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Huynh A, Gray PE, Sullivan A, Mackie J, Guerin A, Rao G, Pathmanandavel K, Mina ED, Hollway G, Hobbs M, Enthoven K, O'Young P, McManus S, Wainwright LH, Higgins M, Noon F, Wong M, Bastard P, Zhang Q, Casanova JL, Hsiao KC, Pinzon-Charry A, Ma CS, Tangye SG. A Novel Case of IFNAR1 Deficiency Identified a Common Canonical Splice Site Variant in DOCK8 in Western Polynesia: The Importance of Validating Variants of Unknown Significance in Under-Represented Ancestries. J Clin Immunol 2024; 44:170. [PMID: 39098944 PMCID: PMC11298505 DOI: 10.1007/s10875-024-01774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 07/23/2024] [Indexed: 08/06/2024]
Abstract
Advanced genomic technologies such as whole exome or whole genome sequencing have improved diagnoses and disease outcomes for individuals with genetic diseases. Yet, variants of unknown significance (VUS) require rigorous validation to establish disease causality or modification, or to exclude them from further analysis. Here, we describe a young individual of Polynesian ancestry who in the first 13 mo of life presented with SARS-CoV-2 pneumonia, severe enterovirus meningitis and adenovirus gastroenteritis, and severe adverse reaction to MMR vaccination. Genomic analysis identified a previously reported pathogenic homozygous variant in IFNAR1 (c.1156G > T, p.Glu386* LOF), which is common in Western Polynesia. Moreover, a new and putatively deleterious canonical splice site variant in DOCK8 was also found in homozygosity (c.3234 + 2T > C). This DOCK8 variant is common in Polynesians and other under-represented ancestries in large genomic databases. Despite in silico bioinformatic predictions, extensive in vitro and ex vivo analysis revealed the DOCK8 variant likely be neutral. Thus, our study reports a novel case of IFNAR1 deficiency, but also highlights the importance of functional validation of VUS, including those predicted to be deleterious, and the pressing need to expand our knowledge of the genomic architecture and landscape of under-represented populations and ancestries.
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Affiliation(s)
- Aimee Huynh
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
| | - Paul E Gray
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- School Medicine, Western Sydney University, Penrith, NSW, Australia
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Randwick, Australia
| | - Anna Sullivan
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
- Clinical Immunogenomics Research Consortium, Australasia, Australia
| | - Joseph Mackie
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Antoine Guerin
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Geetha Rao
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Karrnan Pathmanandavel
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Erika Della Mina
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Georgina Hollway
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Matthew Hobbs
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Karen Enthoven
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Patrick O'Young
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
| | - Sam McManus
- Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | | | | | - Fallon Noon
- Genetic Health Queensland, Brisbane, Australia
| | - Melanie Wong
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Department of Allergy and Immunology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- University of Paris, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- University of Paris, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, Paris, France
- Howard Hughes Medical Institute, New York, USA
| | - Kuang-Chih Hsiao
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Starship Child Health, Auckland, New Zealand
- Department of Paediatrics, University of Auckland, Auckland, New Zealand
| | - Alberto Pinzon-Charry
- Queensland Paediatric Immunology and Allergy Service, Children's Health Queensland, Brisbane, QLD, 4101, Australia
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Griffith University and University of Queensland, Queensland, Australia
| | - Cindy S Ma
- Clinical Immunogenomics Research Consortium, Australasia, Australia
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Stuart G Tangye
- Clinical Immunogenomics Research Consortium, Australasia, Australia.
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW, 2010, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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2
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O'Donovan CJ, Tan LT, Abidin MAZ, Roderick MR, Grammatikos A, Bernatoniene J. Diagnosis of Chronic Granulomatous Disease: Strengths and Challenges in the Genomic Era. J Clin Med 2024; 13:4435. [PMID: 39124702 DOI: 10.3390/jcm13154435] [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: 06/27/2024] [Revised: 07/17/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Chronic granulomatous disease (CGD) is a group of rare primary inborn errors of immunity characterised by a defect in the phagocyte respiratory burst, which leads to severe and life-threatening infective and inflammatory complications. Despite recent advances in our understanding of the genetic and molecular pathophysiology of X-linked and autosomal recessive CGD, and growth in the availability of functional and genetic testing, there remain significant barriers to early and accurate diagnosis. In the current review, we provide an up-to-date summary of CGD pathophysiology, underpinning current methods of diagnostic testing for CGD and closely related disorders. We present an overview of the benefits of early diagnosis and when to suspect and test for CGD. We discuss current and historical methods for functional testing of NADPH oxidase activity, as well as assays for measuring protein expression of NADPH oxidase subunits. Lastly, we focus on genetic and genomic methods employed to diagnose CGD, including gene-targeted panels, comprehensive genomic testing and ancillary methods. Throughout, we highlight general limitations of testing, and caveats specific to interpretation of results in the context of CGD and related disorders, and provide an outlook for newborn screening and the future.
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Affiliation(s)
- Conor J O'Donovan
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Upper Maudlin Street, Bristol BS2 8BJ, UK
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Lay Teng Tan
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Upper Maudlin Street, Bristol BS2 8BJ, UK
- Department of Paediatrics, University Malaya Medical Center, Lembah Pantai, Kuala Lumpur 59100, Malaysia
| | - Mohd A Z Abidin
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Upper Maudlin Street, Bristol BS2 8BJ, UK
- Department of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Marion R Roderick
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Upper Maudlin Street, Bristol BS2 8BJ, UK
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Alexandros Grammatikos
- Department of Immunology, Southmead Hospital, North Bristol NHS Trust, Bristol BS10 5NB, UK
| | - Jolanta Bernatoniene
- Department of Paediatric Immunology and Infectious Diseases, Bristol Royal Hospital for Children, University Hospitals Bristol and Weston NHS Foundation Trust, Upper Maudlin Street, Bristol BS2 8BJ, UK
- School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol BS8 1TD, UK
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3
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Aykut A, Durmaz A, Karaca N, Gulez N, Genel F, Celmeli F, Cogurlu MT, Akcan M, Cicek D, Cipe FE, Kiykim A, Yıldıran A, Unluhizarci K, Kilic SS, Aksu G, Ardeniz O, Kutukculer N. Primary immune regulatory disorders (PIRD): expanding the mutation spectrum in Turkey and identification of sixteen novel variants. Immunol Res 2024:10.1007/s12026-024-09477-6. [PMID: 38644452 DOI: 10.1007/s12026-024-09477-6] [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: 10/13/2023] [Accepted: 04/01/2024] [Indexed: 04/23/2024]
Abstract
Human Inborn Errors of Immunity (IEIs) encompass a clinically and genetically heterogeneous group of disorders, ranging from mild cases to severe, life-threatening types. Among these, Primary Immune Regulatory Disorders (PIRDs) constitute a subset of IEIs characterized by diverse clinical phenotypes, prominently featuring severe atopy, autoimmunity, lymphoproliferation, hyperinflammation, autoinflammation, and susceptibility to malignancies. According to the latest report from the International Union of Immunological Societies (IUIS), PIRDs arise from mutations in various genes including LYST, RAB27A, AP3B1, AP3D1, PRF1, UNC13D, STX11, STXBP2, FAAP24, SLC7A7, RASGRP1, CD70, CTPS1, RLTPR, ITK, MAGT1, PRKCD, TNFRSF9, SH2DIA, XIAP, CD27 (TNFRSF7), FAS (TNFRSF6), FASLG (TNFSF6), CASP10, CASP8, FADD, LRBA, STAT3, AIRE, ITCH, ZAP70, TPP2, JAK1, PEPD, FOXP3, IL2RA, CTLA4, BACH2, IL2RB, DEF6, FERMT1, IL10, IL10RA, IL10RB, NFAT5, TGFB1, and RIPK1 genes. We designed a targeted next-generation sequencing (TNGS) workflow using the Ion AmpliSeq™ Primary Immune Deficiency Research Panel to sequence 264 genes associated with IEIs on the Ion S5™ Sequencer. In this study, we report the identification of 38 disease-causing variants, including 16 novel ones, detected in 40 patients across 15 distinct PIRD genes. The application of next-generation sequencing enabled rapid and precise diagnosis of patients with PIRDs.
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Affiliation(s)
- Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey.
| | - Asude Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Bornova, Izmir, Turkey
| | - Neslihan Karaca
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Nesrin Gulez
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Ferah Genel
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University, Uz Pediatric Diseases and Surgery Training and Research Hospital, Dr. Behcet, Izmir, Turkey
| | - Fatih Celmeli
- Immunology and Allergy Diseases, Saglık Bilimleri University, Antalya Training and Research Hospital Pediatric, Antalya, Turkey
| | - M Tuba Cogurlu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Saglık Bilimleri University, Kocaeli Derince Training and Research Hospital, Kocaeli, Turkey
| | - Mediha Akcan
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Dilek Cicek
- Department of Pediatric Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Funda Erol Cipe
- Pediatric Immunology and Allergy Diseases, Saglık Bilimleri University Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Ayca Kiykim
- Department of Pediatric Health and Diseases, Cerrahpasa Faculty of Medicine, Pediatric Allergy Immunology, Istanbul, Turkey
| | - Alisan Yıldıran
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ondokuz Mayıs University, Samsun, Turkey
| | - Kursad Unluhizarci
- Department of Endocrinology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Sara Sebnem Kilic
- Department of Pediatric Immunology and Rheumatology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Guzide Aksu
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Omur Ardeniz
- Department of Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Necil Kutukculer
- Department of Pediatric Health and Diseases, Department of Pediatric Immunology, Faculty of Medicine, Ege University, Izmir, Turkey
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Jiang D, Rosenlind K, Baxter S, Gernsheimer T, Gulsuner S, Allenspach EJ, Keel SB. Evaluating the prevalence of inborn errors of immunity in adults with chronic immune thrombocytopenia or Evans syndrome. Blood Adv 2023; 7:7202-7208. [PMID: 37792884 PMCID: PMC10702780 DOI: 10.1182/bloodadvances.2023011042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 10/06/2023] Open
Abstract
Inborn errors of immunity (IEIs) are monogenic disorders that predispose patients to immune dysregulation, autoimmunity, and infection. Autoimmune cytopenias, such as immune thrombocytopenia (ITP) and Evans syndrome (a combination of ITP and autoimmune hemolytic anemia), are increasingly recognized phenotypes of IEI. Although recent findings suggest that IEIs may commonly underlie pediatric ITP and Evans syndrome, its prevalence in adult patients with these disorders remains undefined. This study sought to estimate the prevalence of underlying IEIs among adults with persistent or chronic ITP or Evans syndrome using a next-generation sequencing panel encompassing >370 genes implicated in IEIs. Forty-four subjects were enrolled from an outpatient adult hematology clinic at a tertiary referral center in the United States, with a median age of 49 years (range, 20-83). Fourteen subjects (31.8%) had secondary ITP, including 8 (18.2%) with Evans syndrome. No cases of IEI were identified despite a high representation of subjects with a personal history of autoimmunity (45.5%) and early onset of disease (median age at diagnosis of 40 years [range, 2-77]), including 20.5% who were initially diagnosed as children. Eight subjects (18.2%) were found to be carriers of pathogenic IEI variants, which, in their heterozygous state, are not disease-causing. One case of TUBB1-related congenital thrombocytopenia was identified. Although systematic screening for IEI has been proposed for pediatric patients with Evans syndrome, findings from this real-world study suggest that inclusion of genetic testing for IEI in the routine work-up of adults with ITP and Evans syndrome has a low diagnostic yield.
