with primary immunodeficiencies. The average diagnostic yield for primary immunodeficiencies is determined to be 29% (range 10-79%) and 38% specifically for whole-exome sequencing (range 15-70%). The significant variation between studies is mainly the result of differences in clinical characteristics of the studied cohorts but is also influenced by varying sequencing approaches and (in silico) gene panel selection. We further discuss other factors contributing to the relatively low yield, including the inherent limitations of whole-exome sequencing, challenges in the interpretation of novel candidate genetic variants, and promises of exploring the non-coding part of the genome. We propose strategies to improve the diagnostic yield leading the way towards expanded personalized treatment in PIDs.
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Affiliation(s)
- Emil E Vorsteveld
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Caspar I van der Made
- Department of Human Genetics, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboudumc Center for Infectious Diseases (RCI), Radboudumc, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Frede N, Rojas-Restrepo J, Caballero Garcia de Oteyza A, Buchta M, Hübscher K, Gámez-Díaz L, Proietti M, Saghafi S, Chavoshzadeh Z, Soler-Palacin P, Galal N, Adeli M, Aldave-Becerra JC, Al-Ddafari MS, Ardenyz Ö, Atkinson TP, Kut FB, Çelmeli F, Rees H, Kilic SS, Kirovski I, Klein C, Kobbe R, Korganow AS, Lilic D, Lunt P, Makwana N, Metin A, Özgür TT, Karakas AA, Seneviratne S, Sherkat R, Sousa AB, Unal E, Patiroglu T, Wahn V, von Bernuth H, Whiteford M, Doffinger R, Jouhadi Z, Grimbacher B. Genetic Analysis of a Cohort of 275 Patients with Hyper-IgE Syndromes and/or Chronic Mucocutaneous Candidiasis. J Clin Immunol 2021; 41:1804-1838. [PMID: 34390440 PMCID: PMC8604890 DOI: 10.1007/s10875-021-01086-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 06/05/2021] [Indexed: 01/24/2023]
Abstract
Hyper-IgE syndromes and chronic mucocutaneous candidiasis constitute rare primary immunodeficiency syndromes with an overlapping clinical phenotype. In recent years, a growing number of underlying genetic defects have been identified. To characterize the underlying genetic defects in a large international cohort of 275 patients, of whom 211 had been clinically diagnosed with hyper-IgE syndrome and 64 with chronic mucocutaneous candidiasis, targeted panel sequencing was performed, relying on Agilent HaloPlex and Illumina MiSeq technologies. The targeted panel sequencing approach allowed us to identify 87 (32 novel and 55 previously described) mutations in 78 patients, which generated a diagnostic success rate of 28.4%. Specifically, mutations in DOCK8 (26 patients), STAT3 (21), STAT1 (15), CARD9 (6), AIRE (3), IL17RA (2), SPINK5 (3), ZNF341 (2), CARMIL2/RLTPR (1), IL12RB1 (1), and WAS (1) have been detected. The most common clinical findings in this cohort were elevated IgE (81.5%), eczema (71.7%), and eosinophilia (62.9%). Regarding infections, 54.7% of patients had a history of radiologically proven pneumonia, and 28.3% have had other serious infections. History of fungal infection was noted in 53% of cases and skin abscesses in 52.9%. Skeletal or dental abnormalities were observed in 46.2% of patients with a characteristic face being the most commonly reported feature (23.1%), followed by retained primary teeth in 18.9% of patients. Targeted panel sequencing provides a cost-effective first-line genetic screening method which allows for the identification of mutations also in patients with atypical clinical presentations and should be routinely implemented in referral centers.
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Affiliation(s)
- Natalie Frede
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jessica Rojas-Restrepo
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrés Caballero Garcia de Oteyza
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mary Buchta
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katrin Hübscher
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Gámez-Díaz
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michele Proietti
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Shiva Saghafi
- Immunology Asthma and Allergy Research Institute Tehran University of Medical Sciences , Tehran, Iran
| | - Zahra Chavoshzadeh
- Pediatric Infectious Research Center, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall D'Hebron, Barcelona, Catalonia, Spain
| | - Nermeen Galal
- Department of Pediatrics, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mehdi Adeli
- Sidra Medicine, Weill Cornell Medicine, Hamad Medical Corporation, Doha, Qatar
| | | | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, University of Abou-Bekr Belkaïd, Tlemcen, Algeria
| | - Ömür Ardenyz
- Division of Allergy and Immunology, Department of Internal Medicine, Faculty of Medicine, Ege University, Izmir, Turkey
| | - T Prescott Atkinson
- Division of Pediatric Allergy & Immunology, University of Alabama At Birmingham, Birmingham, AL, USA
| | - Fulya Bektas Kut
- Departmant of Pediatrics, Division of Pediatric Immunology and Allergy, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Fatih Çelmeli
- Antalya Education and Research Hospital Department of Pediatric Immunology and Allergy, Antalya, Turkey
| | - Helen Rees
- Bristol Royal Hospital for Children, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Sara S Kilic
- Faculty of Medicine, Uludag University, Bursa, Turkey
| | - Ilija Kirovski
- Medical Faculty Skopje, 50 Divizija BB, 1000, Skopje, Macedonia
| | - Christoph Klein
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center , Hamburg-Eppendorf, Germany
| | | | - Desa Lilic
- Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Peter Lunt
- Centre for Academic Child Health, University of Bristol, Bristol, UK
| | - Niten Makwana
- Department of Pediatrics, Sandwell and West, Birmingham Hospitals NHS Trust, Birmingham, UK
| | - Ayse Metin
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Tuba Turul Özgür
- Department of Pediatrics, Division of Immunology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Ayse Akman Karakas
- Department of Dermatology and Venerology, Akdeniz University Medical Faculty, Antalya, Turkey
| | - Suranjith Seneviratne
- Institute of Immunity and Transplantation, Royal Free Hospital and University College London, London, UK
| | - Roya Sherkat
- Acquired Immunodeficiency Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ana Berta Sousa
- Serviço de Genética, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, and Laboratório de Imunologia Básica, Faculdade de Medicina de Lisboa, Universidade de Lisboa, Lisboa, Portugal
| | - Ekrem Unal
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Erciyes University, 38010, Melikgazi, Kayseri, Turkey.,Deparment of Molecular Biology and Genetics, Gevher Nesibe Genom and Stem Cell Institution, GENKOK Genome and Stem Cell Center, Erciyes University, 38010, Melikgazi, Kayseri, Turkey
| | - Turkan Patiroglu
- Department of Pediatrics, Division of Pediatric Immunology, Faculty of Medicine, Erciyes University, 38010, Melikgazi, Kayseri, Turkey
| | - Volker Wahn
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Department of Immunology, Labor Berlin GmbH, Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health (BIH), Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Margo Whiteford
- Department of Clinical Genetics, Queen Elizabeth University Hospital, Glasgow, G51 4TF, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | - Zineb Jouhadi
- Department of Pediatric Infectious Diseases, Children's Hospital CHU Ibn Rochd, University Hassan 2, Casablanca, Morocco
| | - Bodo Grimbacher
- Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,Institute for Immunodeficiency, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,German Center for Infection Research (DZIF), Satellite Center Freiburg, Freiburg, Germany. .,CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany. .,RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany. .,CCI-Center for Chronic Immunodeficiency, Universitätsklinikum Freiburg, Breisacher Straße 115, 79106, Freiburg, Germany.
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9
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Stephens Z, Milosevic D, Kipp B, Grebe S, Iyer RK, Kocher JPA. PB-Motif-A Method for Identifying Gene/Pseudogene Rearrangements With Long Reads: An Application to CYP21A2 Genotyping. Front Genet 2021; 12:716586. [PMID: 34394200 PMCID: PMC8355628 DOI: 10.3389/fgene.2021.716586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022] Open
Abstract
Long read sequencing technologies have the potential to accurately detect and phase variation in genomic regions that are difficult to fully characterize with conventional short read methods. These difficult to sequence regions include several clinically relevant genes with highly homologous pseudogenes, many of which are prone to gene conversions or other types of complex structural rearrangements. We present PB-Motif, a new method for identifying rearrangements between two highly homologous genomic regions using PacBio long reads. PB-Motif leverages clustering and filtering techniques to efficiently report rearrangements in the presence of sequencing errors and other systematic artifacts. Supporting reads for each high-confidence rearrangement can then be used for copy number estimation and phased variant calling. First, we demonstrate PB-Motif's accuracy with simulated sequence rearrangements of PMS2 and its pseudogene PMS2CL using simulated reads sweeping over a range of sequencing error rates. We then apply PB-Motif to 26 clinical samples, characterizing CYP21A2 and its pseudogene CYP21A1P as part of a diagnostic assay for congenital adrenal hyperplasia. We successfully identify damaging variation and patient carrier status concordant with clinical diagnosis obtained from multiplex ligation-dependent amplification (MLPA) and Sanger sequencing. The source code is available at: github.com/zstephens/pb-motif.
