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Erman B, Aba U, Ipsir C, Pehlivan D, Aytekin C, Cildir G, Cicek B, Bozkurt C, Tekeoglu S, Kaya M, Aydogmus C, Cipe F, Sucak G, Eltan SB, Ozen A, Barıs S, Karakoc-Aydiner E, Kıykım A, Karaatmaca B, Kose H, Uygun DFK, Celmeli F, Arikoglu T, Ozcan D, Keskin O, Arık E, Aytekin ES, Cesur M, Kucukosmanoglu E, Kılıc M, Yuksek M, Bıcakcı Z, Esenboga S, Ayvaz DÇ, Sefer AP, Guner SN, Keles S, Reisli I, Musabak U, Demirbas ND, Haskologlu S, Kilic SS, Metin A, Dogu F, Ikinciogulları A, Tezcan I. Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye. J Clin Immunol 2024; 44:157. [PMID: 38954121 PMCID: PMC11219406 DOI: 10.1007/s10875-024-01759-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/22/2024] [Indexed: 07/04/2024]
Abstract
Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients' long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.
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Affiliation(s)
- Baran Erman
- Institute of Child Health, Hacettepe University, Ankara, Turkey.
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey.
| | - Umran Aba
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Canberk Ipsir
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Damla Pehlivan
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Caner Aytekin
- Pediatric Immunology, SBU Ankara Dr Sami Ulus Maternity Child Health and Diseases Training and Research Hospital, Ankara, Turkey
| | - Gökhan Cildir
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5000, Australia
| | - Begum Cicek
- Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Ceren Bozkurt
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Sidem Tekeoglu
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Melisa Kaya
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Turkey
| | - Cigdem Aydogmus
- Department of Pediatric Allergy and Clinical Immunology, University of Health Sciences, Istanbul Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Funda Cipe
- Department of Pediatric Allergy and Clinical Immunology, Altinbas University School of Medicine, Istanbul, Turkey
| | - Gulsan Sucak
- Medical Park Bahçeşehir Hospital, Clinic of Hematology and Transplantation, İstanbul, Turkey
| | - Sevgi Bilgic Eltan
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ahmet Ozen
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Safa Barıs
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Elif Karakoc-Aydiner
- Marmara University, Faculty of Medicine, Department of Pediatric Allergy and Immunology, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, Turkey
| | - Ayca Kıykım
- Pediatric Allergy and Immunology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Betul Karaatmaca
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Hulya Kose
- Department of Pediatric Immunology, Diyarbakir Children Hospital, Diyarbakır, Turkey
| | - Dilara Fatma Kocacık Uygun
- Division of Allergy Immunology, Department of Pediatrics, Akdeniz University Faculty of Medicine, Antalya, Turkey
| | - Fatih Celmeli
- Republic of Turkey Ministry of Health Antalya Training and Research Hospital Pediatric Immunology and Allergy Diseases, Antalya, Turkey
| | - Tugba Arikoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Mersin University, Mersin, Turkey
| | - Dilek Ozcan
- Division of Pediatric Allergy and Immunology, Faculty of Medicine, Balcali Hospital, Cukurova University, Adana, Turkey
| | - Ozlem Keskin
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Arık
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Elif Soyak Aytekin
- Department of Pediatric Allergy and Immunology, Etlik City Hospital, Ankara, Turkey
| | - Mahmut Cesur
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ercan Kucukosmanoglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Mehmet Kılıc
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, University of Firat, Elazığ, Turkey
| | - Mutlu Yuksek
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, Turkey
| | - Zafer Bıcakcı
- Department of Pediatric Hematology, Faculty of Medicine, Ataturk University, Erzurum, Turkey
| | - Saliha Esenboga
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Deniz Çagdaş Ayvaz
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
- Section of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Asena Pınar Sefer
- Department of Pediatric Allergy and Immunology, Şanlıurfa Training and Research Hospital, Şanlıurfa, Turkey
| | - Sukrü Nail Guner
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sevgi Keles
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ismail Reisli
- Department of Pediatric Immunology and Allergy, Medicine Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Ugur Musabak
- Department of Immunology and Allergy, Baskent University School of Medicine, Ankara, Turkey
| | - Nazlı Deveci Demirbas
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sule Haskologlu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Sara Sebnem Kilic
- Division of Pediatric Immunology-Rheumatology, Bursa Uludag University Faculty of Medicine, Bursa, Turkey
- Translational Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ayse Metin
- Department of Pediatric Allergy and Immunology, University of Health Sciences, Ankara Bilkent City Hospital, Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Aydan Ikinciogulları
- Department of Pediatric Immunology and Allergy, Ankara University Faculty of Medicine, Ankara, Turkey
| | - Ilhan Tezcan
- Department of Pediatrics, Division of Pediatric Immunology, Hacettepe University School of Medicine, Ankara, Turkey
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Stojkic I, Prince BT, Kuehn HS, Gil Silva AA, Varga EA, Rosenzweig SD, Ramadesikan S, Supinger R, Marhabaie M, Chang P, Mardis ER, Koboldt DC. A novel IKZF1 variant in a family with autosomal dominant CVID: A case for expanding exon coverage in inborn errors of immunity. Clin Immunol 2024; 264:110244. [PMID: 38734037 DOI: 10.1016/j.clim.2024.110244] [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: 04/05/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Common variable immune deficiency (CVID) is a heterogenous group of disorders characterized by varying degrees of hypogammaglobulinemia, recurrent infections, and autoimmunity. Currently, pathogenic variants are identified in approximately 20-30% of CVID cases. Here we report a 3-generation family with autosomal dominant Common Variable Immunodeficiency (CVID) diagnosed in 9 affected individuals. Although primary immune deficiency panels and exome sequencing were non-diagnostic, whole genome sequencing revealed a novel, pathogenic c.499C > T: p.His167Tyr variant in IKZF1, a critical regulator of B cell development. Functional testing done through pericentromeric heterochromatin localization and light shift chemiluminescent electrophoretic mobility shift assay confirmed the variant's deleterious effect via a haploinsufficiency mechanism. Our findings expand the spectrum of known IKZF1 mutations and contribute to a more comprehensive understanding of CVID's genetic heterogeneity. Furthermore, this case underscores the importance of considering whole genome sequencing for comprehensive genetic diagnosis when concern for a monogenic inborn errors of immunity is high.