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MESH Headings
- Humans
- Adult
- Child
- Young Adult
- Middle Aged
- Aged
- Aged, 80 and over
- Child, Preschool
- Adolescent
- Anemia, Hemolytic, Autoimmune/epidemiology
- Anemia, Hemolytic, Autoimmune/genetics
- Anemia, Hemolytic, Autoimmune/complications
- Purpura, Thrombocytopenic, Idiopathic/epidemiology
- Purpura, Thrombocytopenic, Idiopathic/genetics
- Purpura, Thrombocytopenic, Idiopathic/complications
- Autoimmunity
- Prevalence
- Thrombocytopenia/epidemiology
- Thrombocytopenia/genetics
- Thrombocytopenia/complications
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Affiliation(s)
- Debbie Jiang
- Division of Hematology, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Center, Seattle, WA
- Division of Hematology, Massachusetts General Hospital, Boston, MA
| | | | - Sarah Baxter
- Division of Rheumatology, Seattle Children’s Hospital, Seattle, WA
| | - Terry Gernsheimer
- Division of Hematology, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Center, Seattle, WA
| | | | | | - Siobán B. Keel
- Division of Hematology, University of Washington, Seattle, WA
- Fred Hutchinson Cancer Center, Seattle, WA
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Peng X, Kaviany S. Approach to Diagnosing Inborn Errors of Immunity. Rheum Dis Clin North Am 2023; 49:731-739. [PMID: 37821192 DOI: 10.1016/j.rdc.2023.06.001] [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] [Indexed: 10/13/2023]
Abstract
Inborn errors of immunity are now understood to encompass manifold features including but not limited to immunodeficiency, autoimmunity, autoinflammation, atopy, bone marrow defects, and/or increased malignancy risk. As such, it is essential to maintain a high index of suspicion, as these disorders are not limited to specific demographics such as children or those with recurrent infections. Clinical presentations and standard immunophenotyping are informative for suggesting potential underlying etiologies, but integration of data from multimodal approaches including genomics is often required to achieve diagnosis.
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Affiliation(s)
- Xiao Peng
- McKusick-Nathans, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Blalock 1008, Baltimore, MD 21287, USA
| | - Saara Kaviany
- The University of Chicago & Biological Sciences, Department of Pediatrics, University of Chicago, 5841 South Maryland Avenue, Chicago, IL 60637, USA.
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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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Ferreira CS, Francisco Junior RDS, Gerber AL, Guimarães APDC, de Carvalho FAA, Dos Reis BCS, Pinto-Mariz F, de Souza MS, de Vasconcelos ZFM, Goudouris ES, Vasconcelos ATR. Genetic screening in a Brazilian cohort with inborn errors of immunity. BMC Genom Data 2023; 24:47. [PMID: 37592284 PMCID: PMC10433585 DOI: 10.1186/s12863-023-01148-z] [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: 11/25/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Inherited genetic defects in immune system-related genes can result in Inborn Errors of Immunity (IEI), also known as Primary Immunodeficiencies (PID). Diagnosis of IEI disorders is challenging due to overlapping clinical manifestations. Accurate identification of disease-causing germline variants is crucial for appropriate treatment, prognosis, and genetic counseling. However, genetic sequencing is challenging in low-income countries like Brazil. This study aimed to perform genetic screening on patients treated within Brazil's public Unified Health System to identify candidate genetic variants associated with the patient's phenotype. METHODS Thirteen singleton unrelated patients from three hospitals in Rio de Janeiro were enrolled in this study. Genomic DNA was extracted from the peripheral blood lymphocytes of each patient, and whole exome sequencing (WES) analyses were conducted using Illumina NextSeq. Germline genetic variants in IEI-related genes were prioritized using a computational framework considering their molecular consequence in coding regions; minor allele frequency ≤ 0.01; pathogenicity classification based on American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines gathered from the VarSome clinical database; and IEI-related phenotype using the Franklin tool. The genes classification into IEI categories follows internationally recognized guidelines informed by the International Union of Immunological Societies Expert Committee. Additional methods for confirmation of the variant included Sanger sequencing, phasing analysis, and splice site prediction. RESULTS A total of 16 disease-causing variants in nine genes, encompassing six different IEI categories, were identified. X-Linked Agammaglobulinemia, caused by BTK variations, emerged as the most prevalent IEI disorder in the cohort. However, pathogenic and likely pathogenic variants were also reported in other known IEI-related genes, namely CD40LG, CARD11, WAS, CYBB, C6, and LRBA. Interestingly, two patients with suspected IEI exhibited pathogenic variants in non-IEI-related genes, ABCA12 and SLC25A13, potentially explaining their phenotypes. CONCLUSIONS Genetic screening through WES enabled the detection of potentially harmful variants associated with IEI disorders. These findings contribute to a better understanding of patients' clinical manifestations by elucidating the genetic basis underlying their phenotypes.
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Affiliation(s)
- Cristina Santos Ferreira
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Ronaldo da Silva Francisco Junior
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Alexandra Lehmkuhl Gerber
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Ana Paula de Campos Guimarães
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil
| | - Flavia Amendola Anisio de Carvalho
- Allergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Bárbara Carvalho Santos Dos Reis
- Allergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Fernanda Pinto-Mariz
- Allergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG) - Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Monica Soares de Souza
- Allergy and Immunology Sector of the Pediatric Service of the Federal Hospital of Rio de Janeiro State (HFSE) - Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Zilton Farias Meira de Vasconcelos
- Laboratory of High Complexity of the Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF/FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ekaterini Simões Goudouris
- Allergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG) - Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ana Tereza Ribeiro Vasconcelos
- Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha CEP: 25651-075, Petrópolis, Rio de Janeiro, Brazil.
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8
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Zhang C, Han X, Jin Y, Chen X, Gong C, Peng J, Wang Y, Luo X, Yang Z, Zhang Y, Wan W, Liu X, Mao J, Yu H, Li J, Liu L, Sun L, Yang S, An Y, Liu Z, Gao E, Zhu H, Chen Y, Yu X, Zhou Q, Liu Z. Pathogenic Gene Spectrum and Clinical Implication in Chinese Patients with Lupus Nephritis. Clin J Am Soc Nephrol 2023; 18:869-880. [PMID: 37099456 PMCID: PMC10356117 DOI: 10.2215/cjn.0000000000000185] [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: 11/02/2022] [Accepted: 04/14/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Lupus nephritis is a rare immunological disorder. Genetic factors are considered important in its causation. We aim to systematically investigate the rare pathogenic gene variants in patients with lupus nephritis. METHODS Whole-exome sequencing was used to screen pathogenic gene variants in 1886 probands with lupus nephritis. Variants were interpreted on the basis of known pathogenic variants or the American College of Medical Genetics and Genomics guidelines and studied by functional analysis, including RNA sequencing, quantitative PCR, cytometric bead array, and Western blotting. RESULTS Mendelian form of lupus nephritis was confirmed in 71 probands, involving 63 variants in 39 pathogenic genes. The detection yield was 4%. The pathogenic genes enriched in nuclear factor kappa-B (NF-κB), type I interferon, phosphatidylinositol-3-kinase/serine/threonine kinase Akt (PI3K/AKT), Ras GTPase/mitogen-activated protein kinase (RAS/MAPK), and Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathways. Clinical manifestation patterns were diverse among different signaling pathways. More than 50% of the pathogenic gene variants were reported to be associated with lupus or lupus nephritis for the first time. The identified pathogenic gene variants of lupus nephritis overlapped with those of autoinflammatory and immunodeficiency diseases. Inflammatory signatures, such as cytokine levels of IL-6, IL-8, IL-1 β , IFN α , IFN γ , and IP10 in serum and transcriptional levels of interferon-stimulated genes in blood, were significantly higher in patients with pathogenic gene variants compared with controls. The overall survival rate of patients with pathogenic gene variants was lower than those without pathogenic gene variants. CONCLUSIONS A small fraction of patients with lupus nephritis had identifiable pathogenic gene variants, primarily in NF-κB, type I interferon, PI3K/AKT, JAK/STAT, RAS/MAPK, and complement pathways.
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Affiliation(s)
- Changming Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xu Han
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Ying Jin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiang Chen
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Cheng Gong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Jiahui Peng
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yusha Wang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Xiaoxin Luo
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Zhaohui Yang
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Yangyang Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Weiguo Wan
- Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaohui Liu
- Jiangxi Provincial Children's Hospital, Nanchang, China
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Haiguo Yu
- Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jingyi Li
- Department of Rheumatology and Immunology, First Affiliated Hospital (Southwest Hospital) of Army Medical University, Chongqing, China
| | - Li Liu
- Children's Hospital of Tianjin University, Tianjin, China
| | - Li Sun
- Department of Rheumatology, Children's Hospital of Fudan University, Shanghai, China
| | - Sirui Yang
- Department of Pediatric Rheumatology and Allergy, The First Hospital of Jilin University, Changchun, China
| | - Yu An
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhengzhao Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Erzhi Gao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Honghao Zhu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Yinghua Chen
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiaomin Yu
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Zhejiang Laboratory for Systems and Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Qing Zhou
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
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9
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Beers BJ, Similuk MN, Ghosh R, Seifert BA, Jamal L, Kamen M, Setzer MR, Jodarski C, Duncan R, Hunt D, Mixer M, Cao W, Bi W, Veltri D, Karlins E, Zhang L, Li Z, Oler AJ, Jevtich K, Yu Y, Hullfish H, Bielekova B, Frischmeyer-Guerrerio P, Dang Do A, Huryn LA, Olivier KN, Su HC, Lyons JJ, Zerbe CS, Rao VK, Keller MD, Freeman AF, Holland SM, Franco LM, Walkiewicz MA, Yan J. Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity. Front Immunol 2023; 14:1172004. [PMID: 37215141 PMCID: PMC10196392 DOI: 10.3389/fimmu.2023.1172004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
Purpose Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI. Methods We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings. Results Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone. Conclusion Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.