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Affiliation(s)
- Zachary Stephens
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | | | | | | | - Ravishankar K Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
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10
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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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11
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Asano T, Khourieh J, Zhang P, Rapaport F, Spaan AN, Li J, Lei WT, Pelham SJ, Hum D, Chrabieh M, Han JE, Guérin A, Mackie J, Gupta S, Saikia B, Baghdadi JEI, Fadil I, Bousfiha A, Habib T, Marr N, Ganeshanandan L, Peake J, Droney L, Williams A, Celmeli F, Hatipoglu N, Ozcelik T, Picard C, Abel L, Tangye SG, Boisson-Dupuis S, Zhang Q, Puel A, Béziat V, Casanova JL, Boisson B. Human STAT3 variants underlie autosomal dominant hyper-IgE syndrome by negative dominance. J Exp Med 2021; 218:212397. [PMID: 34137790 PMCID: PMC8217968 DOI: 10.1084/jem.20202592] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022] Open
Abstract
Most patients with autosomal dominant hyper-IgE syndrome (AD-HIES) carry rare heterozygous STAT3 variants. Only six of the 135 in-frame variants reported have been experimentally shown to be dominant negative (DN), and it has been recently suggested that eight out-of-frame variants operate by haploinsufficiency. We experimentally tested these 143 variants, 7 novel out-of-frame variants found in HIES patients, and other STAT3 variants from the general population. Strikingly, all 15 out-of-frame variants were DN via their encoded (1) truncated proteins, (2) neoproteins generated from a translation reinitiation codon, and (3) isoforms from alternative transcripts or a combination thereof. Moreover, 128 of the 135 in-frame variants (95%) were also DN. The patients carrying the seven non-DN STAT3 in-frame variants have not been studied for other genetic etiologies. Finally, none of the variants from the general population tested, including an out-of-frame variant, were DN. Overall, our findings show that heterozygous STAT3 variants, whether in or out of frame, underlie AD-HIES through negative dominance rather than haploinsufficiency.
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Affiliation(s)
- Takaki Asano
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Joëlle Khourieh
- Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - András N Spaan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Juan Li
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Wei-Te Lei
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Simon J Pelham
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - David Hum
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Maya Chrabieh
- Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY
| | - Antoine Guérin
- Garvan Institute of Medical Research, Darlinghurst, Australia.,St. Vincent's Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Joseph Mackie
- Garvan Institute of Medical Research, Darlinghurst, Australia.,St. Vincent's Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Sudhir Gupta
- Division of Basic and Clinical Immunology, Department of Medicine, School of Medicine, University of California, Irvine, Irvine, CA
| | - Biman Saikia
- Department of Immunopathology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Ilham Fadil
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco.,Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, Averroes University Hospital Center, Casablanca, Morocco
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco.,Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, Averroes University Hospital Center, Casablanca, Morocco
| | - Tanwir Habib
- Research Branch, Sidra Medicine, Qatar Foundation, Doha, Qatar
| | - Nico Marr
- Research Branch, Sidra Medicine, Qatar Foundation, Doha, Qatar.,College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Luckshman Ganeshanandan
- Department of Clinical Immunology, PathWest Laboratory Medicine Western Australia, Fiona Stanley Hospital, Perth, Australia
| | - Jane Peake
- Queensland Children's Hospital, South Brisbane, Australia
| | - Luke Droney
- Department of Clinical Immunology, Princess Alexandra Hospital, Brisbane, Australia
| | - Andrew Williams
- Immunology Laboratory, Children's Hospital Westmead, Westmead, Australia
| | - Fatih Celmeli
- Department of Allergy and Immunology, University of Medical Science Antalya Education and Research Hospital, Antalya, Turkey
| | - Nevin Hatipoglu
- Bakirkoy Dr Sadi Konuk Education and Training Hospital, Istanbul, Turkey
| | - Tayfun Ozcelik
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Capucine Picard
- Université de Paris, Paris, France.,Study Center for Primary Immunodeficiencies, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.,Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Institut National de la Santé et de la Recherche Médicale UMR 1163, Imagine Institute, Paris, France.,Pediatric Immunology-Hematology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Australia.,St. Vincent's Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, Australia
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France.,Howard Hughes Medical Institute, New York, NY
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY.,Paris University, Imagine Institute, Paris, France.,Laboratory of Human Genetics of Infectious Disease, Necker Branch, Institut National de la Santé et de la Recherche Médicale U1163, Paris, France
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12
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Aghamohammadi A, Rezaei N, Yazdani R, Delavari S, Kutukculer N, Topyildiz E, Ozen A, Baris S, Karakoc-Aydiner E, Kilic SS, Kose H, Gulez N, Genel F, Reisli I, Djenouhat K, Tahiat A, Boukari R, Ladj S, Belbouab R, Ferhani Y, Belaid B, Djidjik R, Kechout N, Attal N, Saidani K, Barbouche R, Bousfiha A, Sobh A, Rizk R, Elnagdy MH, Al-Ahmed M, Al-Tamemi S, Nasrullayeva G, Adeli M, Al-Nesf M, Hassen A, Mehawej C, Irani C, Megarbane A, Quinn J, Maródi L, Modell V, Modell F, Al-Herz W, Geha RS, Abolhassani H. Consensus Middle East and North Africa Registry on Inborn Errors of Immunity. J Clin Immunol 2021; 41:1339-1351. [PMID: 34052995 PMCID: PMC8310844 DOI: 10.1007/s10875-021-01053-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/26/2021] [Indexed: 01/03/2023]
Abstract
Background Inborn errors of immunity (IEIs) are a heterogeneous group of genetic defects of immunity, which cause high rates of morbidity and mortality mainly among children due to infectious and non-infectious complications. The IEI burden has been critically underestimated in countries from middle- and low-income regions and the majority of patients with IEI in these regions lack a molecular diagnosis. Methods We analyzed the clinical, immunologic, and genetic data of IEI patients from 22 countries in the Middle East and North Africa (MENA) region. The data was collected from national registries and diverse databases such as the Asian Pacific Society for Immunodeficiencies (APSID) registry, African Society for Immunodeficiencies (ASID) registry, Jeffrey Modell Foundation (JMF) registry, J Project centers, and International Consortium on Immune Deficiency (ICID) centers. Results We identified 17,120 patients with IEI, among which females represented 39.4%. Parental consanguinity was present in 60.5% of cases and 27.3% of the patients were from families with a confirmed previous family history of IEI. The median age of patients at the onset of disease was 36 months and the median delay in diagnosis was 41 months. The rate of registered IEI patients ranges between 0.02 and 7.58 per 100,000 population, and the lowest rates were in countries with the highest rates of disability-adjusted life years (DALY) and death rates for children. Predominantly antibody deficiencies were the most frequent IEI entities diagnosed in 41.2% of the cohort. Among 5871 patients genetically evaluated, the diagnostic yield was 83% with the majority (65.2%) having autosomal recessive defects. The mortality rate was the highest in patients with non-syndromic combined immunodeficiency (51.7%, median age: 3.5 years) and particularly in patients with mutations in specific genes associated with this phenotype (RFXANK, RAG1, and IL2RG). Conclusions This comprehensive registry highlights the importance of a detailed investigation of IEI patients in the MENA region. The high yield of genetic diagnosis of IEI in this region has important implications for prevention, prognosis, treatment, and resource allocation. Supplementary Information The online version contains supplementary material available at 10.1007/s10875-021-01053-z.