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Affiliation(s)
- Ivana Stojkic
- Division of Pediatric Rheumatology, Nationwide Children's Hospital, Columbus, OH, USA.
| | - Benjamin T Prince
- Division of Allergy and Immunology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Hye Sun Kuehn
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Agustin A Gil Silva
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Elizabeth A Varga
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Swetha Ramadesikan
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Rachel Supinger
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Mohammad Marhabaie
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Peter Chang
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Elaine R Mardis
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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Chen Y, Li D, Yin J, Xiong J, Xu M, Qi Q, Yang W. Diagnostic yield of next-generation sequencing in suspect primary immunodeficiencies diseases: a systematic review and meta-analysis. Clin Exp Med 2024; 24:131. [PMID: 38890201 PMCID: PMC11189333 DOI: 10.1007/s10238-024-01392-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
To determine the diagnostic yield of Next-generation sequencing (NGS) in suspect Primary Immunodeficiencies Diseases (PIDs). This systematic review was conducted following PRISMA criteria. Searching Pubmed and Web of Science databases, the following keywords were used in the search: ("Next-generation sequencing") OR "whole exome sequencing" OR "whole genome sequencing") AND ("primary immunodeficiency disease" OR "PIDs"). We used STARD items to assess the risk of bias in the included studies. The meta-analysis included 29 studies with 5847 patients, revealing a pooled positive detection rate of 42% (95% CI 0.29-0.54, P < 0.001) for NGS in suspected PID cases. Subgroup analyses based on family history demonstrated a higher detection rate of 58% (95% CI 0.43-0.71) in patients with a family history compared to 33% (95% CI 0.21-0.46) in those without (P < 0.001). Stratification by disease types showed varied detection rates, with Severe Combined Immunodeficiency leading at 58% (P < 0.001). Among 253 PID-related genes, RAG1, ATM, BTK, and others constituted major contributors, with 34 genes not included in the 2022 IUIS gene list. The application of NGS in suspected PID patients can provide significant diagnostic results, especially in patients with a family history. Meanwhile, NGS performs excellently in accurately diagnosing disease types, and early identification of disease types can benefit patients in treatment.
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Affiliation(s)
- Yingying Chen
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Dongrui Li
- The First Clinical College of Guangzhou Medical University, Guangzhou, 510180, China
| | - Jiawen Yin
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Jinglin Xiong
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Min Xu
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Qing Qi
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China
| | - Wenlin Yang
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
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von Hardenberg S, Klefenz I, Steinemann D, Di Donato N, Baumann U, Auber B, Klemann C. Current genetic diagnostics in inborn errors of immunity. Front Pediatr 2024; 12:1279112. [PMID: 38659694 PMCID: PMC11039790 DOI: 10.3389/fped.2024.1279112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
New technologies in genetic diagnostics have revolutionized the understanding and management of rare diseases. This review highlights the significant advances and latest developments in genetic diagnostics in inborn errors of immunity (IEI), which encompass a diverse group of disorders characterized by defects in the immune system, leading to increased susceptibility to infections, autoimmunity, autoinflammatory diseases, allergies, and malignancies. Various diagnostic approaches, including targeted gene sequencing panels, whole exome sequencing, whole genome sequencing, RNA sequencing, or proteomics, have enabled the identification of causative genetic variants of rare diseases. These technologies not only facilitated the accurate diagnosis of IEI but also provided valuable insights into the underlying molecular mechanisms. Emerging technologies, currently mainly used in research, such as optical genome mapping, single cell sequencing or the application of artificial intelligence will allow even more insights in the aetiology of hereditary immune defects in the near future. The integration of genetic diagnostics into clinical practice significantly impacts patient care. Genetic testing enables early diagnosis, facilitating timely interventions and personalized treatment strategies. Additionally, establishing a genetic diagnosis is necessary for genetic counselling and prognostic assessments. Identifying specific genetic variants associated with inborn errors of immunity also paved the way for the development of targeted therapies and novel therapeutic approaches. This review emphasizes the challenges related with genetic diagnosis of rare diseases and provides future directions, specifically focusing on IEI. Despite the tremendous progress achieved over the last years, several obstacles remain or have become even more important due to the increasing amount of genetic data produced for each patient. This includes, first and foremost, the interpretation of variants of unknown significance (VUS) in known IEI genes and of variants in genes of unknown significance (GUS). Although genetic diagnostics have significantly contributed to the understanding and management of IEI and other rare diseases, further research, exchange between experts from different clinical disciplines, data integration and the establishment of comprehensive guidelines are crucial to tackle the remaining challenges and maximize the potential of genetic diagnostics in the field of rare diseases, such as IEI.