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Affiliation(s)
- Breanna J. Beers
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Morgan N. Similuk
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rajarshi Ghosh
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bryce A. Seifert
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Leila Jamal
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Michael Kamen
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael R. Setzer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Colleen Jodarski
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rylee Duncan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Devin Hunt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Madison Mixer
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Wenjia Cao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Weimin Bi
- Baylor Genetics, Houston, TX, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Daniel Veltri
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eric Karlins
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingwen Zhang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Zhiwen Li
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew J. Oler
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kathleen Jevtich
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yunting Yu
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haley Hullfish
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Bibiana Bielekova
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Pamela Frischmeyer-Guerrerio
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - An Dang Do
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Laryssa A. Huryn
- National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kenneth N. Olivier
- Division of Pulmonary Diseases and Critical Care Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Helen C. Su
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jonathan J. Lyons
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christa S. Zerbe
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - V. Koneti Rao
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael D. Keller
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alexandra F. Freeman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Steven M. Holland
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Luis M. Franco
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Magdalena A. Walkiewicz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jia Yan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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10
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Yaakoubi R, Mekki N, Ben-Mustapha I, Ben-Khemis L, Bouaziz A, Ben Fraj I, Ammar J, Hamzaoui A, Turki H, Boussofara L, Denguezli M, Haddad S, Ouederni M, Bejaoui M, Chan KW, Lau YL, Mellouli F, Barbouche MR, Ben-Ali M. Diagnostic challenge in a series of eleven patients with hyper IgE syndromes. Front Immunol 2023; 13:1057679. [PMID: 36703986 PMCID: PMC9871884 DOI: 10.3389/fimmu.2022.1057679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/22/2022] [Indexed: 01/12/2023] Open
Abstract
Hyper IgE syndromes (HIES) is a heterogeneous group of Inborn Errors of Immunity characterized by eczema, recurrent skin and lung infections associated with eosinophilia and elevated IgE levels. Autosomal dominant HIES caused by loss of function mutations in Signal transducer and activator of transcription 3 (STAT3) gene is the prototype of these disorders. Over the past two decades, advent in genetic testing allowed the identification of ten other etiologies of HIES. Although Dedicator of Cytokinesis 8 (DOCK8) deficiency is no more classified among HIES etiologies but as a combined immunodeficiency, this disease, characterized by severe viral infections, food allergies, autoimmunity, and increased risk of malignancies, shares some clinical features with STAT3 deficiency. The present study highlights the diagnostic challenge in eleven patients with the clinical phenotype of HIES in a resource-limited region. Candidate gene strategy supported by clinical features, laboratory findings and functional investigations allowed the identification of two heterozygous STAT3 mutations in five patients, and a bi-allelic DOCK8 mutation in one patient. Whole Exome Sequencing allowed to unmask atypical presentations of DOCK8 deficiency in two patients presenting with clinical features reminiscent of STAT3 deficiency. Our study underlies the importance of the differential diagnosis between STAT3 and DOCK8 deficiencies in order to improve diagnostic criteria and to propose appropriate therapeutic approaches. In addition, our findings emphasize the role of NGS in detecting mutations that induce overlapping phenotypes.
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Affiliation(s)
- Roukaya Yaakoubi
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia,Faculty of Medicine, Tunis El Manar University, Tunis, Tunisia
| | - Najla Mekki
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia,Faculty of Medicine, Tunis El Manar University, Tunis, Tunisia
| | - Imen Ben-Mustapha
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia,Faculty of Medicine, Tunis El Manar University, Tunis, Tunisia
| | - Leila Ben-Khemis
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia
| | - Asma Bouaziz
- Department of Pediatrics, Ben Arous Hospital of Tunis, Tunis, Tunisia
| | - Ilhem Ben Fraj
- Department of Pediatrics, National Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Jamel Ammar
- Pulmonology B Department, AbderrahmenMami Hospital, Ariana, Tunisia
| | - Agnès Hamzaoui
- Pulmonology B Department, AbderrahmenMami Hospital, Ariana, Tunisia
| | - Hamida Turki
- Department of Dermatology, HédiChaker Hospital of SFAX, Sfax, Tunisia
| | - Lobna Boussofara
- Department of Dermatology, Farhat Hached Hospital, Sousse, Tunisia
| | | | - Samir Haddad
- Department of Pediatrics, Children Hospital of Tunis, Tunis, Tunisia
| | - Monia Ouederni
- Department of Pediatrics, National Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Mohamed Bejaoui
- Department of Pediatrics, National Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Koon Wing Chan
- Department of Pediatrics and Adolescent Medicine, Li KaShing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yu Lung Lau
- Department of Pediatrics and Adolescent Medicine, Li KaShing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fethi Mellouli
- Department of Pediatrics, National Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Mohamed-Ridha Barbouche
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia,Department of Microbiology, Immunology and Infectious Diseases, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Meriem Ben-Ali
- Laboratory of Transmission, Control and Immunobiology of Infections, Institut Pasteur de Tunis, University Tunis El-Manar, Tunis, Tunisia,*Correspondence: Meriem Ben-Ali,
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11
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Michniacki TF, Walkovich K, DeMeyer L, Saad N, Hannibal M, Basiaga ML, Horst KK, Mohan S, Chen L, Brodeur K, Du Y, Frame D, Ngo S, Simoneau J, Brown N, Lee PY. SOCS1 Haploinsufficiency Presenting as Severe Enthesitis, Bone Marrow Hypocellularity, and Refractory Thrombocytopenia in a Pediatric Patient with Subsequent Response to JAK Inhibition. J Clin Immunol 2022; 42:1766-1777. [PMID: 35976468 PMCID: PMC9381392 DOI: 10.1007/s10875-022-01346-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022]
Abstract
Haploinsufficiency of suppressor of cytokine signaling 1 (SOCS1) is a recently discovered autoinflammatory disorder with significant rheumatologic, immunologic, and hematologic manifestations. Here we report a case of SOCS1 haploinsufficiency in a 5-year-old child with profound arthralgias and immune-mediated thrombocytopenia unmasked by SARS-CoV-2 infection. Her clinical manifestations were accompanied by excessive B cell activity, eosinophilia, and elevated IgE levels. Uniquely, this is the first report of SOCS1 haploinsufficiency in the setting of a chromosomal deletion resulting in complete loss of a single SOCS1 gene with additional clinical findings of bone marrow hypocellularity and radiologic evidence of severe enthesitis. Immunologic profiling showed a prominent interferon signature in the patient's peripheral blood mononuclear cells, which were also hypersensitive to stimulation by type I and type II interferons. The patient showed excellent clinical and functional laboratory response to tofacitinib, a Janus kinase inhibitor that disrupts interferon signaling. Our case highlights the need to utilize a multidisciplinary diagnostic approach and consider a comprehensive genetic evaluation for inborn errors of immunity in patients with an atypical immune-mediated thrombocytopenia phenotype.
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Affiliation(s)
- Thomas F Michniacki
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA.
| | - Kelly Walkovich
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Lauren DeMeyer
- Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Nadine Saad
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Mark Hannibal
- Division of Genetics, Metabolism & Genomic Medicine, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Matthew L Basiaga
- Division of Pediatric Rheumatology, Department of Pediatrics, Mayo Clinic, Rochester, MN, USA
| | - Kelly K Horst
- Division of Pediatric Radiology, Department of Radiology, Mayo Clinic, Rochester, MN, USA
| | - Smriti Mohan
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Liang Chen
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kailey Brodeur
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yan Du
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David Frame
- Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Sandra Ngo
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Jillian Simoneau
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Noah Brown
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Pui Y Lee
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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12
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Ochiai S, Hayakawa I, Ohashi E, Hamano S, Miyata Y, Sakuma H, Hogetsu K, Gocho Y, Ogura M, Uchiyama T, Abe Y. Fatal X-linked lymphoproliferative disease type 1-associated limbic encephalitis with positive anti-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor antibody. Brain Dev 2022; 44:630-634. [PMID: 35778314 DOI: 10.1016/j.braindev.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/31/2022] [Accepted: 06/15/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND X-linked lymphoproliferative disease type 1 (XLP1) is a rare monogenic immune dysregulation disorder caused by a deficiency of a signaling lymphocyte activation molecule-associated protein (SAP). While many patients with XLP1 present with fatal hemophagocytic lymphohistiocytosis upon Epstein Barr virus (EBV) infection, a small fraction present with limbic encephalitis in the absence of EBV infection. It is poorly understood why SAP deficiency may cause limbic encephalitis in XLP1. CASE A 12-year-old boy presented with seizures, changes in personality, memory loss, and cognitive deficits during treatment for interstitial pneumonia. A diagnosis of limbic encephalitis was made. Despite treatment against CD8+ T cell-mediated autoimmunity with intravenous methylprednisolone, dexamethasone, intravenous immunoglobulin, plasma exchange, cyclosporine, weekly etoposide, mycophenolate mofetil, and adalimumab, encephalitis progressed until the patient died after one month of treatment intitiation. Post-mortem genetic testing revealed a de novo SH2D1A truncating mutation. Tests for EBV infection were negative. Initial spinal fluid revealed markedly elevated protein levels, mild pleocytosis, and elevation of two chemokines (C-X-C motif chemokine ligand [CXCL] 10 and CXCL 13). Moreover, initial spinal fluid was tested positive for anti-alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) autoantibody. DISCUSSION In XLP1-associated limbic encephalitis, anti-AMPAR autoantibody production by the dysregulated immune system due to SAP deficiency might be a pathogenic mechanism of central nervous system manifestations. In addition to the standard treatment for XLP1, targeted treatment against B-cell-mediated immunity might be indicated for patients with XLP1-associated limbic encephalitis.
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Affiliation(s)
- Satoru Ochiai
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Teikyo University, Tokyo, Japan
| | - Itaru Hayakawa
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, University of Tokyo, Tokyo, Japan.
| | - Eri Ohashi
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
| | - Sho Hamano
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - Yohane Miyata
- Department of Pediatrics, Kyorin University School of Medicine, Tokyo, Japan
| | - Hiroshi Sakuma
- Department of Brain & Neurosciences, Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan
| | - Keita Hogetsu
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshihiro Gocho
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Masao Ogura
- Department of Nephrology, National Center for Child Health and Development, Tokyo, Japan
| | - Toru Uchiyama
- Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Yuichi Abe
- Division of Neurology, National Center for Child Health and Development, Tokyo, Japan
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13
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Mørup SB, Nazaryan-Petersen L, Gabrielaite M, Reekie J, Marquart HV, Hartling HJ, Marvig RL, Katzenstein TL, Masmas TN, Lundgren J, Murray DD, Helleberg M, Borgwardt L. Added Value of Reanalysis of Whole Exome- and Whole Genome Sequencing Data From Patients Suspected of Primary Immune Deficiency Using an Extended Gene Panel and Structural Variation Calling. Front Immunol 2022; 13:906328. [PMID: 35874679 PMCID: PMC9302041 DOI: 10.3389/fimmu.2022.906328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Knowledge of the genetic variation underlying Primary Immune Deficiency (PID) is increasing. Reanalysis of genome-wide sequencing data from undiagnosed patients with suspected PID may improve the diagnostic rate. Methods We included patients monitored at the Department of Infectious Diseases or the Child and Adolescent Department, Rigshospitalet, Denmark, for a suspected PID, who had been analysed previously using a targeted PID gene panel (457 PID-related genes) on whole exome- (WES) or whole genome sequencing (WGS) data. A literature review was performed to extend the PID gene panel used for reanalysis of single nucleotide variation (SNV) and small indels. Structural variant (SV) calling was added on WGS data. Results Genetic data from 94 patients (86 adults) including 36 WES and 58 WGS was reanalysed a median of 23 months after the initial analysis. The extended gene panel included 208 additional PID-related genes. Genetic reanalysis led to a small increase in the proportion of patients with new suspicious PID related variants of uncertain significance (VUS). The proportion of patients with a causal genetic diagnosis was constant. In total, five patients (5%, including three WES and two WGS) had a new suspicious PID VUS identified due to reanalysis. Among these, two patients had a variant added due to the expansion of the PID gene panel, and three patients had a variant reclassified to a VUS in a gene included in the initial PID gene panel. The total proportion of patients with PID related VUS, likely pathogenic, and pathogenic variants increased from 43 (46%) to 47 (50%), as one patient had a VUS detected in both initial- and reanalysis. In addition, we detected new suspicious SNVs and SVs of uncertain significance in PID candidate genes with unknown inheritance and/or as heterozygous variants in genes with autosomal recessive inheritance in 8 patients. Conclusion These data indicate a possible diagnostic gain of reassessing WES/WGS data from patients with suspected PID. Reasons for the possible gain included improved knowledge of genotype-phenotype correlation, expanding the gene panel, and adding SV analyses. Future studies of genotype-phenotype correlations may provide additional knowledge on the impact of the new suspicious VUSs.