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Affiliation(s)
- Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Delavari
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Necil Kutukculer
- Department of Pediatric Immunology, Ege University Faculty of Medicine, Bornova-İzmir, Turkey
| | - Ezgi Topyildiz
- Department of Pediatric Immunology, Ege University Faculty of Medicine, Bornova-İzmir, Turkey
| | - Ahmet Ozen
- Faculty of Medicine, Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Safa Baris
- Faculty of Medicine, Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Faculty of Medicine, Pediatric Allergy and Immunology, Marmara University, Istanbul, Turkey.,The Isil Berat Barlan Center for Translational Medicine, Istanbul Jeffrey Modell Foundation Diagnostic Center for Primary Immune Deficiencies, Istanbul, Turkey
| | - Sara Sebnem Kilic
- Uludag University, Medical Faculty, Department of Pediatric Immunology and Rheumatology, Bursa, Turkey
| | - Hulya Kose
- Uludag University, Medical Faculty, Department of Pediatric Immunology and Rheumatology, Bursa, Turkey
| | - Nesrin Gulez
- Department of Pediatric Immunology and Allergy, University of Health Sciences Dr. Behçet Uz Children's Hospital, İzmir, Turkey
| | - Ferah Genel
- Department of Pediatric Immunology and Allergy, University of Health Sciences Dr. Behçet Uz Children's Hospital, İzmir, Turkey
| | - Ismail Reisli
- Department of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Kamel Djenouhat
- Laboratory of Immunology, Department of Medical Biology, Rouiba Hospital, Algiers, Algeria
| | - Azzeddine Tahiat
- Laboratory of Immunology, Department of Medical Biology, Rouiba Hospital, Algiers, Algeria
| | - Rachida Boukari
- Department of Pediatrics, Mustapha Pacha University Hospital, University of Algiers, Algiers, Algeria
| | - Samir Ladj
- Department of Pediatrics, Mustapha Pacha University Hospital, University of Algiers, Algiers, Algeria
| | - Reda Belbouab
- Department of Pediatrics, Mustapha Pacha University Hospital, University of Algiers, Algiers, Algeria
| | - Yacine Ferhani
- Department of Pediatrics, Mustapha Pacha University Hospital, University of Algiers, Algiers, Algeria
| | - Brahim Belaid
- Department of Medical Immunology, University Hospital Center of Beni Messous, University of Algiers, Algiers, Algeria
| | - Reda Djidjik
- Department of Medical Immunology, University Hospital Center of Beni Messous, University of Algiers, Algiers, Algeria
| | - Nadia Kechout
- Department of Immunology, Pasteur Institute of Algeria/Faculty of Medicine, Algiers, Algeria
| | - Nabila Attal
- Department of Immunology, Pasteur Institute of Algeria/Faculty of Medicine, Algiers, Algeria
| | - Khalissa Saidani
- Department of Immunology, Pasteur Institute of Algeria/Faculty of Medicine, Algiers, Algeria
| | - Ridha Barbouche
- Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, Casablanca, Morocco
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Ragheed Rizk
- Department of Pediatrics, Mansoura University Children's Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Marwa H Elnagdy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Mona Al-Ahmed
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.,Department of Allergy, Al-Rashid Allergy Center, Kuwait University, Kuwait City, Kuwait
| | - Salem Al-Tamemi
- Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Gulnara Nasrullayeva
- Department Immunology Research Laboratory, Azerbaijan Medical University, Baku, Azerbaijan
| | - Mehdi Adeli
- Allergy and Immunology Division, Pediatrics Department, Sidra Medicine, Doha, Qatar
| | - Maryam Al-Nesf
- Allergy and Immunology Section, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Amel Hassen
- Allergy and Immunology Division, Pediatrics Department, Sidra Medicine, Doha, Qatar
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Carla Irani
- Internal Medicine and Clinical Immunology, Hotel Dieu de France Hospital, Saint Joseph University, Beirut, Lebanon
| | - Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Jessica Quinn
- Jeffrey Modell Foundation (JMF), New York City, NY, USA
| | | | - László Maródi
- PID Clinical Unit and Laboratory, Department of Dermatology, Semmelweis University, Budapest, Hungary.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University, New York, NY, USA
| | - Vicki Modell
- Jeffrey Modell Foundation (JMF), New York City, NY, USA
| | - Fred Modell
- Jeffrey Modell Foundation (JMF), New York City, NY, USA
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat 13110, PO Box 24923, Kuwait City, Kuwait. .,Allergy and Clinical Immunology Unit, Pediatric Department, Al-Sabah Hospital, Kuwait City, Kuwait.
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, 1 Blackfan Circle, Karp, Bldg, 10th Floor, Boston, MA, 02115, USA.
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran. .,Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, 14186, Huddinge, Stockholm, Sweden.
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13
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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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14
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Erman B, Çipe F. Genetic Screening of the Patients with Primary Immunodeficiency by Whole-Exome Sequencing. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2021; 33:19-24. [PMID: 33406023 DOI: 10.1089/ped.2019.1097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Primary immunodeficiencies (PIDs) are a heterogeneous group of congenital disorders characterized by susceptibility to recurrent infections, allergy, malignancies and autoimmunity. The identification of disease-causing genetic defects is critically important for treatment options. In last decade, next-generation sequencing (NGS)-based methods has enabled the rapid genetic screening and the discovery of new genetic defects in PIDs. In this study, we investigated causative mutations in patients with PID by NGS. Methods: We applied whole-exome sequencing in 8 PID patients. Detected mutations by NGS were validated by Sanger sequencing. Results: We made a genetic diagnosis in 5 of 8 (63%) patients, including 3 novel disease-causing variants. The identified mutations were found in RAG1, RAG2, JAK3, RFXANK, and CYBA genes. Conclusions: Our results show that whole-exome sequencing can facilitate the genetic diagnosis of the patients with PID.
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Affiliation(s)
- Baran Erman
- Department of Molecular Biology and Genetics, Istınye University, Istanbul, Turkey.,Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Funda Çipe
- Department of Pediatrics, Medical School, Istinye University, Istanbul, Turkey
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15
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Lamb CC, Wang Y. PHYSICIAN CHARACTERISTICS THAT INFLUENCE PATIENT PARTICIPATION IN THE TREATMENT OF PRIMARY IMMUNODEFICIENCY. PATIENT EDUCATION AND COUNSELING 2020; 103:2280-2289. [PMID: 32475713 DOI: 10.1016/j.pec.2020.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 05/15/2020] [Accepted: 05/16/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Shared decision making (SDM) is recommended to improve healthcare quality. Physicians who use a rational decision-making style and patient-centric approach are more likely to incorporate SDM into clinical practice. This paper explores how certain physician characteristics such as gender, age, race, experience, and specialty explain patient participation. METHODS A multi-group structural equation model tested the relationship between physician decision-making styles, patient-centered care, physician characteristics, and patient participation in clinical treatment decisions. A survey was completed by 330 physicians who treat primary immunodeficiency. Sample group responses were compared between groups across specialty, age, race, experience, or gender. RESULTS A patient-centric approach was the main factor that encouraged SDM independent of physician decision-making style with both treatment protocols and product choices. The positive effect of patient-centrism is stronger for immunologists, more experienced physicians, or male physicians. A rational decision-making style increases participation for non-immunologists, older physicians, white physicians, less-experienced physicians and female physicians. CONCLUSION A patient-centric approach, rational decision-making and certain physician characteristics help explain patient participation in clinical decisions. Practice Implications Future SDM research and policy initiatives should focus on physician adoption of patient-centric approaches to chronic care diseases and the potential bias associated with physician characteristics and decision-making style.
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Affiliation(s)
- Christopher C Lamb
- BioSolutions Services, Englewood Cliffs, New Jersey, United States; Department of Management and Entrepreneurship, Silberman College of Business, Fairleigh Dickinson University, Teaneck, New Jersey, United States; Weatherhead School of Management, Case Western Reserve University, Cleveland, Ohio, USA.
| | - Yunmei Wang
- Case Cardiovascular Research Institute, Case Western Reserve University School of Medicine and Harrington Heart &Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio 44106, USA
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16
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Chinn IK, Orange JS. A 2020 update on the use of genetic testing for patients with primary immunodeficiency. Expert Rev Clin Immunol 2020; 16:897-909. [DOI: 10.1080/1744666x.2020.1814145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ivan K. Chinn
- Department of Pediatrics, Section of Immunology, Allergy, and Retrovirology, Baylor College of Medicine, Houston, TX, USA
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, TX, USA
| | - Jordan S. Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY, USA
- NewYork-Presbyterian Morgan Stanley Children's Hospita, New York, USA
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17
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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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18
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Quinn J, Modell V, Holle J, Truty R, Aradhya S, Johnson B, Orange J, Modell F. Jeffrey's insights: Jeffrey Modell Foundation's global genetic sequencing pilot program to identify specific primary immunodeficiency defects to optimize disease management and treatment. Immunol Res 2020; 68:126-134. [PMID: 32462469 PMCID: PMC7335369 DOI: 10.1007/s12026-020-09131-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Primary immunodeficiencies (PI) are genetic defects of the immune system that result in chronic and often life-threatening infections and/or life-threatening autoimmunity if not diagnosed and treated. Patients with a suspected PI, but without a genetic diagnosis, commonly undergo a diagnostic odyssey that is costly, time-consuming, and arduous. This delay in diagnosis prevents appropriate disease management and treatment, contributing to prolonged suffering and decreased quality of life. Although next generation sequencing (NGS) can provide these patients with relief from such a diagnostic odyssey, it is often unavailable, mainly due to cost and inaccessibility. In January 2019, the Jeffrey Modell Foundation (JMF) launched a free genetic sequencing pilot program for Jeffrey Modell Centers Network (JMCN) patients clinically diagnosed with an underlying PI. A total of 21 sites within the JMCN were invited to participate. JMF collaborated with Invitae, and testing was comprised of Invitae's Primary Immunodeficiency Panel, which currently includes 207 genes. A questionnaire was disseminated to each participating physician to evaluate barriers to access to genetic sequencing and changes in disease management and treatment after testing. One hundred fifty-eight patients and 29 family members were tested in this pilot study. Twenty-one percent of patients with a suspected monogenic disorder received a molecular diagnosis, and others received potentially useful diagnostic leads. Based on the results of genetic sequencing, clinical diagnosis was altered in 45% of patients, disease management was altered in 40%, treatment was altered in 36%, and genetic counseling was altered in 62%. The results of this pilot program demonstrate the utility, cost-efficiency, and critical importance of NGS for PI and make the case for broad scale sequence-based diagnostics for PI patients when requested by expert immunologists.