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Affiliation(s)
| | - Isabel Klefenz
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nataliya Di Donato
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ulrich Baumann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Christian Klemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
- Department of Pediatric Immunology, Rheumatology and Infectiology, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
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Rayzan E, Mirbeyk M, Pezeshki PS, Mohammadpour M, Yaghmaie B, Hassani SA, Sharifzadeh M, Tahernia L, Rezaei N. Whole-exome sequencing to identify undiagnosed primary immunodeficiency disorders in children with community-acquired sepsis, admitted in the pediatric intensive care unit. Pediatr Allergy Immunol 2023; 34:e14066. [PMID: 38146112 DOI: 10.1111/pai.14066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
BACKGROUND Whole-exome sequencing (WES) provides a powerful diagnostic tool for identifying primary immunodeficiency diseases (PIDs). This study explores the utility of this approach in uncovering previously undiagnosed PIDs in children with community-acquired sepsis (CAS), with a medical history of recurrent infections or a family history of PIDs. METHODS We performed WES on DNA samples extracted from the blood of the 34 enrolled patients, followed by bioinformatic analysis for variant calling, annotation, and prioritization. We also performed a segregation analysis in available family members to confirm the inheritance patterns and assessed the potential impact of the identified variants on protein function. RESULTS From 34 patients enrolled in the study, 29 patients (85%) with previously undiagnosed genetic diseases, including 28 patients with PIDs and one patient with interstitial lung and liver disease, were identified. We identified two patients with severe combined immunodeficiency (SCID), patients with combined immunodeficiency (CID), six patients with combined immunodeficiency with syndromic features (CID-SF), four patients with defects in intrinsic and innate immunity, four patients with congenital defects of phagocyte function (CPDF), and six patients with the disease of immune dysregulation. Autoinflammatory disorders and predominantly antibody deficiency were diagnosed in one patient each. CONCLUSION Our findings demonstrate the potential of WES in identifying undiagnosed PIDs in children with CAS. Implementing WES in the clinical evaluation of CAS patients with a warning sign for PIDs can aid in their timely diagnosis and potentially lead to improved patient care.
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Affiliation(s)
- Elham Rayzan
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
- International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Boston, Massachusetts, USA
| | - Mona Mirbeyk
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Parmida Sadat Pezeshki
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Masoud Mohammadpour
- Division of Pediatric Intensive Care Unit, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahareh Yaghmaie
- Division of Pediatric Intensive Care Unit, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Abbas Hassani
- Division of Pediatric Intensive Care Unit, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Meisam Sharifzadeh
- Division of Pediatric Intensive Care Unit, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Tahernia
- Division of Pediatric Intensive Care Unit, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
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Fujiyoshi J, Inoue H, Sawano T, Mushimoto Y, Motomura Y, Nishiyama K, Kaku N, Nagata H, Yamamura K, Ishimura M, Koga Y, Ochiai M, Sakai Y, Tajiri T, Ohga S. Critical diseases in neonates after discharge home from birth hospital: A retrospective study from a tertiary hospital in Japan. Early Hum Dev 2023; 186:105869. [PMID: 37774632 DOI: 10.1016/j.earlhumdev.2023.105869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
INTRODUCTION To establish actionable neonatal screening during the first month of life, we investigated critical diseases in seemingly healthy newborns discharged from birth hospitals. METHODS This retrospective study enrolled previously healthy full-term infants who visited our hospital, a tertiary hospital in Japan, from home between 5 and 28 days after birth from 2009 to 2018. Infants with known perinatal or congenital diseases, positive newborn screening results, or accidental injuries were excluded. Data were collected from electronic medical records, including principal diagnosis, clinical details, and prognosis at 18 months of age. RESULTS Ninety-seven (58 %) of 168 eligible neonates were admitted to the hospital, and 71 (42 %) were not. The median admission rate in patients with disease onset at ≤14 days after birth (80 %) was significantly higher than that in patients with disease onset at ≥15 days (42 %). Among 45 patients who received intensive medical care, 5 died and 10 developed neurodevelopmental sequelae. Four of 5 patients died by 100 days. Among 25 diseases treated in intensive care unit, 17 (68 %) diseases had a prevalence of <1 per 2000 live births. The commonly used diagnostic methods were imaging (n = 58, 35 %) and physical examination (n = 34, 20 %). CONCLUSION Critical diseases due to rare and heterogeneous causes in ostensibly healthy newborns occurred predominantly in the first two weeks of life. Optimal newborn screening and health check-up protocols may benefit from the wide spectrum of life-threatening diseases occurring in home after birth.