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Affiliation(s)
- Sara Bohnstedt Mørup
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Migle Gabrielaite
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joanne Reekie
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hanne V. Marquart
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hans Jakob Hartling
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rasmus L. Marvig
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Terese L. Katzenstein
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Tania N. Masmas
- The Child and Adolescent Department, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jens Lundgren
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Daniel D. Murray
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marie Helleberg
- Centre of Excellence for Health, Immunity, and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Line Borgwardt
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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14
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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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15
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Rawat A, Sharma M, Vignesh P, Jindal AK, Suri D, Das J, Joshi V, Tyagi R, Sharma J, Kaur G, Lau YL, Imai K, Nonoyama S, Lenardo M, Singh S. Utility of targeted next generation sequencing for inborn errors of immunity at a tertiary care centre in North India. Sci Rep 2022; 12:10416. [PMID: 35729272 PMCID: PMC9213413 DOI: 10.1038/s41598-022-14522-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/08/2022] [Indexed: 11/09/2022] Open
Abstract
Inborn errors of immunity (IEI) are a heterogeneous group of monogenic disorders that include primary immunodeficiency's and other disorders affecting different aspects of the immune system. Next-Generation Sequencing (NGS) is an essential tool to diagnose IEI. We report our 3-year experience in setting up facilities for NGS for diagnosis of IEI in Chandigarh, North India. We used a targeted, customized gene panel of 44 genes known to result in IEI. Variant analysis was done using Ion Reporter software. The in-house NGS has enabled us to offer genetic diagnoses to patients with IEI at minimal costs. Of 121 patients who were included pathogenic variants were identified in 77 patients. These included patients with Chronic Granulomatous Disease, Severe Combined Immune Deficiency, leukocyte adhesion defect, X-linked agammaglobulinemia, Ataxia Telangiectasia, Hyper-IgE syndrome, Wiskott Aldrich syndrome, Mendelian susceptibility to mycobacterial diseases, Hyper-IgM syndrome, autoimmune lymphoproliferative syndrome, and GATA-2 deficiency. This manuscript discusses the challenges encountered while setting up and running targeted NGS for IEI in our unit. Genetic diagnosis has helped our patients with IEI in genetic counselling, prenatal diagnosis, and accessing appropriate therapeutic options.
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Affiliation(s)
- Amit Rawat
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Madhubala Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Pandiarajan Vignesh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ankur Kumar Jindal
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Deepti Suri
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jhumki Das
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Vibhu Joshi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Rahul Tyagi
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Jyoti Sharma
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Gurjit Kaur
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kohsuke Imai
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Shigeaki Nonoyama
- Department of Pediatric, Perinatal and Maternal Medicine, Tokyo Medical and Dental University, National Defence Medical College, Tokyo, 113-8519, Japan
| | - Michael Lenardo
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892-1892, USA
| | - Surjit Singh
- Allergy Immunology Unit, Department of Pediatrics, Advanced Pediatrics Centre, Post Graduate Institute of Medical Education and Research, Chandigarh, 160012, India
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16
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Kuijpers TW, Tromp SAM, van Leeuwen EMM, de Bree GJ. Case Report: A Highly Variable Clinical and Immunological Presentation of IKAROS Deficiency in a Single Family. Front Immunol 2022; 13:865838. [PMID: 35479066 PMCID: PMC9036438 DOI: 10.3389/fimmu.2022.865838] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
Here we describe a novel mutation in the IKZF gene encoding IKAROS, as the cause of common variable immunodeficiency (CVID). The identification of the same defect in the IKZF gene with manifestations of asymptomatic selective IgA deficiency and chronic ITP in the father and her younger brother, respectively, demonstrates the large variability of this genetic defect in one single family, while living in the same environment with a relatively similar genetic background. As discussed, clinical penetrance of the molecular defects identified by mutations in IKZF and other common gene defects in CVID in familial immune-related abnormalities makes genetic testing a necessary step for diagnosis, management, and counseling, as part of the routine immunological workup.
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Affiliation(s)
- Taco W. Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory of Immunology, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Samantha A. M. Tromp
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Samantha A. M. Tromp,
| | - Ester M. M. van Leeuwen
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Godelieve J. de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
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17
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Weber K, Zeißig Y, Haag C, Schmelz R, Pazmandi J, Kalinichenko A, Boztug K, Zeißig S, Aust D, Laass MW, Schuetz C. [Chronic or severe enteropathy and immunodeficiency: be prepared for a rara avis]. ZEITSCHRIFT FUR GASTROENTEROLOGIE 2022; 60:1668-1677. [PMID: 35297030 DOI: 10.1055/a-1709-5024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the work-up of chronic enteropathies an underlying inborn error of immunity (IEI) should be considered in certain cases. IEI are rare, but approximately 10% of patients may present with symptoms of inflammatory bowel disease (IBD), which is a much more common entity. Patients with IEI associated IBD may show extraintestinal symptoms or signs, and are often refractory to conventional anti-inflammatory treatment. In case of early-onset bowel inflammation and other intestinal or extraintestinal manifestations, an IEI should be excluded. A small fraction of monogenic IEI can be amenable to targeted therapies, or even corrected by allogeneic stem cell transplantation. Therefore, early diagnosis is crucial. This paper shows examples of clinical - gastrointestinal as well as extraintestinal - signs and findings which require immunological and possibly genetic workup.
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Affiliation(s)
- Katrin Weber
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Yvonne Zeißig
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Cornelie Haag
- Universitätsklinikum Carl Gustav Carus Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - Renate Schmelz
- Universitätsklinikum Carl Gustav Carus Medizinische Klinik und Poliklinik I, Dresden, Germany
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Artem Kalinichenko
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,St. Anna Kinderspital und Universitätsklinik für Kinder und Jugendliche, Medizinische Universitat Wien, Wien, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Sebastian Zeißig
- Center for Regenerative Therapies Dresden, Dresden, Germany.,Klinik und Poliklinik für Innere Medizin I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Daniela Aust
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Martin W Laass
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Catharina Schuetz
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
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18
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Elsink K, Huibers MMH, Hollink IHIM, Simons A, Zonneveld-Huijssoon E, van der Veken LT, Leavis HL, Henriet SSV, van Deuren M, van de Veerdonk FL, Potjewijd J, Berghuis D, Dalm VASH, Vermont CL, van de Ven AAJM, Lambeck AJA, Abbott KM, van Hagen PM, de Bree GJ, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers. Front Immunol 2022; 12:780134. [PMID: 34992599 PMCID: PMC8724043 DOI: 10.3389/fimmu.2021.780134] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 01/07/2023] Open
Abstract
Objective Inborn errors of immunity (IEI) are a heterogeneous group of disorders, affecting different components of the immune system. Over 450 IEI related genes have been identified, with new genes continually being recognized. This makes the early application of next-generation sequencing (NGS) as a diagnostic method in the evaluation of IEI a promising development. We aimed to provide an overview of the diagnostic yield and time to diagnosis in a cohort of patients suspected of IEI and evaluated by an NGS based IEI panel early in the diagnostic trajectory in a multicenter setting in the Netherlands. Study Design We performed a prospective observational cohort study. We collected data of 165 patients with a clinical suspicion of IEI without prior NGS based panel evaluation that were referred for early NGS using a uniform IEI gene panel. The diagnostic yield was assessed in terms of definitive genetic diagnoses, inconclusive diagnoses and patients without abnormalities in the IEI gene panel. We also assessed time to diagnosis and clinical implications. Results For children, the median time from first consultation to diagnosis was 119 days versus 124 days for adult patients (U=2323; p=0.644). The median turn-around time (TAT) of genetic testing was 56 days in pediatric patients and 60 days in adult patients (U=1892; p=0.191). A definitive molecular diagnosis was made in 25/65 (24.6%) of pediatric patients and 9/100 (9%) of adults. Most diagnosed disorders were identified in the categories of immune dysregulation (n=10/25; 40%), antibody deficiencies (n=5/25; 20%), and phagocyte diseases (n=5/25; 20%). Inconclusive outcomes were found in 76/165 (46.1%) patients. Within the patient group with a genetic diagnosis, a change in disease management occurred in 76% of patients. Conclusion In this cohort, the highest yields of NGS based evaluation for IEI early in the diagnostic trajectory were found in pediatric patients, and in the disease categories immune dysregulation and phagocyte diseases. In cases where a definitive diagnosis was made, this led to important disease management implications in a large majority of patients. More research is needed to establish a uniform diagnostic pathway for cases with inconclusive diagnoses, including variants of unknown significance.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Manon M H Huibers
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Iris H I M Hollink
- Department of Clinical Genetics, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annet Simons
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Radboud University, Nijmegen, Netherlands.,Radboud Institute for Oncology, Radboud University Medical Center, Radboud University, Nijmegen, Netherlands
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lars T van der Veken
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Helen L Leavis
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Stefanie S V Henriet
- Department of Pediatric Infectious Diseases and Immunology, Amalia's Children Hospital, Radboud University Nijmegen Medical Centre, Radboud University, Nijmegen, Netherlands
| | - Marcel van Deuren
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Frank L van de Veerdonk
- Department of Internal Medicine, Radboud University Medical Center, Radboud Center for Infectious Diseases, Nijmegen, Netherlands
| | - Judith Potjewijd
- Department of Nephrology and Clinical Immunology, Maastricht University Medical Center, Maastricht University, Maastricht, Netherlands
| | - Dagmar Berghuis
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden University, Leiden, Netherlands
| | - Virgil A S H Dalm
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Clementien L Vermont
- Department of Pediatric Infectious Diseases, Immunology and Rheumatology, Sophia Children's Hospital, Erasmus Medical Center, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Annick A J M van de Ven
- Department of Internal Medicine and Allergology, Rheumatology and Clinical Immunology, University Medical Center Groningen, Groningen, Netherlands
| | - Annechien J A Lambeck
- Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Kristin M Abbott
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - P Martin van Hagen
- Department of Internal Medicine, Division of Allergy & Clinical Immunology; Department of Immunology, Erasmus University Medical Center Rotterdam, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Institute for Infection and Immunity, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina's Children Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
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19
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Tengsujaritkul M, Suratannon N, Ittiwut C, Ittiwut R, Chatchatee P, Suphapeetiporn K, Shotelersuk V. Phenotypic heterogeneity and genotypic spectrum of inborn errors of immunity identified through whole exome sequencing in a Thai patient cohort. Pediatr Allergy Immunol 2022; 33:e13701. [PMID: 34796988 DOI: 10.1111/pai.13701] [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] [Received: 08/03/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Inborn errors of immunity (IEI) comprise more than 400 rare diseases with potential life-threatening conditions. Clinical manifestations and genetic defects are heterogeneous and diverse among populations. Here, we aimed to characterize the clinical, immunologic, and genetic features of Thai pediatric patients with IEI. The use of whole-exome sequencing (WES) in diagnosis and clinical decision making was also assessed. METHODS Thirty six unrelated patients with clinical and laboratory findings consistent with IEI were recruited from January 2010 to December 2020. WES was performed to identify the underlying genetic defects. RESULTS The median age of disease onset was 4 months (range: 1 month to 13 years), and 24 were male (66.7%). Recurrent sinopulmonary tract infection was the most common clinical presentation followed by septicemia and severe pneumonia. Using WES, we successfully identified the underlying genetic defects in 18 patients (50%). Of the 20 variants identified, six have not been previously described (30%). According to the International Union of Immunological Societies (IUIS), 38.9% of these detected cases (7/18) were found to harbor variants associated with genes in combined immunodeficiencies with associated or syndromic features (Class II). CONCLUSION The diagnostic yield of WES in this patient cohort was 50%. Six novel genetic variants in IEI genes were identified. The clinical usefulness of WES in IEI was demonstrated, emphasizing it as an effective diagnostic strategy in these genetically heterogeneous disorders.