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Affiliation(s)
- Jessica Quinn
- Jeffrey Modell Foundation, 780 Third Avenue, 47th Floor, New York City, NY, 10017, USA
| | - Vicki Modell
- Jeffrey Modell Foundation, 780 Third Avenue, 47th Floor, New York City, NY, 10017, USA
| | | | | | | | | | - Jordan Orange
- Jeffrey Modell Foundation, 780 Third Avenue, 47th Floor, New York City, NY, 10017, USA
| | - Fred Modell
- Jeffrey Modell Foundation, 780 Third Avenue, 47th Floor, New York City, NY, 10017, USA.
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19
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McLean KC, Mandal M. It Takes Three Receptors to Raise a B Cell. Trends Immunol 2020; 41:629-642. [PMID: 32451219 DOI: 10.1016/j.it.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
As the unique source of diverse immunoglobulin repertoires, B lymphocytes are an indispensable part of humoral immunity. B cell progenitors progress through sequential and mutually exclusive states of proliferation and recombination, coordinated by cytokines and chemokines. Mutations affecting the crucial pre-B cell checkpoint result in immunodeficiency, autoimmunity, and leukemia. This checkpoint was previously modeled by the signaling of two opposing receptors, IL-7R and the pre-BCR. We provide an update to this model in which three receptors, IL-7R, pre-BCR, and CXCR4, work in concert to coordinate both the proper positioning of B cell progenitors in the bone marrow (BM) microenvironment and their progression through the pre-B checkpoint. Furthermore, signaling initiated by all three receptors directly instructs cell fate and developmental progression.
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Affiliation(s)
- Kaitlin C McLean
- Section of Rheumatology, and Gwen Knapp Center for Lupus and Immunology Research, Department of Medicine, University of Chicago, IL 60637, USA
| | - Malay Mandal
- Section of Rheumatology, and Gwen Knapp Center for Lupus and Immunology Research, Department of Medicine, University of Chicago, IL 60637, USA.
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20
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Sun J, Yang L, Lu Y, Wang H, Peng X, Dong X, Cheng G, Cao Y, Wu B, Wang X, Zhou W. Screening for primary immunodeficiency diseases by next-generation sequencing in early life. Clin Transl Immunology 2020; 9:e1138. [PMID: 32431812 PMCID: PMC7231820 DOI: 10.1002/cti2.1138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Objective We aimed to use next-generation sequencing (NGS) for the early diagnosis of primary immunodeficiency diseases (PIDs) and define its effects on medical management for an infant cohort in early life. Methods A single-centre study was conducted from November 2015 to April 2018. Infants less than 3 months old with infections or abnormal white blood cell counts were enrolled in the study. Gene variants were analysed by NGS, and once a mutation was found in a PID-associated gene, the immune functions associated with this mutation were detected. The diagnosis rate of PIDs in the cohort was the main outcome. The patients received corresponding management and follow-up treatments. Results Among 2392 patients who were genetically tested with NGS, 51 infants were diagnosed with PIDs. Seven types of PIDs were detected, and the most common (25/51, 49%) were combined immunodeficiencies with associated or syndromic features. Thirty-five patients (68.6%) were cured or had improved outcomes after being diagnosed with PID. The NGS cost was US$280 per case. Conclusions This study not only highlighted the potential of NGS to rapidly deliver molecular diagnoses of PIDs but also indicated that the prevalence of PIDs is underestimated. With broader use, this approach has the potential to alter clinical strategies.
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Affiliation(s)
- Jinqiao Sun
- Department of Clinical Immunology Children's Hospital of Fudan University Shanghai China
| | - Lin Yang
- Clinical Genetic Center Children's Hospital of Fudan University Shanghai China
| | - Yulan Lu
- Children's Hospital & Institutes of Biomedical Sciences Fudan university Shanghai China.,Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xiaomin Peng
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xinran Dong
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Guoqiang Cheng
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
| | - Yun Cao
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects The Translational Medicine Center of Children Development and Disease of Fudan University Children's Hospital of Fudan University Shanghai China
| | - Xiaochuan Wang
- Department of Clinical Immunology Children's Hospital of Fudan University Shanghai China
| | - Wenhao Zhou
- Department of Neonatology Children's Hospital of Fudan University Shanghai China
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21
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Streata I, Riza AL, Sosoi S, Burada F, Ioana M. Phenotype Heterogeneity in 3q29 Microduplication Syndrome. CURRENT HEALTH SCIENCES JOURNAL 2020; 46:193-197. [PMID: 32874693 PMCID: PMC7445637 DOI: 10.12865/chsj.46.02.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/15/2020] [Indexed: 11/05/2022]
Abstract
3q29 microduplication syndrome is characterized by widely variable clinical presentation, but generally mild features. Developmental delay, particularly speech, and intellectual disability, eye abnormalities and heart defects are more frequently seen in affected individuals, although it is difficult to delineate a recognisable pattern. We describe a clinical case with a 1.65Mb duplication at 3q29 (chr3:195,979,518-197,638,922, GRCh37) identified by aCGH. The uncharacteristically late onset of the 34 years-old woman is marked by mild intellectual disability, progressive cortical atrophy and recurrent mucosal infections with Candida albicans. The gene content of the duplicated region-29 genes, including PAK2, DLG1, BDH1, FBXO45 and TFRC-seems closely linked to neuronal development and synaptic function, explaining brain and eye development related findings. We speculate on the possible involvement of genes like RNF168 in the aetiology of immunodeficiency. In-depth studies are needed to understand the pathophysiological mechanisms leading to the traits seen in this very rare syndrome.
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Affiliation(s)
- Ioana Streata
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital Craiova, Romania
| | - Anca-Lelia Riza
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital Craiova, Romania
| | - Simona Sosoi
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital Craiova, Romania
| | - Florin Burada
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital Craiova, Romania
| | - Mihai Ioana
- Human Genomics Laboratory, University of Medicine and Pharmacy of Craiova, Romania
- Regional Centre of Medical Genetics Dolj, County Clinical Emergency Hospital Craiova, Romania
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22
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Lewandowicz-Uszyńska A, Pasternak G, Świerkot J, Bogunia-Kubik K. Primary Immunodeficiencies: Diseases of Children and Adults - A Review. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1289:37-54. [PMID: 32803731 DOI: 10.1007/5584_2020_556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Primary immunodeficiencies (PIDs) belong to a group of rare congenital diseases occurring all over the world that may be seen in both children and adults. In most cases, genetic predispositions are already known. As shown in this review, genetic abnormalities may be related to dysfunction of the immune system, which manifests itself as recurrent infections, increased risk of cancer, and autoimmune diseases. This article reviews the various forms of PIDs, including their characterization, management strategies, and complications. Novel aspects of the diagnostics and monitoring of PIDs are presented.
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Affiliation(s)
- Aleksandra Lewandowicz-Uszyńska
- Third Department and Clinic of Pediatrics, Immunology and Rheumatology of Developmental Age, Wroclaw Medical University, Wroclaw, Poland. .,Department of Immunology and Pediatrics, The J. Gromkowski Provincial Hospital, Wroclaw, Poland.
| | - Gerard Pasternak
- Third Department and Clinic of Pediatrics, Immunology and Rheumatology of Developmental Age, Wroclaw Medical University, Wroclaw, Poland
| | - Jerzy Świerkot
- Department and Clinic of Rheumatology and Internal Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Bogunia-Kubik
- Laboratory of Clinical Immunogenetics and Pharmacogenetics, The Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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23
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Lye JJ, Williams A, Baralle D. Exploring the RNA Gap for Improving Diagnostic Yield in Primary Immunodeficiencies. Front Genet 2019; 10:1204. [PMID: 31921280 PMCID: PMC6917654 DOI: 10.3389/fgene.2019.01204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Challenges in diagnosing primary immunodeficiency are numerous and diverse, with current whole-exome and whole-genome sequencing approaches only able to reach a molecular diagnosis in 25–60% of cases. We assess these problems and discuss how RNA-focused analysis has expanded and improved in recent years and may now be utilized to gain an unparalleled insight into cellular immunology. We review how investigation into RNA biology can give information regarding the differential expression, monoallelic expression, and alternative splicing—which have important roles in immune regulation and function. We show how this information can inform bioinformatic analysis pipelines and aid in the variant filtering process, expediting the identification of causal variants—especially those affecting splicing—and enhance overall diagnostic ability. We also demonstrate the challenges, which remain in the design of this type of investigation, regarding technological limitation and biological considerations and suggest potential directions for the clinical applications.