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Affiliation(s)
- Junko Fujiyoshi
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Comprehensive Maternity and Perinatal Care Center, Kyushu University Hospital, Fukuoka, Japan
| | - Hirosuke Inoue
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Comprehensive Maternity and Perinatal Care Center, Kyushu University Hospital, Fukuoka, Japan.
| | - Toru Sawano
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Comprehensive Maternity and Perinatal Care Center, Kyushu University Hospital, Fukuoka, Japan
| | - Yuichi Mushimoto
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshitomo Motomura
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kei Nishiyama
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriyuki Kaku
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Emergency & Critical Care Center, Kyushu University Hospital, Fukuoka, Japan
| | - Hazumu Nagata
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenichiro Yamamura
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Perinatal and Pediatric Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masataka Ishimura
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuhki Koga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masayuki Ochiai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Similuk M, Kuijpers T. Nature and nurture: understanding phenotypic variation in inborn errors of immunity. Front Cell Infect Microbiol 2023; 13:1183142. [PMID: 37780853 PMCID: PMC10538643 DOI: 10.3389/fcimb.2023.1183142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
The overall disease burden of pediatric infection is high, with widely varying clinical outcomes including death. Among the most vulnerable children, those with inborn errors of immunity, reduced penetrance and variable expressivity are common but poorly understood. There are several genetic mechanisms that influence phenotypic variation in inborn errors of immunity, as well as a body of knowledge on environmental influences and specific pathogen triggers. Critically, recent advances are illuminating novel nuances for fundamental concepts on disease penetrance, as well as raising new areas of inquiry. The last few decades have seen the identification of almost 500 causes of inborn errors of immunity, as well as major advancements in our ability to characterize somatic events, the microbiome, and genotypes across large populations. The progress has not been linear, and yet, these developments have accumulated into an enhanced ability to diagnose and treat inborn errors of immunity, in some cases with precision therapy. Nonetheless, many questions remain regarding the genetic and environmental contributions to phenotypic variation both within and among families. The purpose of this review is to provide an updated summary of key concepts in genetic and environmental contributions to phenotypic variation within inborn errors of immunity, conceptualized as including dynamic, reciprocal interplay among factors unfolding across the key dimension of time. The associated findings, potential gaps, and implications for research are discussed in turn for each major influencing factor. The substantial challenge ahead will be to organize and integrate information in such a way that accommodates the heterogeneity within inborn errors of immunity to arrive at a more comprehensive and accurate understanding of how the immune system operates in health and disease. And, crucially, to translate this understanding into improved patient care for the millions at risk for serious infection and other immune-related morbidity.
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Affiliation(s)
- Morgan Similuk
- Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Taco Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children’s Hospital, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
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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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Ricci S, Abu-Rumeileh S, Campagna N, Barbati F, Stagi S, Canessa C, Lodi L, Palterer B, Maggi L, Matucci A, Vultaggio A, Annunziato F, Azzari C. Case Report: A child with NFKB1 haploinsufficiency explaining the linkage between immunodeficiency and short stature. Front Immunol 2023; 14:1224603. [PMID: 37600787 PMCID: PMC10434558 DOI: 10.3389/fimmu.2023.1224603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
We report the case of a patient with common variable immunodeficiency (CVID) presenting with short stature and treated with recombinant human growth hormone (rhGH). Whole exome sequencing revealed a novel single-nucleotide duplication in the NFKB1 gene (c.904dup, p.Ser302fs), leading to a frameshift and thus causing NFKB1 haploinsufficiency. The variant was considered pathogenic and was later found in the patient's mother, also affected by CVID. This is the first reported case of a patient with CVID due to NFKB1 mutation presenting with short stature. We analyzed the interconnection between NFKB1 and GH - IGF-1 pathways and we hypothesized a common ground for both CVID and short stature in our patient.