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Affiliation(s)
- Maliwan Tengsujaritkul
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, the Thai Red Cross Society, Bangkok, Thailand
| | - Chupong Ittiwut
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Rungnapa Ittiwut
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand.,Department of Pediatrics, Faculty of Medicine, Center of Excellence for Medical Genomics, Medical Genomics Cluster, Chulalongkorn University, Bangkok, Thailand
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20
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Walkovich K. Understanding neutropenia secondary to intrinsic or iatrogenic immune dysregulation. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2021; 2021:504-513. [PMID: 34889406 PMCID: PMC8791120 DOI: 10.1182/hematology.2021000285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As a key member of the innate and adaptive immune response, neutrophils provide insights into the hematopoietic and inflammatory manifestations of inborn errors of immunity (IEI) and the consequences of immunotherapy. The facile recognition of IEI presenting with neutropenia provides an avenue for hematologists to facilitate early diagnosis and expedite biologically rationale care. Moreover, enhancing the understanding of the molecular mechanisms driving neutropenia in IEI-decreased bone marrow reserves, diminished egress from the bone marrow, and decreased survival-offers an opportunity to further dissect the pathophysiology driving neutropenia secondary to iatrogenic immune dysregulation, eg, immune checkpoint inhibitors and chimeric antigen receptor T-cell therapy.
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Affiliation(s)
- Kelly Walkovich
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
- Correspondence Kelly Walkovich, Department of Pediatrics, University of Michigan, 1540 E Medical Center Dr, Ann Arbor, MI 48109; e-mail:
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21
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Ripen AM, Chiow MY, Rama Rao PR, Mohamad SB. Revealing Chronic Granulomatous Disease in a Patient With Williams-Beuren Syndrome Using Whole Exome Sequencing. Front Immunol 2021; 12:778133. [PMID: 34804071 PMCID: PMC8599285 DOI: 10.3389/fimmu.2021.778133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Blended phenotypes exhibited by a patient may present a challenge to the establishment of diagnosis. In this study, we report a seven-year-old Murut girl with unusual features of Williams-Beuren syndrome (WBS), including recurrent infections and skin abscesses. Considering the possibility of a second genetic disorder, a mutation screening for genes associated with inborn errors of immunity (IEI) was conducted using whole exome sequencing (WES). Analysis of copy number variations (CNVs) from the exome data revealed a 1.53Mb heterozygous deletion on chromosome 7q11.23, corresponding to the known WBS. We also identified a biallelic loss of NCF1, which indicated autosomal recessive chronic granulomatous disease (CGD). Dihydrorhodamine (DHR) flow cytometric assay demonstrated abnormally low neutrophil oxidative burst activity. Coamplification of NCF1 and its pseudogenes identified a GT-deletion (ΔGT) at the start of exon 2 in NCF1 (NM_000265.7: c.75_76delGT: p.Tyr26Hisfs*26). Estimation of NCF1-to-NCF1 pseudogenes ratio using ΔGT and 20-bp gene scans affirmed nil copies of NCF1 in the patient. While the father had a normal ratio of 2:4, the mother had a ratio of 1:5, implicating the carrier of ΔGT-containing NCF1. Discovery of a 7q11.23 deletion involving one NCF1 allele and a ΔGT in the second NCF1 allele explained the coexistence of WBS and CGD in our patient. This study highlights the capability of WES to establish a molecular diagnosis for a case with blended phenotypes, enabling the provision of appropriate prophylactic treatment.
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Affiliation(s)
- Adiratna Mat Ripen
- Primary Immunodeficiency Unit, Allergy and Immunology Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Selangor, Malaysia
| | - Mei Yee Chiow
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Prakash Rao Rama Rao
- Pediatrics Department, Keningau Hospital, Ministry of Health Malaysia, Sabah, Malaysia
| | - Saharuddin Bin Mohamad
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.,Centre of Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), University of Malaya, Kuala Lumpur, Malaysia
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22
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Very Elevated IgE, Atopy, and Severe Infection: A Genomics-Based Diagnostic Approach to a Spectrum of Diseases. Case Reports Immunol 2021; 2021:2767012. [PMID: 34603803 PMCID: PMC8486527 DOI: 10.1155/2021/2767012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/05/2021] [Indexed: 11/20/2022] Open
Abstract
Elevated IgE has been long recognized as an important clinical marker of atopy but can be seen in a myriad of conditions. The discovery of autosomal dominant STAT3 deficiency marked the first recognition of hyper-IgE syndrome (HIES) and the first primary immunodeficiency linked to elevated IgE. Since then, genomic testing has increased the number of defects with associated mutations causing hyper-IgE syndrome and atopic diseases with FLG, DOCK8, SPINK5, and CARD11, among others. A spectrum of recurrent infections and atopy are hallmarks of elevated IgE with significant phenotypic overlap between each underlying condition. As treatment is predicated on early diagnosis, genomic testing is becoming a more commonly used diagnostic tool. We present a 6-year-old male patient with markedly elevated IgE and severe atopic dermatitis presenting with staphylococcal bacteremia found to have a heterozygous variant in FLG (p.S3247X) and multiple variants of unknown significance in BCL11B, ZAP70, LYST, and PTPRC. We review the genetic defects underpinning elevated IgE and highlight the spectrum of atopy and immunodeficiency seen in patients with underlying mutations. Although no one mutation is completely causative of the constellation of symptoms in this patient, we suggest the synergism of these variants is an impetus of disease.
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23
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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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24
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Targeted NGS Yields Plentiful Ultra-Rare Variants in Inborn Errors of Immunity Patients. Genes (Basel) 2021; 12:genes12091299. [PMID: 34573280 PMCID: PMC8469131 DOI: 10.3390/genes12091299] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/18/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Inborn errors of immunity (IEI) include a large group of inherited diseases sharing either poor, dysregulated, or absent and/or acquired function in one or more components of the immune system. Next-generation sequencing (NGS) has driven a rapid increase in the recognition of such defects, though the wide heterogeneity of genetically diverse but phenotypically overlapping diseases has often prevented the molecular characterization of the most complex patients. Two hundred and seventy-two patients were submitted to three successive NGS-based gene panels composed of 58, 146, and 312 genes. Along with pathogenic and likely pathogenic causative gene variants, accounting for the corresponding disorders (37/272 patients, 13.6%), a number of either rare (probably) damaging variants in genes unrelated to patients’ phenotype, variants of unknown significance (VUS) in genes consistent with their clinics, or apparently inconsistent benign, likely benign, or VUS variants were also detected. Finally, a remarkable amount of yet unreported variants of unknown significance were also found, often recurring in our dataset. The NGS approach demonstrated an expected IEI diagnostic rate. However, defining the appropriate list of genes for these panels may not be straightforward, and the application of unbiased approaches should be taken into consideration, especially when patients show atypical clinical pictures.
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25
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Similuk MN, Yan J, Setzer MR, Jamal L, Littel P, Lenardo M, Su HC. Exome sequencing study in a clinical research setting finds general acceptance of study returning secondary genomic findings with little decisional conflict. J Genet Couns 2021; 30:766-773. [PMID: 33320394 PMCID: PMC10478172 DOI: 10.1002/jgc4.1367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 11/10/2020] [Accepted: 11/20/2020] [Indexed: 01/19/2023]
Abstract
The most appropriate strategies for managing secondary genomic findings (SF) in clinical research are being developed and evaluated. We surveyed patients at the National Institute of Allergy and Infectious Diseases (NIAID) to evaluate decisional conflict regarding enrolling in a study that returns SF. Responses were collected using a cross-sectional survey after informed consent but before return of SF. Sixty-six adults of 116 eligible participants responded. No participant explicitly declined because they did not want to possibly receive a SF. Sixty-five of 66 (98%) participants thought it was appropriate to return SFs in research; one participant was unsure. Decisional conflict regarding enrolling in a study returning SF was low overall with 68% of participants reporting a score of less than 10 on a 100-point decisional conflict scale, implying that they felt informed, clear on what they wanted, and supported. Lower genetic literacy was weakly associated with higher decisional conflict (Spearman's rho = -0.297, p = .015). Six participants reported confusion related to the choices about SFs. Our data suggest that participants in our study feel it is appropriate to receive SF and have little decisional conflict about potentially receiving such information; however, some participants may need further education and counseling.
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Affiliation(s)
- Morgan N Similuk
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Jia Yan
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
- Medical Science and Computing, LLC, Rockville, MD, USA
| | - Michael R Setzer
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
- Medical Science and Computing, LLC, Rockville, MD, USA
| | - Leila Jamal
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
- Medical Science and Computing, LLC, Rockville, MD, USA
- Department of Bioethics, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Patricia Littel
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Michael Lenardo
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Helen C Su
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
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26
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Engelbrecht C, Urban M, Schoeman M, Paarwater B, van Coller A, Abraham DR, Cornelissen H, Glashoff R, Esser M, Möller M, Kinnear C, Glanzmann B. Clinical Utility of Whole Exome Sequencing and Targeted Panels for the Identification of Inborn Errors of Immunity in a Resource-Constrained Setting. Front Immunol 2021; 12:665621. [PMID: 34093558 PMCID: PMC8176954 DOI: 10.3389/fimmu.2021.665621] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022] Open
Abstract
Primary immunodeficiency disorders (PIDs) are inborn errors of immunity (IEI) that cause immune system impairment. To date, more than 400 single-gene IEI have been well defined. The advent of next generation sequencing (NGS) technologies has improved clinical diagnosis and allowed for discovery of novel genes and variants associated with IEI. Molecular diagnosis provides clear clinical benefits for patients by altering management, enabling access to certain treatments and facilitates genetic counselling. Here we report on an 8-year experience using two different NGS technologies, namely research-based WES and targeted gene panels, in patients with suspected IEI in the South African healthcare system. A total of 52 patients' had WES only, 26 had a targeted gene panel only, and 2 had both panel and WES. Overall, a molecular diagnosis was achieved in 30% (24/80) of patients. Clinical management was significantly altered in 67% of patients following molecular results. All 24 families with a molecular diagnosis received more accurate genetic counselling and family cascade testing. Results highlight the clinical value of expanded genetic testing in IEI and its relevance to understanding the genetic and clinical spectrum of the IEI-related disorders in Africa. Detection rates under 40% illustrate the complexity and heterogeneity of these disorders, especially in an African population, thus highlighting the need for expanded genomic testing and research to further elucidate this.