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Affiliation(s)
- Jed J Lye
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom
| | - Anthony Williams
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Wessex Investigational Sciences Hub Laboratory (WISH Lab), Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Faculty of Medicine, Highfield Campus, University of Southampton, Southampton, United Kingdom
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24
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Lamb CC, Wang Y, Lyytinen K. Shared decision making: Does a physician's decision-making style affect patient participation in treatment choices for primary immunodeficiency? J Eval Clin Pract 2019; 25:1102-1110. [PMID: 31115958 PMCID: PMC6900116 DOI: 10.1111/jep.13162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 12/22/2022]
Abstract
Overall health care spending in the United States is equivalent to more than 15% of GDP, yet outcomes rank below the top 25 in most quality categories when compared with other Organization for Economic Cooperation and Development (OECD) countries. The majority of spending is consumed by small patient populations with chronic diseases. Experts believe increased patient-physician shared decision making (SDM) should result in better overall longitudinal care but understanding the physician's role in facilitating SDM is limited. Structural equation modelling was applied to results of a 2016 questionnaire-based survey of 330 US physicians who treat approximately 55% of primary immune deficiency requiring immune globulin therapy; it tested the relationship between slow/rational vs fast/intuitive decision-making styles and SDM as mediated by patient-centric care and moderated by physician's trust in the patient. The results showed a statistically significant relationship between slow/rational decision making and SDM. The results also suggest differences related to age, gender, education, and race but no differences related to trust.
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Affiliation(s)
- Christopher C Lamb
- BioSolutions Services LLC, Cambridge, Massachusetts.,Weatherhead School of Management, Case Western Reserve University, Cleveland, Ohio
| | - Yunmei Wang
- Case Cardiovascular Research Institute, Case Western Reserve University School of Medicine and Harrington Heart &Vascular Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Kalle Lyytinen
- Weatherhead School of Management, Case Western Reserve University, Cleveland, Ohio
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25
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Chinn IK, Chan AY, Chen K, Chou J, Dorsey MJ, Hajjar J, Jongco AM, Keller MD, Kobrynski LJ, Kumanovics A, Lawrence MG, Leiding JW, Lugar PL, Orange JS, Patel K, Platt CD, Puck JM, Raje N, Romberg N, Slack MA, Sullivan KE, Tarrant TK, Torgerson TR, Walter JE. Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol 2019; 145:46-69. [PMID: 31568798 DOI: 10.1016/j.jaci.2019.09.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022]
Abstract
Genetic testing has become an integral component of the diagnostic evaluation of patients with suspected primary immunodeficiency diseases. Results of genetic testing can have a profound effect on clinical management decisions. Therefore clinical providers must demonstrate proficiency in interpreting genetic data. Because of the need for increased knowledge regarding this practice, the American Academy of Allergy, Asthma & Immunology Primary Immunodeficiency Diseases Committee established a work group that reviewed and summarized information concerning appropriate methods, tools, and resources for evaluating variants identified by genetic testing. Strengths and limitations of tests frequently ordered by clinicians were examined. Summary statements and tables were then developed to guide the interpretation process. Finally, the need for research and collaboration was emphasized. Greater understanding of these important concepts will improve the diagnosis and management of patients with suspected primary immunodeficiency diseases.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex.
| | - Alice Y Chan
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Karin Chen
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Janet Chou
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Morna J Dorsey
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Joud Hajjar
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Artemio M Jongco
- Departments of Medicine and Pediatrics, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Great Neck, NY; Center for Health Innovations and Outcomes Research, Feinstein Institute for Medical Research, Great Neck, NY; Division of Allergy & Immunology, Cohen Children's Medical Center of New York, Great Neck, NY
| | - Michael D Keller
- Department of Allergy and Immunology, Children's National Hospital, Washington, DC
| | - Lisa J Kobrynski
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Attila Kumanovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Monica G Lawrence
- Department of Medicine, Division of Asthma, Allergy and Immunology, University of Virginia Health System, Charlottesville, Va
| | - Jennifer W Leiding
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Cancer and Blood Disorders Institute, Johns Hopkins-All Children's Hospital, St Petersburg, Fla
| | - Patricia L Lugar
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, NC
| | - 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
| | - Kiran Patel
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Craig D Platt
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Jennifer M Puck
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Nikita Raje
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Mo; Division of Allergy/Asthma/Immunology, Children's Mercy Hospital, Kansas City, Mo
| | - Neil Romberg
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Maria A Slack
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY; Department of Pediatrics, Division of Pediatric Allergy and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Kathleen E Sullivan
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Teresa K Tarrant
- Department of Medicine, Division of Rheumatology and Immunology, Duke University Medical Center, Durham, NC
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Jolan E Walter
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Division of Pediatric Allergy Immunology, Massachusetts General Hospital, Boston, Mass
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26
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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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27
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Jaeken J, Lefeber DJ, Matthijs G. Clinical Utility Gene Card for: PGM3 defective congenital disorder of glycosylation. Eur J Hum Genet 2019; 27:1757-1760. [PMID: 31231132 DOI: 10.1038/s41431-019-0453-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 05/20/2019] [Accepted: 05/31/2019] [Indexed: 11/10/2022] Open
Abstract
Review of the analytical and clinical validity as well as of the clinical utility of DNA-based testing for mutations in PGM3 in diagnostic, predictive and prenatal settings, and for risk assessment in relatives.
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Affiliation(s)
- Jaak Jaeken
- Department of Regeneration and Development, Center for Metabolic Diseases, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium.
| | - Dirk J Lefeber
- Department of Neurology, Translational Metabolic Laboratory, Radboudumc, Nijmegen, The Netherlands
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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28
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Exome sequencing in routine diagnostics: a generic test for 254 patients with primary immunodeficiencies. Genome Med 2019; 11:38. [PMID: 31203817 PMCID: PMC6572765 DOI: 10.1186/s13073-019-0649-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/17/2019] [Indexed: 12/18/2022] Open
Abstract
Background Diagnosis of primary immunodeficiencies (PIDs) is complex and cumbersome yet important for the clinical management of the disease. Exome sequencing may provide a genetic diagnosis in a significant number of patients in a single genetic test. Methods In May 2013, we implemented exome sequencing in routine diagnostics for patients suffering from PIDs. This study reports the clinical utility and diagnostic yield for a heterogeneous group of 254 consecutively referred PID patients from 249 families. For the majority of patients, the clinical diagnosis was based on clinical criteria including rare and/or unusual severe bacterial, viral, or fungal infections, sometimes accompanied by autoimmune manifestations. Functional immune defects were interpreted in the context of aberrant immune cell populations, aberrant antibody levels, or combinations of these factors. Results For 62 patients (24%), exome sequencing identified pathogenic variants in well-established PID genes. An exome-wide analysis diagnosed 10 additional patients (4%), providing diagnoses for 72 patients (28%) from 68 families altogether. The genetic diagnosis directly indicated novel treatment options for 25 patients that received a diagnosis (34%). Conclusion Exome sequencing as a first-tier test for PIDs granted a diagnosis for 28% of patients. Importantly, molecularly defined diagnoses indicated altered therapeutic options in 34% of cases. In addition, exome sequencing harbors advantages over gene panels as a truly generic test for all genetic diseases, including in silico extension of existing gene lists and re-analysis of existing data. Electronic supplementary material The online version of this article (10.1186/s13073-019-0649-3) contains supplementary material, which is available to authorized users.
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29
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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: 34] [Impact Index Per Article: 6.8] [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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30
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Heimall J. Genetic Testing to Diagnose Primary Immunodeficiency Disorders and to Identify Targeted Therapy. Immunol Allergy Clin North Am 2019; 39:129-140. [DOI: 10.1016/j.iac.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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31
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Winkler TH, Mårtensson IL. The Role of the Pre-B Cell Receptor in B Cell Development, Repertoire Selection, and Tolerance. Front Immunol 2018; 9:2423. [PMID: 30498490 PMCID: PMC6249383 DOI: 10.3389/fimmu.2018.02423] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022] Open
Abstract
Around four decades ago, it had been observed that there were cell lines as well as cells in the fetal liver that expressed antibody μ heavy (μH) chains in the apparent absence of bona fide light chains. It was thus possible that these cells expressed another molecule(s), that assembled with μH chains. The ensuing studies led to the discovery of the pre-B cell receptor (pre-BCR), which is assembled from Ig μH and surrogate light (SL) chains, together with the signaling molecules Igα and β. It is expressed on a fraction of pro-B (pre-BI) cells and most large pre-B(II) cells, and has been implicated in IgH chain allelic exclusion and down-regulation of the recombination machinery, assessment of the expressed μH chains and shaping the IgH repertoire, transition from the pro-B to pre-B stage, pre-B cell expansion, and cessation.