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Affiliation(s)
- S. Ricci
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Florence, Italy
| | - S. Abu-Rumeileh
- Department of Health Sciences, University of Florence, Florence, Italy
| | - N. Campagna
- Department of Health Sciences, University of Florence, Florence, Italy
| | - F. Barbati
- Department of Health Sciences, University of Florence, Florence, Italy
| | - S. Stagi
- Department of Health Sciences, University of Florence, Florence, Italy
- Endocrinology Division, Section of Pediatrics, Meyer Children’s Hospital Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Florence, Italy
| | - C. Canessa
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Florence, Italy
| | - L. Lodi
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Florence, Italy
| | - B. Palterer
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - L. Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - A. Matucci
- Immunoallergology Unit, Careggi University Hospital, Florence, Italy
| | - A. Vultaggio
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Immunoallergology Unit, Careggi University Hospital, Florence, Italy
| | - F. Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Flow Cytometry Diagnostic Center and Immunotherapy, Careggi University Hospital, Florence, Italy
| | - C. Azzari
- Department of Health Sciences, University of Florence, Florence, Italy
- Immunology Division, Section of Pediatrics, Meyer Children’s Hospital Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Florence, Italy
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10
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Kwon SS, Cho YK, Hahn S, Oh J, Won D, Shin S, Kang JM, Ahn JG, Lee ST, Choi JR. Genetic diagnosis of inborn errors of immunity using clinical exome sequencing. Front Immunol 2023; 14:1178582. [PMID: 37325673 PMCID: PMC10264570 DOI: 10.3389/fimmu.2023.1178582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Inborn errors of immunity (IEI) include a variety of heterogeneous genetic disorders in which defects in the immune system lead to an increased susceptibility to infections and other complications. Accurate, prompt diagnosis of IEI is crucial for treatment plan and prognostication. In this study, clinical utility of clinical exome sequencing (CES) for diagnosis of IEI was evaluated. For 37 Korean patients with suspected symptoms, signs, or laboratory abnormalities associated with IEI, CES that covers 4,894 genes including genes related to IEI was performed. Their clinical diagnosis, clinical characteristics, family history of infection, and laboratory results, as well as detected variants, were reviewed. With CES, genetic diagnosis of IEI was made in 15 out of 37 patients (40.5%). Seventeen pathogenic variants were detected from IEI-related genes, BTK, UNC13D, STAT3, IL2RG, IL10RA, NRAS, SH2D1A, GATA2, TET2, PRF1, and UBA1, of which four variants were previously unreported. Among them, somatic causative variants were identified from GATA2, TET2, and UBA1. In addition, we identified two patients incidentally diagnosed IEI by CES, which was performed to diagnose other diseases of patients with unrecognized IEI. Taken together, these results demonstrate the utility of CES for the diagnosis of IEI, which contributes to accurate diagnosis and proper treatments.
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Affiliation(s)
- Soon Sung Kwon
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Youn Keong Cho
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungmin Hahn
- Department of Pediatric Hemato-oncology, Yonsei Cancer Center, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jiyoung Oh
- Division of Clinical Genetics, Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongju Won
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Man Kang
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
- Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome, Seoul, Republic of Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
- Dxome, Seoul, Republic of Korea
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11
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Nurchis MC, Raspolini GM, Heidar Alizadeh A, Altamura G, Radio FC, Tartaglia M, Dallapiccola B, Damiani G. Organizational Aspects of the Implementation and Use of Whole Genome Sequencing and Whole Exome Sequencing in the Pediatric Population in Italy: Results of a Survey. J Pers Med 2023; 13:899. [PMID: 37373888 DOI: 10.3390/jpm13060899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/16/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
This study explores the organizational aspects of whole genome sequencing (WGS) implementation for pediatric patients with suspected genetic disorders in Italy, comparing it with whole exome sequencing (WES). Health professionals' opinions were collected through an internet-based survey and analyzed using a qualitative summative content analysis methodology. Among the 16 respondents, most were clinical geneticists performing only WES, while 5 also used WGS. The key differences identified include higher needs for analyzing genome rearrangements following WES, greater data storage and security requirements for WGS, and WGS only being performed in specific research studies. No difference was detected in centralization and decentralization issues. The main cost factors included genetic consultations, library preparation and sequencing, bioinformatic analysis, interpretation and confirmation, data storage, and complementary diagnostic investigations. Both WES and WGS decreased the need for additional diagnostic analyses when not used as last-resort tests. Organizational aspects were similar for WGS and WES, but economic evidence gaps may exist for WGS in clinical settings. As sequencing costs decline, WGS will likely replace WES and traditional genetic testing. Tailored genomic policies and cost-effectiveness analyses are needed for WGS implementation in health systems. WGS shows promise for enhancing genetics knowledge and expediting diagnoses for pediatric patients with genetic disorders.
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | | | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146 Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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12
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Nurchis MC, Altamura G, Riccardi MT, Radio FC, Chillemi G, Bertini ES, Garlasco J, Tartaglia M, Dallapiccola B, Damiani G. Whole genome sequencing diagnostic yield for paediatric patients with suspected genetic disorders: systematic review, meta-analysis, and GRADE assessment. Arch Public Health 2023; 81:93. [PMID: 37231492 DOI: 10.1186/s13690-023-01112-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND About 80% of the roughly 7,000 known rare diseases are single gene disorders, about 85% of which are ultra-rare, affecting less than one in one million individuals. NGS technologies, in particular whole genome sequencing (WGS) in paediatric patients suffering from severe disorders of likely genetic origin improve the diagnostic yield allowing targeted, effective care and management. The aim of this study is to perform a systematic review and meta-analysis to assess the effectiveness of WGS, with respect to whole exome sequencing (WES) and/or usual care, for the diagnosis of suspected genetic disorders among the paediatric population. METHODS A systematic review of the literature was conducted querying relevant electronic databases, including MEDLINE, EMBASE, ISI Web of Science, and Scopus from January 2010 to June 2022. A random-effect meta-analysis was run to inspect the diagnostic yield of different techniques. A network meta-analysis was also performed to directly assess the comparison between WGS and WES. RESULTS Of the 4,927 initially retrieved articles, thirty-nine met the inclusion criteria. Overall results highlighted a significantly higher pooled diagnostic yield for WGS, 38.6% (95% CI: [32.6 - 45.0]), in respect to WES, 37.8% (95% CI: [32.9 - 42.9]) and usual care, 7.8% (95% CI: [4.4 - 13.2]). The meta-regression output suggested a higher diagnostic yield of the WGS compared to WES after controlling for the type of disease (monogenic vs non-monogenic), with a tendency to better diagnostic performances for Mendelian diseases. The network meta-analysis showed a higher diagnostic yield for WGS compared to WES (OR = 1.54, 95%CI: [1.11 - 2.12]). CONCLUSIONS Although whole genome sequencing for the paediatric population with suspected genetic disorders provided an accurate and early genetic diagnosis in a high proportion of cases, further research is needed for evaluating costs, effectiveness, and cost-effectiveness of WGS and achieving an informed decision-making process. TRIAL REGISTRATION This systematic review has not been registered.