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Affiliation(s)
- Clair Engelbrecht
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michael Urban
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mardelle Schoeman
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brandon Paarwater
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Ansia van Coller
- Immunology Unit, Division of Medical Microbiology, National Health Laboratory Service and Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa
| | - Deepthi Raju Abraham
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa
| | - Helena Cornelissen
- Division of Haematopathology, National Health Laboratory Service, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa
| | - Richard Glashoff
- Immunology Unit, Division of Medical Microbiology, National Health Laboratory Service and Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa
| | - Monika Esser
- Immunology Unit, Division of Medical Microbiology, National Health Laboratory Service and Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa.,Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town, South Africa
| | - Marlo Möller
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Craig Kinnear
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,SAMRC Genomics Centre, Cape Town, South Africa
| | - Brigitte Glanzmann
- SAMRC Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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27
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Zhu T, Gong X, Bei F, Ma L, Sun J, Wang J, Qiu G, Sun J, Sun Y, Zhang Y. Primary immunodeficiency-related genes in neonatal intensive care unit patients with various genetic immune abnormalities: a multicentre study in China. Clin Transl Immunology 2021; 10:e1266. [PMID: 33777394 PMCID: PMC7984964 DOI: 10.1002/cti2.1266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/01/2021] [Accepted: 02/28/2021] [Indexed: 11/10/2022] Open
Abstract
Objectives The present phenotype-based disease classification causes ambiguity in diagnosing and determining timely, effective treatment options for primary immunodeficiency (PID). In this study, we aimed to examine the characteristics of early-onset PID and proposed a JAK-STATopathy subgroup based on their molecular defects. Methods We reviewed 72 patients (< 100 days) retrospectively. These patients exhibited various immune-related phenotypes and received a definitive molecular diagnosis by next-generation sequencing (NGS)-based tests. We evaluated the PID-causing genes and clinical parameters. We assessed the genes that shared the JAK-STAT signalling pathway. We also examined the potential high risks related to the 180-day death rate. Results We identified PID disorders in 25 patients (34.72%, 25/72). The 180-day mortality was 26.39% (19/72). Early onset of disease (cut-off value of 3.5 days of age) was associated with a high 180-day death rate (P = 0.009). Combined immunodeficiency with associated or syndromic features comprised the most common PID class (60.00%, 15/25). Patients who presented life-threatening infections were most likely to exhibit PID (odds ratio [OR] = 2.864; 95% confidence interval [CI]: 1.047-7.836). Twelve out of 72 patients shared JAK-STAT pathway defects. Seven JAK-STATopathy patients were categorised as PID. They were admitted to NICUs as immunological emergencies. Most of them experienced severe infections and thrombocytopenia, with 4 succumbing to an early death. Conclusions This study confirmed that NGS can be utilised as an aetiological diagnostic method of complex immune-related conditions in early life. Through the classification of PID as pathway-based subtypes, we see an opportunity to dissect the heterogeneity and to direct targeted therapies.
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Affiliation(s)
- Tianwen Zhu
- Department of Neonatology Xinhua Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Xiaohui Gong
- Department of Neonatology Shanghai Children's Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Fei Bei
- Department of Neonatology Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Li Ma
- Department of Neonatology Shanghai Children's Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jingjing Sun
- Department of Neonatology Shanghai Children's Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory Shanghai Children's Medical Center Shanghai Jiaotong University School of Medicine Shanghai China
| | - Gang Qiu
- Department of Neonatology Shanghai Children's Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Jianhua Sun
- Department of Neonatology Shanghai Children's Medical Center Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yu Sun
- Department of Pediatric Endocrinology/Genetics Xinhua Hospital Shanghai Jiao Tong University School of Medicine Shanghai Institute for Pediatric Research Shanghai China
| | - Yongjun Zhang
- Department of Neonatology Xinhua Hospital Shanghai Jiao Tong University School of Medicine Shanghai China
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28
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Rispoli F, Valencic E, Girardelli M, Pin A, Tesser A, Piscianz E, Boz V, Faletra F, Severini GM, Taddio A, Tommasini A. Immunity and Genetics at the Revolving Doors of Diagnostics in Primary Immunodeficiencies. Diagnostics (Basel) 2021; 11:532. [PMID: 33809703 PMCID: PMC8002250 DOI: 10.3390/diagnostics11030532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/14/2022] Open
Abstract
Primary immunodeficiencies (PIDs) are a large and growing group of disorders commonly associated with recurrent infections. However, nowadays, we know that PIDs often carry with them consequences related to organ or hematologic autoimmunity, autoinflammation, and lymphoproliferation in addition to simple susceptibility to pathogens. Alongside this conceptual development, there has been technical advancement, given by the new but already established diagnostic possibilities offered by new genetic testing (e.g., next-generation sequencing). Nevertheless, there is also the need to understand the large number of gene variants detected with these powerful methods. That means advancing beyond genetic results and resorting to the clinical phenotype and to immunological or alternative molecular tests that allow us to prove the causative role of a genetic variant of uncertain significance and/or better define the underlying pathophysiological mechanism. Furthermore, because of the rapid availability of results, laboratory immunoassays are still critical to diagnosing many PIDs, even in screening settings. Fundamental is the integration between different specialties and the development of multidisciplinary and flexible diagnostic workflows. This paper aims to tell these evolving aspects of immunodeficiencies, which are summarized in five key messages, through introducing and exemplifying five clinical cases, focusing on diseases that could benefit targeted therapy.
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Affiliation(s)
- Francesco Rispoli
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (F.R.); (V.B.); (A.T.); (A.T.)
| | - Erica Valencic
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Martina Girardelli
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Alessia Pin
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Alessandra Tesser
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Elisa Piscianz
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Valentina Boz
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (F.R.); (V.B.); (A.T.); (A.T.)
| | - Flavio Faletra
- Department of Diagnostics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Giovanni Maria Severini
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Andrea Taddio
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (F.R.); (V.B.); (A.T.); (A.T.)
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
| | - Alberto Tommasini
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (F.R.); (V.B.); (A.T.); (A.T.)
- Department of Pediatrics, Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (M.G.); (A.P.); (A.T.); (E.P.); (G.M.S.)
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29
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Lee K, Abraham RS. Next-generation sequencing for inborn errors of immunity. Hum Immunol 2021; 82:871-882. [PMID: 33715910 DOI: 10.1016/j.humimm.2021.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022]
Abstract
Inborn errors of immunity (IEIs) include several hundred gene defects affecting various components of the immune system. As with other constitutional disorders, next-generation sequencing (NGS) is a powerful tool for the diagnosis of these diseases. While NGS can provide molecular confirmation of disease in a patient with a suspected or classic phenotype, it can also identify new molecular defects of the immune system, expand gene-disease phenotypes, clarify mechanism of disease, pattern of inheritance or identify new gene-disease associations. Multiple clinical specialties are involved in the diagnosis and management of patients with IEI, and most have no formal genetic training or expertise. To effectively utilize NGS tools and data in clinical practice, it is relevant and pragmatic to obtain a modicum of knowledge about genetic terminology, the variety of platforms and tools available for high-throughput genomic analysis, the interpretation and implementation of such data in clinical practice. There is considerable variability not only in the technologies and analytical tools used for NGS but in the bioinformatics approach to variant identification and interpretation. The ability to provide a molecular basis for disease has the potential to alter therapeutic management and longer-term treatment of the disease, including developing personalized approaches with molecularly targeted therapies. This review is intended for the clinical specialist or diagnostic immunologist who works in the area of inborn errors of immunity, and provides an overview of the need for genetic testing in these patients (the "why" aspect), the various technologies and analytical approaches, bioinformatics tools, resources, and challenges (the "how" aspect), and the clinical evidence for identifying which patients might be best served by such testing (the "when" aspect).
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Affiliation(s)
- Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Roshini S Abraham
- Diagnostic Immunology Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA.
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30
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Fusaro M, Rosain J, Grandin V, Lambert N, Hanein S, Fourrage C, Renaud N, Gil M, Chevalier S, Chahla WA, Bader-Meunier B, Barlogis V, Blanche S, Boutboul D, Castelle M, Comont T, Diana JS, Fieschi C, Galicier L, Hermine O, Lefèvre-Utile A, Malphettes M, Merlin E, Oksenhendler E, Pasquet M, Suarez F, André I, Béziat V, De Saint Basile G, De Villartay JP, Kracker S, Lagresle-Peyrou C, Latour S, Rieux-Laucat F, Mahlaoui N, Bole C, Nitschke P, Hulier-Ammar E, Fischer A, Moshous D, Neven B, Alcais A, Vogt G, Bustamante J, Picard C. Improving the diagnostic efficiency of primary immunodeficiencies with targeted next-generation sequencing. J Allergy Clin Immunol 2021; 147:734-737. [DOI: 10.1016/j.jaci.2020.05.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 01/09/2023]
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Buchbinder D, Walter JE, Butte MJ, Chan WY, Chitty Lopez M, Dimitriades VR, Dorsey MJ, Nugent DJ, Puck JM, Singh J, Collins CA. When Screening for Severe Combined Immunodeficiency (SCID) with T Cell Receptor Excision Circles Is Not SCID: a Case-Based Review. J Clin Immunol 2021; 41:294-302. [PMID: 33411155 PMCID: PMC8179373 DOI: 10.1007/s10875-020-00931-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Newborn screening efforts focusing on the quantification of T cell receptor excision circles (TRECs), as a biomarker for abnormal thymic production of T cells, have allowed for the identification and definitive treatment of severe combined immunodeficiency (SCID) in asymptomatic neonates. With the adoption of TREC quantification in Guthrie cards across the USA and abroad, typical, and atypical SCID constitutes only ~ 10% of cases identified with abnormal TRECs associated with T cell lymphopenia. Several other non-SCID-related conditions may be identified by newborn screening in a term infant. Thus, it is important for physicians to recognize that other factors, such as prematurity, are often associated with low TRECs initially, but often improve with age. This paper focuses on a challenge that immunologists face: the diagnostic evaluation and management of cases in which abnormal TRECs are associated with variants of T cell lymphopenia in the absence of a genetically defined form of typical or atypical SCID. Various syndromes associated with T cell impairment, secondary forms of T cell lymphopenia, and idiopathic T cell lymphopenia are identified using this screening approach. Yet there is no consensus or guidelines to assist in the evaluation and management of these newborns, despite representing 90% of the patients identified, resulting in significant work for the clinical teams until a diagnosis is made. Using a case-based approach, we review pearls relevant to the evaluation of these newborns, as well as the management dilemmas for the families and team related to the resolution of genetic ambiguities.
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Affiliation(s)
- David Buchbinder
- Department of Hematology, Children's Hospital of Orange County, Orange, CA, USA.