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Affiliation(s)
- Thomas H Winkler
- Chair of Genetics, Department of Biology, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Inga-Lill Mårtensson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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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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Eleven percent intact PGM3 in a severely immunodeficient patient with a novel splice-site mutation, a case report. BMC Pediatr 2018; 18:285. [PMID: 30157810 PMCID: PMC6114780 DOI: 10.1186/s12887-018-1258-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 08/17/2018] [Indexed: 12/28/2022] Open
Abstract
Background A novel immunodeficiency, frequently accompanied by high serum-IgE, and caused by mutations in the PGM3 gene was described in 2014. To date there are no unique phenotype characteristics for PGM3 deficiency. PGM3 encodes a carbohydrate-modifying enzyme, phosphoglucomutase 3. Null-mutations are quite likely lethal, and to date only missense mutations or small deletions have been reported. Such mutations frequently cause a combination of reduced enzyme activity and protein instability, complicating determination of the enzyme level needed for survival. Here we present the first patient with a homozygous splice-modifying mutation in the PGM3 gene. An A > G substitution at position c.871 + 3 (transcript NM_001199917) is causing a deletion of exon 7 in the majority of PGM3 transcripts. In addition, this case further increases the clinical phenotypes of immunodeficiency caused by PGM3 mutations. Case presentation We describe the symptoms of a 3-year-old girl who was severely growth retarded, had vascular malformations, extensive eczema, multiple food-allergies, and was prone to infections. Unlike the majority of reported PGM3 deficient patients she lacked skeletal dysplasia and had normal neurocognitive development. In addition to the high serum-IgE, she displayed altered T cell numbers with reduced naïve CD4+ and CD8+ T-cells, increased number of activated effector memory CD8+ T cells and aberrant T-cell functions. The patient was homozygous for a new hypomorphic, splice-modifying mutation in the PGM3 gene, causing severely reduced mRNA levels. In the patient’s cells, we observed 5% intact mRNA and approximately 11% of the protein levels seen in healthy controls. Treatment with allogeneic hematopoietic stem cell therapy was planned, but unfortunately the clinical condition deteriorated with multi-organ failure, which led to her death at 3 years of age. Conclusions There is still no specific phenotype identified that distinguishes immunodeficiency caused by PGM3 mutations from other forms of immunodeficiency. The patient described here yields new information on the phenotypic variability among these patients. In addition, since all the synthesized protein is wild-type, it is possible for the first time to estimate the enzyme activity in vivo. The results suggest that1/10 of the normal PGM3 level is sufficient for survival but that it is insufficient for accurate carbohydrate processing. Electronic supplementary material The online version of this article (10.1186/s12887-018-1258-9) contains supplementary material, which is available to authorized users.
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Rahmani ES, Azarpara Н, Karimipoor M, Rahimi Н. Whole exome analysis of primary immunodeficiency. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The human primary immunodeficiency diseases (PIDs) refer to a rare heterogeneous group of single-gene inherited disorders causing malfunctions in the immune system, and thus the affected patients have a predisposition to severe life-threatening infections. The heterogeneous nature of PIDs, which involves at list 300 different genes, makes diagnosis of the disease a complex issue. Although studies revealed that six million people have a kind of PID, but due to a complex diagnosis procedure many affected individuals have not gotten a correct diagnosis. However, thanks to advancing in the DNA sequencing method and availability of sophisticated sequencers molecular characterization of genetic disorders have been revolutionized. The whole exome sequencing (WES) method can help clinicians detect Mendelian disease and other complex genetic disorders. The presented study used WES to investigate two infants with symptoms of primary immunodeficiency including hemophagocytic lymphohistiocytosis (HLH) and severe combined immunodeficiency (SCID). It has been shown that the HLH patient had a mutation in the UNC13D gene (NM_199242.2:c.627delT), and the SCID patient had a mutation in the RAG1 gene (NM_000448.2:c.322C>G). It has been demonstrated that WES is a fast and cost-effective method facilitating genetic diagnosis in PID sufferers.
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Nunes-Santos CDJ, Rosenzweig SD. Bacille Calmette-Guerin Complications in Newly Described Primary Immunodeficiency Diseases: 2010-2017. Front Immunol 2018; 9:1423. [PMID: 29988375 PMCID: PMC6023996 DOI: 10.3389/fimmu.2018.01423] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/07/2018] [Indexed: 12/25/2022] Open
Abstract
Bacille Calmette–Guerin (BCG) vaccine is widely used as a prevention strategy against tuberculosis. BCG is a live vaccine, usually given early in life in most countries. While safe to most recipients, it poses a risk to immunocompromised patients. Several primary immunodeficiency diseases (PIDD) have been classically associated with complications related to BCG vaccine. However, a number of new inborn errors of immunity have been described lately in which little is known about adverse reactions following BCG vaccination. The aim of this review is to summarize the existing data on BCG-related complications in patients diagnosed with PIDD described since 2010. When BCG vaccination status or complications were not specifically addressed in those manuscripts, we directly contacted the corresponding authors for further clarification. We also analyzed data on other mycobacterial infections in these patients. Based on our analysis, around 8% of patients with gain-of-function mutations in STAT1 had mycobacterial infections, including localized complications in 3 and disseminated disease in 4 out of 19 BCG-vaccinated patients. Localized BCG reactions were also frequent in activated PI3Kδ syndrome type 1 (3/10) and type 2 (2/18) vaccinated children. Also, of note, no BCG-related complications have been described in either CTLA4 or LRBA protein-deficient patients; and not enough information on BCG-vaccinated NFKB1 or NFKB2-deficient patients was available to drive any conclusions about these diseases. Despite the high prevalence of environmental mycobacterial infections in GATA2-deficient patients, only one case of BCG reaction has been reported in a patient who developed disseminated disease. In conclusion, BCG complications could be expected in some particular, recently described PIDD and it remains a preventable risk factor for pediatric PIDD patients.
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Affiliation(s)
- Cristiane de Jesus Nunes-Santos
- Faculdade de Medicina, Instituto da Crianca, Universidade de São Paulo, São Paulo, Brazil.,Immunology Service, Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, United States
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36
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Abolhassani H, Aghamohammadi A, Fang M, Rezaei N, Jiang C, Liu X, Pan-Hammarström Q, Hammarström L. Clinical implications of systematic phenotyping and exome sequencing in patients with primary antibody deficiency. Genet Med 2018; 21:243-251. [PMID: 29921932 DOI: 10.1038/s41436-018-0012-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 11/20/2017] [Accepted: 03/20/2018] [Indexed: 02/08/2023] Open
Abstract
PURPOSE The etiology of 80% of patients with primary antibody deficiency (PAD), the second most common type of human immune system disorder after human immunodeficiency virus infection, is yet unknown. METHODS Clinical/immunological phenotyping and exome sequencing of a cohort of 126 PAD patients (55.5% male, 95.2% childhood onset) born to predominantly consanguineous parents (82.5%) with unknown genetic defects were performed. The American College of Medical Genetics and Genomics criteria were used for validation of pathogenicity of the variants. RESULTS This genetic approach and subsequent immunological investigations identified potential disease-causing variants in 86 patients (68.2%); however, 27 of these patients (31.4%) carried autosomal dominant (24.4%) and X-linked (7%) gene defects. This genetic approach led to the identification of new phenotypes in 19 known genes (38 patients) and the discovery of a new genetic defect (CD70 pathogenic variants in 2 patients). Medical implications of a definite genetic diagnosis were reported in ~50% of the patients. CONCLUSION Due to misclassification of the conventional approach for targeted sequencing, employing next-generation sequencing as a preliminary step of molecular diagnostic approach to patients with PAD is crucial for management and treatment of the patients and their family members.