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Grants
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
- RF-2018-12,366,391, 2018 Ministero della Salute
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Affiliation(s)
- Mario Cesare Nurchis
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- School of Economics, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
| | - Maria Teresa Riccardi
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Giovanni Chillemi
- Department for Innovation in Biological Agro-Food and Forest Systems (DIBAF), University of Tuscia, 01100, Viterbo, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale Delle Ricerche, 70126, Bari, Italy
| | - Enrico Silvio Bertini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Jacopo Garlasco
- Department of Public Health Sciences and Paediatrics, University of Turin, 10126, Turin, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy
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13
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Knoflach K, Rapp CK, Schwerk N, Carlens J, Wetzke M, Emiralioğlu N, Kiper N, Ring AM, Buchvald F, Manali E, Papiris S, Reu-Hofer S, Kappler M, Schieber A, Seidl E, Gothe F, Robinson PN, Griese M. Diffuse alveolar hemorrhage in children with interstitial lung disease: Determine etiologies! Pediatr Pulmonol 2023; 58:1106-1121. [PMID: 36588100 DOI: 10.1002/ppul.26301] [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: 05/17/2022] [Revised: 11/11/2022] [Accepted: 12/27/2022] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Diffuse alveolar hemorrhage (DAH) in children is a rare condition resulting from different underlying diseases. This study aimed at describing characteristics and diagnostic measures in children with ILD (children's interstitial lung disease, chILD) and DAH to improve the diagnostic approach by increasing clinician's awareness of diagnostic shortcomings. PATIENTS AND METHODS A retrospective data analysis of patients with ILD and DAH treated in our own or collaborating centers between 01/07/1997 and 31/12/2020 was performed. Data on clinical courses and diagnostic measures were systematically retrieved as case-vignettes and investigated. To assess suitability of diagnostic software-algorithms, the Human Phenotype Ontology (HPO) was revised and expanded to optimize conditions of its associated tool the "Phenomizer." RESULTS For 97 (74%) of 131 patients, etiology of pulmonary hemorrhage was clarified. For 34 patients (26%), no underlying condition was found (termed as idiopathic pulmonary hemorrhage, IPH). Based on laboratory findings or clinical phenotype/comorbidities, 20 of these patients were assigned to descriptive clusters: IPH associated with autoimmune features (9), eosinophilia (5), renal disease (3) or multiorgan involvement (3). For 14 patients, no further differentiation was possible. CONCLUSION Complete and sometimes repeated diagnostics are essential for establishing the correct diagnosis in children with DAH. We suggest assignment of patients with IPH to descriptive clusters, which may also guide further research. Digital tools such as the Phenomizer/HPO are promising, but need to be extended to increase diagnostic accuracy.
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Affiliation(s)
- Katrin Knoflach
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Christina Katharina Rapp
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Nicolaus Schwerk
- Department of Pediatrics, Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.,German Center for Lung Research (DLZ), Partner Site Hannover (BREATH), Hanover, Germany
| | - Julia Carlens
- Department of Pediatrics, Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Martin Wetzke
- Department of Pediatrics, Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Nagehan Emiralioğlu
- Department of Pediatric Pulmonology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Nural Kiper
- Department of Pediatric Pulmonology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Astrid Madsen Ring
- Pediatric Pulmonary Service, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Frederik Buchvald
- Pediatric Pulmonary Service, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Effrosyni Manali
- Department of Respiratory Medicine, 'Attikon' University Hospital, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Spyros Papiris
- Department of Respiratory Medicine, 'Attikon' University Hospital, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Simone Reu-Hofer
- Institute of Pathology, University of Würzburg, Würzburg, Germany
| | - Matthias Kappler
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Alexandra Schieber
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Elias Seidl
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Florian Gothe
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Matthias Griese
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-University (LMU) Munich, Munich, Germany.,German center for Lung Research (DLZ), Partner Site Munich, Munich, Germany
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14
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Nishimura M, Miyata J, Tanigaki T, Nomura S, Serizawa Y, Igarashi S, Itou K, Ohno T, Kurata Y, Kimizuka Y, Fujikura Y, Sekinaka Y, Sekinaka K, Matsukuma S, Nonoyama S, Kawana A. Successful Treatment of Granulomatous-lymphocytic Interstitial Lung Disease in a Patient with CTLA-4 Deficiency. Intern Med 2023; 62:871-875. [PMID: 35945007 PMCID: PMC10076143 DOI: 10.2169/internalmedicine.0076-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Common variable immunodeficiency (CVID) causes granulomatous-lymphocytic interstitial lung disease (GLILD) and has a poor prognosis. We herein report a case of GLILD in a 49-year-old woman with CTLA-4 deficiency-associated CVID. The patient presented with dyspnea that had worsened over the past two years. A laboratory examination revealed hypoglobulinemia and pancytopenia. Chest computed tomography showed diffuse infiltrative and granular shadows in the bilateral interstitium. A flow cytometric analysis of blood cells and genetic testing confirmed CTLA-4 deficiency. We performed video-assisted thoracoscopic surgery for the pathological diagnosis of GLILD and to exclude infection and malignancy. Corticosteroid treatment successfully improved the condition of the patient.