- Department of Pediatrics, University of California at Irvine, Orange, CA, USA.
| | - Jolan E Walter
- Division of Pediatric, University of South Florida at Johns Hopkins All Children's Hospital, Allergy/ Immunology, St. Petersburg, FL, USA
- Division of Pediatric Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA
| | - Wan-Yin Chan
- Department of Allergy & Immunology, Children's Hospital of Orange County, Orange, CA, USA
| | - Maria Chitty Lopez
- Division of Pediatric, University of South Florida at Johns Hopkins All Children's Hospital, Allergy/ Immunology, St. Petersburg, FL, USA
| | - Victoria R Dimitriades
- Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, Sacramento, CA, USA
| | - Morna J Dorsey
- Department of Allergy & Immunology, University of California, San Francisco, CA, USA
| | - Diane J Nugent
- Department of Hematology, Children's Hospital of Orange County, Orange, CA, USA
- Department of Pediatrics, University of California at Irvine, Orange, CA, USA
| | - Jennifer M Puck
- Department of Allergy & Immunology, University of California, San Francisco, CA, USA
| | - Jasjit Singh
- Department of Infectious Disease, Children's Hospital of Orange County, Orange, CA, USA
| | - Cathleen A Collins
- Department of Pediatrics, Division of Allergy Immunology, University of California at San Diego, La Jolla, CA, USA
- Department of Pediatrics, Division of Allergy Immunology, Rady Children's Hospital, San Diego, CA, USA
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Mone F, Eberhardt RY, Morris RK, Hurles ME, McMullan DJ, Maher ER, Lord J, Chitty LS, Giordano JL, Wapner RJ, Kilby MD. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: prospective cohort study and systematic review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:43-51. [PMID: 32388881 DOI: 10.1002/uog.22072] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To determine the incremental yield of antenatal exome sequencing (ES) over chromosomal microarray analysis (CMA) or conventional karyotyping in prenatally diagnosed congenital heart disease (CHD). METHODS A prospective cohort study of 197 trios undergoing ES following CMA or karyotyping owing to CHD identified prenatally and a systematic review of the literature were performed. MEDLINE, EMBASE, CINAHL and ClinicalTrials.gov (January 2000 to October 2019) databases were searched electronically for studies reporting on the diagnostic yield of ES in prenatally diagnosed CHD. Selected studies included those with more than three cases, with initiation of testing based upon prenatal phenotype only and that included cases in which CMA or karyotyping was negative. The incremental diagnostic yield of ES was assessed in: (1) all cases of CHD; (2) isolated CHD; (3) CHD associated with extracardiac anomaly (ECA); and (4) CHD according to phenotypic subgroup. RESULTS In our cohort, ES had an additional diagnostic yield in all CHD, isolated CHD and CHD associated with ECA of 12.7% (25/197), 11.5% (14/122) and 14.7% (11/75), respectively (P = 0.81). The corresponding pooled incremental yields from 18 studies (encompassing 636 CHD cases) included in the systematic review were 21% (95% CI, 15-27%), 11% (95% CI, 7-15%) and 37% (95% CI, 18-56%), respectively. The results did not differ significantly when subanalysis was limited to studies including more than 20 cases, except for CHD associated with ECA, in which the incremental yield was greater (49% (95% CI, 17-80%)). In cases of CHD associated with ECA in the primary analysis, the most common extracardiac anomalies associated with a pathogenic variant were those affecting the genitourinary system (23/52 (44.2%)). The greatest incremental yield was in cardiac shunt lesions (41% (95% CI, 19-63%)), followed by right-sided lesions (26% (95% CI, 9-43%)). In the majority (68/96 (70.8%)) of instances, pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease genes. The most common (19/96 (19.8%)) monogenic syndrome identified was Kabuki syndrome. CONCLUSIONS There is an apparent incremental yield of prenatal ES in CHD. While the greatest yield is in CHD associated with ECA, consideration could also be given to performing ES in the presence of an isolated cardiac abnormality. A policy of routine application of ES would require the adoption of robust bioinformatic, clinical and ethical pathways. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- F Mone
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - R K Morris
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - D J McMullan
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - E R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - J Lord
- Wellcome Sanger Institute, Hinxton, UK
| | - L S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health, London, UK
| | - J L Giordano
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - R J Wapner
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Columbia University Vagelos Medical Center, New York, NY, USA
| | - M D Kilby
- West Midlands Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
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Więsik-Szewczyk E, Jahnz-Różyk K. From infections to autoimmunity: Diagnostic challenges in common variable immunodeficiency. World J Clin Cases 2020; 8:3942-3955. [PMID: 33024751 PMCID: PMC7520788 DOI: 10.12998/wjcc.v8.i18.3942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 05/29/2020] [Accepted: 08/26/2020] [Indexed: 02/05/2023] Open
Abstract
Common variable immunodeficiency (CVID) is the most common clinically significant primary antibody deficiency diagnosed in adults. The early symptoms are not specific. They include common infections, mainly of the respiratory tract, caused by typical microorganisms, so cases can be missed in primary care. In the majority of patients increased susceptibility to infections coexists with signs or symptoms of autoimmunity, inflammation or polyclonal lymphoproliferation, which can divert diagnosis from immune deficiency. The overall incidence of malignancy is increased in CVID and certain cancers are significantly more common. Lymphomas and gastric carcinoma are the most frequently reported malignancies in CVID, so a high index of suspicion is recommended. Diagnostic delay in CVID is seen worldwide. The main goal of this paper is to increase the awareness about CVID among health care professionals. We aim to present features which can be helpful in CVID diagnosis in order to shorten the “latency” of proper management of CVID patients. We review clinical symptoms, complications and laboratory abnormalities of CVID. Immunoglobulin replacement therapy is regarded as the cornerstone of pharmacological intervention. New modes of Ig application, mainly subcutaneously and via the hyaluronidase-facilitated subcutaneous route, help to adjust therapy to patients’ needs and preferences. Still there remain unmet needs. It remains to be seen whether CVID complications can be avoided by earlier diagnosis, treatment and thorough monitoring in the context of increased risk of malignancy. Development of patient tailored protocols depending on the clinical phenotype and risk factors might be more appropriate. The most important consideration is to diagnose suspected cases and stratify patients in a precise and timely way. Work is needed to define features predictive of unfavorable prognosis.
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Affiliation(s)
- Ewa Więsik-Szewczyk
- Department of Internal Medicine, Pulmonology, Allergy and Clinical Immunology, Central Clinical Hospital of the Ministry of National Defense, Military Institute of Medicine, Warsaw 04-141, Poland
| | - Karina Jahnz-Różyk
- Department of Internal Medicine, Pulmonology, Allergy and Clinical Immunology, Central Clinical Hospital of the Ministry of National Defense, Military Institute of Medicine, Warsaw 04-141, Poland
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34
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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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35
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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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36
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Sakata S, Tsumura M, Matsubayashi T, Karakawa S, Kimura S, Tamaura M, Okano T, Naruto T, Mizoguchi Y, Kagawa R, Nishimura S, Imai K, Le Voyer T, Casanova JL, Bustamante J, Morio T, Ohara O, Kobayashi M, Okada S. Autosomal recessive complete STAT1 deficiency caused by compound heterozygous intronic mutations. Int Immunol 2020; 32:663-671. [PMID: 32603428 DOI: 10.1093/intimm/dxaa043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 06/23/2020] [Indexed: 02/06/2023] Open
Abstract
Autosomal recessive (AR) complete signal transducer and activator of transcription 1 (STAT1) deficiency is an extremely rare primary immunodeficiency that causes life-threatening mycobacterial and viral infections. Only seven patients from five unrelated families with this disorder have been so far reported. All causal STAT1 mutations reported are exonic and homozygous. We studied a patient with susceptibility to mycobacteria and virus infections, resulting in identification of AR complete STAT1 deficiency due to compound heterozygous mutations, both located in introns: c.128+2 T>G and c.542-8 A>G. Both mutations were the first intronic STAT1 mutations to cause AR complete STAT1 deficiency. Targeted RNA-seq documented the impairment of STAT1 mRNA expression and contributed to the identification of the intronic mutations. The patient's cells showed a lack of STAT1 expression and phosphorylation, and severe impairment of the cellular response to IFN-γ and IFN-α. The case reflects the importance of accurate clinical diagnosis and precise evaluation, to include intronic mutations, in the comprehensive genomic study when the patient lacks molecular pathogenesis. In conclusion, AR complete STAT1 deficiency can be caused by compound heterozygous and intronic mutations. Targeted RNA-seq-based systemic gene expression assay may help to increase diagnostic yield in inconclusive cases after comprehensive genomic study.
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Affiliation(s)
- Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | | | - Shuhei Karakawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shunsuke Kimura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Moe Tamaura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tsubasa Okano
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Naruto
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Mizoguchi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Reiko Kagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shiho Nishimura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Kohsuke Imai
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tom Le Voyer
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France.,Paris University, Imagine Institute, Paris, EU, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France.,Paris University, Imagine Institute, Paris, EU, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, EU, France.,Study Center of Immunodeficiencies, Necker Hospital for Sick Children, Paris EU, France.,Howard Hughes Medical Institute, New York, NY, USA
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France.,Paris University, Imagine Institute, Paris, EU, France.,Study Center of Immunodeficiencies, Necker Hospital for Sick Children, Paris EU, France.,Department of Clinical Immunology, Aarhus University Hospital, Aarhus N, EU, Denmark
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kasarazu, Japan
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
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37
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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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38
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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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39
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Suratannon N, van Wijck RTA, Broer L, Xue L, van Meurs JBJ, Barendregt BH, van der Burg M, Dik WA, Chatchatee P, Langerak AW, Swagemakers SMA, Goos JAC, Mathijssen IMJ, Dalm VASH, Suphapeetiporn K, Heezen KC, Drabwell J, Uitterlinden AG, van der Spek PJ, van Hagen PM. Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency. Front Immunol 2020; 11:614. [PMID: 32373116 PMCID: PMC7179678 DOI: 10.3389/fimmu.2020.00614] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Genetic tests for primary immunodeficiency disorders (PIDs) are expensive, time-consuming, and not easily accessible in developing countries. Therefore, we studied the feasibility of a customized single nucleotide variant (SNV) microarray that we developed to detect disease-causing variants and copy number variation (CNV) in patients with PIDs for only 40 Euros. Methods: Probes were custom-designed to genotype 9,415 variants of 277 PID-related genes, and were added to the genome-wide Illumina Global Screening Array (GSA). Data analysis of GSA was performed using Illumina GenomeStudio 2.0, Biodiscovery Nexus 10.0, and R-3.4.4 software. Validation of genotype calling was performed by comparing the GSA with whole-genome sequencing (WGS) data of 56 non-PID controls. DNA samples of 95 clinically diagnosed PID patients, of which 60 patients (63%) had a genetically established diagnosis (by Next-Generation Sequencing (NGS) PID panels or Sanger sequencing), were analyzed to test the performance of the GSA. The additional SNVs detected by GSA were validated by Sanger sequencing. Results: Genotype calling of the customized array had an accuracy rate of 99.7%. The sensitivity for detecting rare PID variants was high (87%). The single sample replication in two runs was high (94.9%). The customized GSA was able to generate a genetic diagnosis in 37 out of 95 patients (39%). These 37 patients included 29 patients in whom the genetic variants were confirmed by conventional methods (26 patients by SNV and 3 by CNV analysis), while in 8 patients a new genetic diagnosis was established (6 patients by SNV and 2 patients suspected for leukemia by CNV analysis). Twenty-eight patients could not be detected due to the limited coverage of the custom probes. However, the diagnostic yield can potentially be increased when newly updated variants are added. Conclusion: Our robust customized GSA seems to be a promising first-line rapid screening tool for PIDs at an affordable price, which opens opportunities for low-cost genetic testing in developing countries. The technique is scalable, allows numerous new genetic variants to be added, and offers the potential for genetic testing not only in PIDs, but also in many other genetic diseases.