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Affiliation(s)
- Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mingyan Fang
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden.,BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Chongyi Jiang
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, Sweden. .,BGI-Shenzhen, Shenzhen, 518083, China. .,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
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37
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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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Pietrucha B, Heropolitańska-Pliszka E, Geffers R, Enßen J, Wieland B, Bogdanova NV, Dörk T. Clinical and Biological Manifestation of RNF168 Deficiency in Two Polish Siblings. Front Immunol 2017; 8:1683. [PMID: 29255463 PMCID: PMC5722808 DOI: 10.3389/fimmu.2017.01683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/15/2017] [Indexed: 11/13/2022] Open
Abstract
Germline mutations in the RING finger protein gene RNF168 have been identified in a combined immunodeficiency disorder called RIDDLE syndrome. Since only two patients have been described with somewhat different phenotypes, there is need to identify further patients. Here, we report on two Polish siblings with RNF168 deficiency due to homozygosity for a novel frameshift mutation, c.295delG, that was identified through exome sequencing. Both patients presented with immunoglobulin deficiency, telangiectasia, cellular radiosensitivity, and increased alpha-fetoprotein (AFP) levels. The younger sibling had a more pronounced neurological and morphological phenotype, and she also carried an ATM gene mutation in the heterozygous state. Immunoblot analyses showed absence of RNF168 protein, whereas ATM levels and function were proficient in lymphoblastoid cells from both patients. Consistent with the absence of RNF168 protein, 53BP1 recruitment to DNA double-strand breaks (DSBs) after irradiation was undetectable in lymphoblasts or primary fibroblasts from either of the two patients. γH2AX foci accumulated normally but they disappeared with significant delay, indicating a severe defect in DSB repair. A comparison with the two previously identified patients indicates immunoglobulin deficiency, cellular radiosensitivity, and increased AFP levels as hallmarks of RNF168 deficiency. The variability in its clinical expression despite similar cellular phenotypes suggests that some manifestations of RNF168 deficiency may be modified by additional genetic or epidemiological factors.
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Affiliation(s)
- Barbara Pietrucha
- Department of Immunology, Children's Memorial Health Institute, Warsaw, Poland
| | | | - Robert Geffers
- Genome Analytics Unit, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Julia Enßen
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Britta Wieland
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Valerijevna Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
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39
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Whole exome sequencing in inborn errors of immunity: use the power but mind the limits. Curr Opin Allergy Clin Immunol 2017; 17:421-430. [DOI: 10.1097/aci.0000000000000398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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40
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Clinical, immunologic, and genetic spectrum of 696 patients with combined immunodeficiency. J Allergy Clin Immunol 2017; 141:1450-1458. [PMID: 28916186 DOI: 10.1016/j.jaci.2017.06.049] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/16/2017] [Accepted: 06/26/2017] [Indexed: 11/21/2022]
Abstract
BACKGROUND Combined immunodeficiencies (CIDs) are diseases of defective adaptive immunity with diverse clinical phenotypes. Although CIDs are more prevalent in the Middle East than Western countries, the resources for genetic diagnosis are limited. OBJECTIVES This study aims to characterize the categories of patients with CIDs in Iran clinically and genetically. METHODS Clinical and laboratory data were obtained from 696 patients with CIDs. Patients were subdivided into those with syndromic (344 patients) and nonsyndromic (352 patients) CIDs. Targeted DNA sequencing was performed on 243 (34.9%) patients. RESULTS The overall diagnostic yield of the 243 sequenced patients was 77.8% (189 patients). The clinical diagnosis of hyper-IgE syndrome (P < .001), onset of disease at greater than 5 years (P = .02), and absence of multiple affected family members (P = .04) were significantly more frequent in the patients without a genetic diagnosis. An autosomal recessive disease was found in 62.9% of patients, reflecting the high rate of consanguinity in this cohort. Mutations impairing VDJ recombination and DNA repair were the most common underlying causes of CIDs. However, in patients with syndromic CIDs, autosomal recessive mutations in ataxia-telangiectasia mutated (ATM), autosomal dominant mutations in signal transducer and activator of transcription 3 (STAT3), and microdeletions in 22q11.21 were the most commonly affected genomic loci. Patients with syndromic CIDs had a significantly lower 5-year survival rate rather than those with nonsyndromic CIDs. CONCLUSIONS This study provides proof of principle for the application of targeted next-generation sequencing panels in countries with limited diagnostic resources. The effect of genetic diagnosis on clinical care requires continued improvements in therapeutic resources for these patients.
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41
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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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Kienzler AK, Hargreaves CE, Patel SY. The role of genomics in common variable immunodeficiency disorders. Clin Exp Immunol 2017; 188:326-332. [PMID: 28236292 DOI: 10.1111/cei.12947] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2017] [Indexed: 01/16/2023] Open
Abstract
The advent of next-generation sequencing (NGS) and 'omic' technologies has revolutionized the field of genetics, and its implementation in health care has the potential to realize precision medicine. Primary immunodeficiencies (PID) are a group of rare diseases which have benefited from NGS, with a massive increase in causative genes identified in the past few years. Common variable immunodeficiency disorders (CVID) are a heterogeneous form of PID and the most common form of antibody failure in children and adults. While a monogenic cause of disease has been identified in a small subset of CVID patients, a genomewide association study and whole genome sequencing have found that, in the majority, a polygenic cause is likely. Other NGS technologies such as RNA sequencing and epigenetic studies have contributed further to our understanding of the contribution of altered gene expression in CVID pathogenesis. We believe that to unravel further the complexities of CVID, a multi-omic approach, combining DNA sequencing with gene expression, methylation, proteomic and metabolomics data, will be essential to identify novel disease-associated pathways and therapeutic targets.
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Affiliation(s)
- A-K Kienzler
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
| | - C E Hargreaves
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
| | - S Y Patel
- NIHR Oxford Biomedical Research Centre, Clinical Immunology Group, Oxford, UK
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43
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Invasive Fungal Infection in Primary Immunodeficiencies Other Than Chronic Granulomatous Disease. CURRENT FUNGAL INFECTION REPORTS 2017. [DOI: 10.1007/s12281-017-0273-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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44
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Rota IA, Dhalla F. FOXN1 deficient nude severe combined immunodeficiency. Orphanet J Rare Dis 2017; 12:6. [PMID: 28077132 PMCID: PMC5225657 DOI: 10.1186/s13023-016-0557-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022] Open
Abstract
Nude severe combined immunodeficiency is a rare inherited disease caused by autosomal recessive loss-of-function mutations in FOXN1. This gene encodes a transcription factor essential for the development of the thymus, the primary lymphoid organ that supports T-cell development and selection. To date nine cases have been reported presenting with the clinical triad of absent thymus resulting in severe T-cell immunodeficiency, congenital alopecia universalis and nail dystrophy. Diagnosis relies on testing for FOXN1 mutations, which allows genetic counselling and guides therapeutic management. Options for treating the underlying immune deficiency include HLA-matched genoidentical haematopoietic cell transplantation containing mature donor T-cells or thymus tissue transplantation. Experience from other severe combined immune deficiency syndromes suggests that early diagnosis, supportive care and definitive management result in better patient outcomes. Without these the prognosis is poor due to early-onset life threatening infections.
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Affiliation(s)
- Ioanna A Rota
- Developmental Immunology Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Fatima Dhalla
- Developmental Immunology Group, Department of Paediatrics, University of Oxford, Oxford, UK. .,Department of Clinical Immunology, Oxford University Hospitals, Oxford, UK.
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45
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Moscato GMF, Giacobbi E, Anemona L, Di Cesare S, Di Matteo G, Andreoni M, Mauriello A, Moschese V. Dysplasia of Granulocytes in a Patient with HPV Disease, Recurrent Infections, and B Lymphopenia: A Novel Variant of WHIM Syndrome? Front Pediatr 2017; 5:95. [PMID: 28512628 PMCID: PMC5411434 DOI: 10.3389/fped.2017.00095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 04/12/2017] [Indexed: 11/13/2022] Open
Abstract
WHIM syndrome is a condition in which affected persons have chronic peripheral neutropenia, lymphopenia, abnormal susceptibility to human papilloma virus infection, and myelokathexis. Myelokathexis refers to the retention of mature neutrophils in the bone marrow (BM), which accounts for degenerative changes and hypersegmentation. Most patients present heterozygous autosomal dominant mutations of the gene encoding CXCR4. Consequently, aberrant CXCL12/CXCR4 signaling impairs the receptor downregulation causing hyperactivation (gain-of-function) that affects BM homing for myelopoiesis and lymphopoiesis and the release of neutrophils in the bloodstream. We report the case of a 26-year-old female with severe foot and hand cutaneous warts since childhood, recalcitrant genital condylomatas, bacterial infections, and intraepithelial cervical neoplasia. Laboratory tests revealed severe B lymphopenia and HPV high and low risk types. HIV testing was negative. Not only CXCR4 but also GATA2, NEMO, and CD40L gene mutations were excluded. BM smears revealed, in the presence of a normal cellularity, hyperplasia of myeloid cells (MPO positive) and karyorrhexis, especially in neutrophils and eosinophils. Of note, neutrophils with altered lobation of nuclei connected by long thin chromatin filaments were observed. Our patient presented a clinical and histological picture reminiscent of WHIM in the presence of normal peripheral neutrophil counts and wild-type CXCR4 gene. Although the BM did not reveal a classical pattern of myelokathexis, the observation of consistent signs of neutrophil dysplasia has fuelled the hypothesis of a novel WHIM variant or a novel immunodeficiency. We speculate that abnormalities that affect CXCR4/CXCL12 pair, including GRK levels or activity, might be responsible for this WHIM-like disorder.