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Affiliation(s)
- Masashi Nishimura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Jun Miyata
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Tomomi Tanigaki
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Sakika Nomura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yusuke Serizawa
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Syunya Igarashi
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Koki Itou
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Tomohiro Ohno
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yuhei Kurata
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yoshifumi Kimizuka
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yuji Fujikura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
| | - Yujin Sekinaka
- Department of Pediatrics, National Defense Medical College, Japan
| | - Kanako Sekinaka
- Department of Pediatrics, National Defense Medical College, Japan
| | - Susumu Matsukuma
- Department of Pathology and Laboratory Medicine, National Defense Medical College, Japan
| | | | - Akihiko Kawana
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Japan
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15
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Al-Tamemi S, Al-Zadjali S, Bruwer Z, Naseem SUR, Al-Siyabi N, ALRawahi M, Alkharusi K, Al-Thihli K, Al-Murshedi F, AlSayegh A, Al-Maawali A, Dennison D. Genetic Causes, Clinical Features, and Survival of Underlying Inborn Errors of Immunity in Omani Patients: a Single-Center Study. J Clin Immunol 2023; 43:452-465. [PMID: 36324046 DOI: 10.1007/s10875-022-01394-3] [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: 05/31/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE Early identification of inborn errors of immunity (IEIs) is crucial due to the significant risk of morbidity and mortality. This study aimed to describe the genetic causes, clinical features, and survival rate of IEIs in Omani patients. METHODS A prospective study of all Omani patients evaluated for immunodeficiency was conducted over a 17-year period. Clinical features and diagnostic immunological findings were recorded. Targeted gene testing was performed in cases of obvious immunodeficiency. For cases with less conclusive phenotypes, a gene panel was performed, followed by whole-exome sequencing if necessary. RESULTS A total of 185 patients were diagnosed with IEIs during the study period; of these, 60.5% were male. Mean ages at symptom onset and diagnosis were 30.0 and 50.5 months, respectively. Consanguinity and a family history of IEIs were present in 86.9% and 50.8%, respectively. Most patients presented with lower respiratory infections (65.9%), followed by growth and development manifestations (43.2%). Phagocytic defects were the most common cause of IEIs (31.9%), followed by combined immunodeficiency (21.1%). Overall, 109 of 132 patients (82.6%) who underwent genetic testing received a genetic diagnosis, while testing was inconclusive for the remaining 23 patients (17.4%). Among patients with established diagnoses, 37 genes and 44 variants were identified. Autosomal recessive inheritance was present in 81.7% of patients with gene defects. Several variants were novel. Intravenous immunoglobulin therapy was administered to 39.4% of patients and 21.6% received hematopoietic stem cell transplantation. The overall survival rate was 75.1%. CONCLUSION This study highlights the genetic causes of IEIs in Omani patients. This information may help in the early identification and management of the disease, thereby improving survival and quality of life.
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Affiliation(s)
- Salem Al-Tamemi
- Clinical Immunology & Allergy Unit, Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman.