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Affiliation(s)
- Narissara Suratannon
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Rogier T A van Wijck
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Linda Broer
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Laixi Xue
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Joyce B J van Meurs
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Barbara H Barendregt
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - Willem A Dik
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Sigrid M A Swagemakers
- Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Pathology & Clinical Bioinformatics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kim C Heezen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jose Drabwell
- International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United Kingdom
| | - André G Uitterlinden
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Peter J van der Spek
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - P Martin van Hagen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
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40
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Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing. Eur J Med Genet 2020; 63:103920. [PMID: 32222431 DOI: 10.1016/j.ejmg.2020.103920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/13/2020] [Accepted: 03/21/2020] [Indexed: 11/22/2022]
Abstract
Autoinflammatory diseases comprise a wide range of syndromes caused by dysregulation of the innate immune response. They are difficult to diagnose due to their phenotypic heterogeneity and variable expressivity. Thus, the genetic origin of the disease remains undetermined for an important proportion of patients. We aim to identify causal genetic variants in patients with suspected autoinflammatory disease and to test the advantages and limitations of the clinical exome gene panels for molecular diagnosis. Twenty-two unrelated patients with clinical features of autoinflammatory diseases were analyzed using clinical exome sequencing (~4800 genes), followed by bioinformatic analyses to detect likely pathogenic variants. By integrating genetic and clinical information, we found a likely causative heterozygous genetic variant in NFKBIA (p.D31N) in a North-African patient with a clinical picture resembling the deficiency of interleukin-1 receptor antagonist, and a heterozygous variant in DNASE2 (p.G322D) in a Spanish patient with a suspected lupus-like monogenic disorder. We also found variants likely to increase the susceptibility to autoinflammatory diseases in three additional Spanish patients: one with an initial diagnosis of juvenile idiopathic arthritis who carries two heterozygous UNC13D variants (p.R727Q and p.A59T), and two with early-onset inflammatory bowel disease harbouring NOD2 variants (p.L221R and p.A728V respectively). Our results show a similar proportion of molecular diagnosis to other studies using whole exome or targeted resequencing in primary immunodeficiencies. Thus, despite its main limitation of not including all candidate genes, clinical exome targeted sequencing can be an appropriate approach to detect likely causative variants in autoinflammatory diseases.
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41
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Elsink K, van Montfrans JM, van Gijn ME, Blom M, van Hagen PM, Kuijpers TW, Frederix GWJ. Cost and impact of early diagnosis in primary immunodeficiency disease: A literature review. Clin Immunol 2020; 213:108359. [PMID: 32035178 DOI: 10.1016/j.clim.2020.108359] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 01/07/2020] [Accepted: 02/04/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND New, innovative, costly diagnostic methods for patients with primary immunodeficiencies (PID) demand upfront insight into their potential cost savings and added value for individual patients. As such, high quality, comparable economic evaluations are of utmost importance to enable informed decisions. The objective of this review was therefore to create an extensive overview of current costing studies and potential cost savings of early diagnosis in primary immunodeficiency disease. METHODS A literature search in PubMed was conducted and studies involving any form of costing study in the field of PIDs were included. Of the included studies, study characteristics, cost parameters and benefits of early diagnosis were extracted and outlined in separate tables. RESULTS Twenty two studies met the inclusion criteria and were included in the review. The papers were categorized according to their subject: neonatal screening for severe combined immunodeficiency (SCID), Ig replacement therapies and studies reporting on costs of general or specific PIDs. Within and between these groups variability in reported costing characteristics was observed. In studies that reported cost savings pre- and post-diagnosis, cost savings ranged from 6500 to 108,463 USD of total costs per patient. CONCLUSION This literature review shows that, regardless of what aspect of PIDs has been studied, in nearly all cases early diagnosis reduces health care consumption and leads to better health outcomes for patients with PIDs. We found considerable variability in costing characteristics of economic evaluations of PID patients, which hampers the comparability of outcomes. More effort is needed to create uniformity and define cost parameters in economic evaluations in the field of PIDs, facilitating further prospective research to extensively assess the benefits of early diagnosis.
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Affiliation(s)
- Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, 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
| | - Mariëlle E van Gijn
- Department of Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Maartje Blom
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - P Martin van Hagen
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - T W Kuijpers
- Department of Internal Medicine/Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands.
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Rudilla F, Franco-Jarava C, Martínez-Gallo M, Garcia-Prat M, Martín-Nalda A, Rivière J, Aguiló-Cucurull A, Mongay L, Vidal F, Solanich X, Irastorza I, Santos-Pérez JL, Tercedor Sánchez J, Cuscó I, Serra C, Baz-Redón N, Fernández-Cancio M, Carreras C, Vagace JM, Garcia-Patos V, Pujol-Borrell R, Soler-Palacín P, Colobran R. Expanding the Clinical and Genetic Spectra of Primary Immunodeficiency-Related Disorders With Clinical Exome Sequencing: Expected and Unexpected Findings. Front Immunol 2019; 10:2325. [PMID: 31681265 PMCID: PMC6797824 DOI: 10.3389/fimmu.2019.02325] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/16/2019] [Indexed: 01/18/2023] Open
Abstract
Primary immunodeficiencies (PIDs) refer to a clinically, immunologically, and genetically heterogeneous group of over 350 disorders affecting development or function of the immune system. The increasing use of next-generation sequencing (NGS) technology has greatly facilitated identification of genetic defects in PID patients in daily clinical practice. Several NGS approaches are available, from the unbiased whole exome sequencing (WES) to specific gene panels. Here, we report on a 3-year experience with clinical exome sequencing (CES) for genetic diagnosis of PIDs. We used the TruSight One sequencing panel, which includes 4,813 disease-associated genes, in 61 unrelated patients (pediatric and adults). The analysis was done in 2 steps: first, we focused on a virtual PID panel and then, we expanded the analysis to the remaining genes. A molecular diagnosis was achieved in 19 (31%) patients: 12 (20%) with mutations in genes included in the virtual PID panel and 7 (11%) with mutations in other genes. These latter cases provided interesting and somewhat unexpected findings that expand the clinical and genetic spectra of PID-related disorders, and are useful to consider in the differential diagnosis. We also discuss 5 patients (8%) with incomplete genotypes or variants of uncertain significance. Finally, we address the limitations of CES exemplified by 7 patients (11%) with negative results on CES who were later diagnosed by other approaches (more specific PID panels, WES, and comparative genomic hybridization array). In summary, the genetic diagnosis rate using CES was 31% (including a description of 12 novel mutations), which rose to 42% after including diagnoses achieved by later use of other techniques. The description of patients with mutations in genes not included in the PID classification illustrates the heterogeneity and complexity of PID-related disorders.
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Affiliation(s)
- Francesc Rudilla
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain.,Transfusional Medicine Group, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Clara Franco-Jarava
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Marina Garcia-Prat
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Andrea Martín-Nalda
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Jacques Rivière
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Aina Aguiló-Cucurull
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Laura Mongay
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain
| | - Francisco Vidal
- Immunogenetics and Histocompatibility Laboratory, Banc de Sang i Teixits, Barcelona, Spain.,Transfusional Medicine Group, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain.,CIBER on Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III (ISCIII), Valencia, Spain
| | - Xavier Solanich
- Adult Immunodeficiencies Unit (UFIPA), Internal Medicine Department, Institut d'Investigació Biomèdica de Bellvitge, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Iñaki Irastorza
- Pediatric Gastroenterology, Cruces University Hospital, Basque Country University, Bilbao, Spain
| | - Juan Luis Santos-Pérez
- Immunodeficiencies and Infectious Disease Unit, Universitary Hospital Virgen de las Nieves, Granada, Spain
| | - Jesús Tercedor Sánchez
- Unidad de Dermatología Pediátrica y Anomalías Vasculares, Servicio de Dermatología, Instituto de Investigación Biosanitaria IBS, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Ivon Cuscó
- Genetics Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Clara Serra
- Genetics Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Noelia Baz-Redón
- Growth and Development Group, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain
| | - Mónica Fernández-Cancio
- Growth and Development Group, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,CIBER Rare Diseases (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carmen Carreras
- Pediatric Hematology and Immunodeficiencies Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - José Manuel Vagace
- Hematology Department, Complejo Hospitalario Universitario de Badajoz, Badajoz, Spain
| | - Vicenç Garcia-Patos
- Dermatology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ricardo Pujol-Borrell
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Pere Soler-Palacín
- Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Autonomous University of Barcelona, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Department of Cell Biology, Physiology and Immunology, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Autonomous University of Barcelona, Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Genetics Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
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Virkud YV, Kelly RS, Wood C, Lasky-Su JA. The nuts and bolts of omics for the clinical allergist. Ann Allergy Asthma Immunol 2019; 123:558-563. [PMID: 31562939 DOI: 10.1016/j.anai.2019.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Omics, aka multi-omics, is an emerging area of research that is advancing the use of personalized medicine in clinical practice and is therefore relevant for the practicing allergist. DATA SOURCES We performed a literature search of a selection of scientific findings in omics and allergy, including variants that may be important to allergy outcomes in the genome, transcriptome, metabolome, microbiome, epigenome, and exposome, among others. STUDY SELECTIONS Basic science papers and review articles. RESULTS The use of multi-omic data in clinical practice is changing how clinicians treat their patients whereby more personalized approaches are becoming standard in medical practice and has the potential to transform the treatment of allergies. CONCLUSION Multi-omic data are relevant and will become increasingly important for the clinical allergist.
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Affiliation(s)
- Yamini V Virkud
- Department of Pediatrics, Massachusetts General Hospital for Children and Harvard Medical School, Boston, Massachusetts; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rachel S Kelly
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Caleb Wood
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts.
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Current status and prospects of primary immunodeficiency diseases in Asia. Genes Dis 2019; 7:3-11. [PMID: 32181271 PMCID: PMC7063407 DOI: 10.1016/j.gendis.2019.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 07/30/2019] [Accepted: 09/04/2019] [Indexed: 11/25/2022] Open
Abstract
Primary Immunodeficiency Diseases (PIDs) are increasingly being reported across the World. Several advances have been made in the diagnostic and therapeutic research related to PIDs. With increasing awareness, the field of PIDs has rapidly evolved in Asia as well. In this review, we summarize the progress that has been made in the field of PIDs in Asian countries; major limitations and challenges faced by the clinicians working in this field in Asia; difference in spectrum of PIDs in Asia from rest of the World; current state of diagnostic and treatment facilities available in various countries in Asia and the future prospects of these diseases in the continent.
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