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Affiliation(s)
- Giusella M F Moscato
- Infectious Diseases Unit, Policlinico Tor Vergata, University of Rome Tor Vergata, Rome, Italy
| | - Erica Giacobbi
- Anatomic Pathology, Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Lucia Anemona
- Anatomic Pathology, Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Silvia Di Cesare
- Department of Medicine of Systems, University of Rome Tor Vergata, Rome, Italy
| | - Gigliola Di Matteo
- Department of Medicine of Systems, University of Rome Tor Vergata, Rome, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, Policlinico Tor Vergata, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Mauriello
- Anatomic Pathology, Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Viviana Moschese
- Department of Medicine of Systems, University of Rome Tor Vergata, Rome, Italy.,Pediatric Immunology Unit, Policlinico Tor Vergata, University of Rome Tor Vergata, Rome, Italy
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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: 196] [Impact Index Per Article: 28.0] [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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47
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Woon ST, Ameratunga R. Comprehensive genetic testing for primary immunodeficiency disorders in a tertiary hospital: 10-year experience in Auckland, New Zealand. Allergy Asthma Clin Immunol 2016; 12:65. [PMID: 27980540 PMCID: PMC5142146 DOI: 10.1186/s13223-016-0169-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/16/2016] [Indexed: 12/04/2022] Open
Abstract
Background and purpose New Zealand is a developed geographically isolated country in the South Pacific with a population of 4.4 million. Genetic diagnosis is the standard of care for most patients with primary immunodeficiency disorders (PIDs). Methods Since 2005, we have offered a comprehensive genetic testing service for PIDs and other immune-related disorders with a published sequence. Here we present results for this program, over the first decade, between 2005 and 2014. Results We undertook testing in 228 index cases and 32 carriers during this time. The three most common test requests were for X-linked lymphoproliferative (XLP), tumour necrosis factor receptor associated periodic syndrome (TRAPS) and haemophagocytic lymphohistiocytosis (HLH). Of the 32 suspected XLP cases, positive diagnoses were established in only 2 patients. In contrast, genetic defects in 8 of 11 patients with suspected X-linked agammaglobulinemia (XLA) were confirmed. Most XLA patients were initially identified from absence of B cells. Overall, positive diagnoses were made in about 23% of all tests requested. The diagnostic rate was lowest for several conditions with locus heterogeneity. Conclusions Thorough clinical characterisation of patients can assist in prioritising which genes should be tested. The clinician-driven customised comprehensive genetic service has worked effectively for New Zealand. Next generation sequencing will play an increasing role in disorders with locus heterogeneity.
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Affiliation(s)
- See-Tarn Woon
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Grafton, Auckland, 1148 New Zealand
| | - Rohan Ameratunga
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Grafton, Auckland, 1148 New Zealand
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48
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Gallo V, Dotta L, Giardino G, Cirillo E, Lougaris V, D'Assante R, Prandini A, Consolini R, Farrow EG, Thiffault I, Saunders CJ, Leonardi A, Plebani A, Badolato R, Pignata C. Diagnostics of Primary Immunodeficiencies through Next-Generation Sequencing. Front Immunol 2016; 7:466. [PMID: 27872624 PMCID: PMC5098274 DOI: 10.3389/fimmu.2016.00466] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Recently, a growing number of novel genetic defects underlying primary immunodeficiencies (PIDs) have been identified, increasing the number of PID up to more than 250 well-defined forms. Next-generation sequencing (NGS) technologies and proper filtering strategies greatly contributed to this rapid evolution, providing the possibility to rapidly and simultaneously analyze large numbers of genes or the whole exome. OBJECTIVE To evaluate the role of targeted NGS and whole exome sequencing (WES) in the diagnosis of a case series, characterized by complex or atypical clinical features suggesting a PID, difficult to diagnose using the current diagnostic procedures. METHODS We retrospectively analyzed genetic variants identified through targeted NGS or WES in 45 patients with complex PID of unknown etiology. RESULTS Forty-seven variants were identified using targeted NGS, while 5 were identified using WES. Newly identified genetic variants were classified into four groups: (I) variations associated with a well-defined PID, (II) variations associated with atypical features of a well-defined PID, (III) functionally relevant variations potentially involved in the immunological features, and (IV) non-diagnostic genotype, in whom the link with phenotype is missing. We reached a conclusive genetic diagnosis in 7/45 patients (~16%). Among them, four patients presented with a typical well-defined PID. In the remaining three cases, mutations were associated with unexpected clinical features, expanding the phenotypic spectrum of typical PIDs. In addition, we identified 31 variants in 10 patients with complex phenotype, individually not causative per se of the disorder. CONCLUSION NGS technologies represent a cost-effective and rapid first-line genetic approach for the evaluation of complex PIDs. WES, despite a moderate higher cost compared to targeted, is emerging as a valuable tool to reach in a timely manner, a PID diagnosis with a considerable potential to draw genotype-phenotype correlation. Nevertheless, a large fraction of patients still remains without a conclusive diagnosis. In these patients, the sum of non-diagnostic variants might be proven informative in future studies with larger cohorts of patients.
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Affiliation(s)
- Vera Gallo
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Laura Dotta
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Giuliana Giardino
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Emilia Cirillo
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Vassilios Lougaris
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Roberta D'Assante
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
| | - Alberto Prandini
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Rita Consolini
- Department of Clinical and Experimental Medicine, University of Pisa , Pisa , Italy
| | - Emily G Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital , Kansas City, MO , USA
| | - Antonio Leonardi
- Department of Molecular Medicine and Medical Biotechnology, Federico II University , Naples , Italy
| | - Alessandro Plebani
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Raffaele Badolato
- Department of Clinical and Experimental Medicine, "Angelo Nocivelli" Institute for Molecular Medicine, University of Brescia , Brescia , Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, Federico II University , Naples , Italy
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49
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Rapid molecular diagnostics of severe primary immunodeficiency determined by using targeted next-generation sequencing. J Allergy Clin Immunol 2016; 138:1142-1151.e2. [PMID: 27484032 DOI: 10.1016/j.jaci.2016.05.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 05/04/2016] [Accepted: 05/31/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Primary immunodeficiency diseases (PIDDs) are inherited disorders of the immune system. The most severe form, severe combined immunodeficiency (SCID), presents with profound deficiencies of T cells, B cells, or both at birth. If not treated promptly, affected patients usually do not live beyond infancy because of infections. Genetic heterogeneity of SCID frequently delays the diagnosis; a specific diagnosis is crucial for life-saving treatment and optimal management. OBJECTIVE We developed a next-generation sequencing (NGS)-based multigene-targeted panel for SCID and other severe PIDDs requiring rapid therapeutic actions in a clinical laboratory setting. METHODS The target gene capture/NGS assay provides an average read depth of approximately 1000×. The deep coverage facilitates simultaneous detection of single nucleotide variants and exonic copy number variants in one comprehensive assessment. Exons with insufficient coverage (<20× read depth) or high sequence homology (pseudogenes) are complemented by amplicon-based sequencing with specific primers to ensure 100% coverage of all targeted regions. RESULTS Analysis of 20 patient samples with low T-cell receptor excision circle numbers on newborn screening or a positive family history or clinical suspicion of SCID or other severe PIDD identified deleterious mutations in 14 of them. Identified pathogenic variants included both single nucleotide variants and exonic copy number variants, such as hemizygous nonsense, frameshift, and missense changes in IL2RG; compound heterozygous changes in ATM, RAG1, and CIITA; homozygous changes in DCLRE1C and IL7R; and a heterozygous nonsense mutation in CHD7. CONCLUSION High-throughput deep sequencing analysis with complete clinical validation greatly increases the diagnostic yield of severe primary immunodeficiency. Establishing a molecular diagnosis enables early immune reconstitution through prompt therapeutic intervention and guides management for improved long-term quality of life.
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50
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Application of extensively targeted next-generation sequencing for the diagnosis of primary immunodeficiencies. J Allergy Clin Immunol 2016; 138:303-305.e3. [DOI: 10.1016/j.jaci.2016.01.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/26/2015] [Accepted: 01/20/2016] [Indexed: 01/03/2023]
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