| | - Shoaib Al-Zadjali
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Zandre Bruwer
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Shafiq-Ur-Rehman Naseem
- Clinical Immunology & Allergy Unit, Department of Child Health, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nabila Al-Siyabi
- Clinical Immunology & Allergy Unit, Directorate of Nursing, Sultan Qaboos University Hospital, Muscat, Oman
| | - Mohammed ALRawahi
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalsa Alkharusi
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Fathiya Al-Murshedi
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Abeer AlSayegh
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Almundher Al-Maawali
- Department of Clinical Genetics, Sultan Qaboos University Hospital, Muscat, Oman
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - David Dennison
- Molecular Hematology Unit, Department of Hematology, Sultan Qaboos University Hospital, Muscat, Oman
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16
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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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17
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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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18
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Rojas-Restrepo J, Caballero-Oteyza A, Huebscher K, Haberstroh H, Fliegauf M, Keller B, Kobbe R, Warnatz K, Ehl S, Proietti M, Grimbacher B. Establishing the Molecular Diagnoses in a Cohort of 291 Patients With Predominantly Antibody Deficiency by Targeted Next-Generation Sequencing: Experience From a Monocentric Study. Front Immunol 2022; 12:786516. [PMID: 34975878 PMCID: PMC8718408 DOI: 10.3389/fimmu.2021.786516] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/29/2021] [Indexed: 12/12/2022] Open
Abstract
Predominantly antibody deficiencies (PAD) are a heterogeneous group of disorders characterized by dysfunctional antibody production, low immunoglobulin levels in serum and impaired vaccine responses. The clinical picture is variable, ranging from mild symptoms to severe complications, which may include autoimmunity, gastrointestinal disease, allergy, and malignancies. If left untreated, PAD patients are at risk of enduring disease progression, irreversible organ damage, and reduced life expectancy. A timely diagnosis has been shown to significantly improve disease prognosis. Here, we report on our experience using targeted gene panel sequencing by employing Agilent’s HaloPlex or SureSelect and Illumina’s MiSeq technologies in a cohort of 291 individuals who presented with low or absent immunoglobulin levels in combination with or without other clinical features. In total, we have detected over 57 novel or previously reported relevant mutations in ADA, ADA2, BTK, CTLA4, LRBA, NFKB1, NFKB2, PIK3CD, STAT3, and TNFRSF13B. Overall, a genetic diagnosis could be made in 24.7% of the investigated patients. The percentage of coverage for the targeted regions ranged from 90% to 98% in this study. Moreover, functional assays were performed on a defined group of the patients carrying candidate variants in CTLA4, LRBA, NFKB1 and BTK, which confirmed their deleterious effect on protein expression and/or function. This study reiterates that the immunological heterogeneity of predominantly antibody deficiencies may have a diverse genetic origin, although certain clinical features may hint towards a specific group of defects. Employing targeted sequencing panels proves to be a very time- and cost-efficient, yet reliable, method for the establishment of a genetic diagnosis in individuals with PAD. However, in case of negative panel results, or if functional testing reveals inconspicuous observations in patients with a clear indication for genetic testing, further work-up including whole exome or whole genome sequencing should be considered.
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Affiliation(s)
- Jessica Rojas-Restrepo
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Andrés Caballero-Oteyza
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Resolving Infection Susceptibility (RESIST) - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Katrin Huebscher
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Hanna Haberstroh
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Manfred Fliegauf
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Baerbel Keller
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
| | - Robin Kobbe
- First Department of Medicine, Division of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Warnatz
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Michele Proietti
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany.,Department of Rheumatology and Immunology, Hannover Medical University, Hannover, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany.,Resolving Infection Susceptibility (RESIST) - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.,Center for Integrative Biological Signaling Studies (CIBSS), University of Freiburg, Freiburg, Germany.,Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany.,German Center for Infection Research (DZIF), Satellite Center Freiburg, Freiburg, Germany
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19
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Haimel M, Pazmandi J, Heredia RJ, Dmytrus J, Bal SK, Zoghi S, van Daele P, Briggs TA, Wouters C, Bader-Meunier B, Aeschlimann FA, Caorsi R, Eleftheriou D, Hoppenreijs E, Salzer E, Bakhtiar S, Derfalvi B, Saettini F, Kusters MAA, Elfeky R, Trück J, Rivière JG, van der Burg M, Gattorno M, Seidel MG, Burns S, Warnatz K, Hauck F, Brogan P, Gilmour KC, Schuetz C, Simon A, Bock C, Hambleton S, de Vries E, Robinson PN, van Gijn M, Boztug K. Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity. J Allergy Clin Immunol 2022; 149:369-378. [PMID: 33991581 PMCID: PMC9346194 DOI: 10.1016/j.jaci.2021.04.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Accurate, detailed, and standardized phenotypic descriptions are essential to support diagnostic interpretation of genetic variants and to discover new diseases. The Human Phenotype Ontology (HPO), extensively used in rare disease research, provides a rich collection of vocabulary with standardized phenotypic descriptions in a hierarchical structure. However, to date, the use of HPO has not yet been widely implemented in the field of inborn errors of immunity (IEIs), mainly due to a lack of comprehensive IEI-related terms. OBJECTIVES We sought to systematically review available terms in HPO for the depiction of IEIs, to expand HPO, yielding more comprehensive sets of terms, and to reannotate IEIs with HPO terms to provide accurate, standardized phenotypic descriptions. METHODS We initiated a collaboration involving expert clinicians, geneticists, researchers working on IEIs, and bioinformaticians. Multiple branches of the HPO tree were restructured and extended on the basis of expert review. Our ontology-guided machine learning coupled with a 2-tier expert review was applied to reannotate defined subgroups of IEIs. RESULTS We revised and expanded 4 main branches of the HPO tree. Here, we reannotated 73 diseases from 4 International Union of Immunological Societies-defined IEI disease subgroups with HPO terms. We achieved a 4.7-fold increase in the number of phenotypic terms per disease. Given the new HPO annotations, we demonstrated improved ability to computationally match selected IEI cases to their known diagnosis, and improved phenotype-driven disease classification. CONCLUSIONS Our targeted expansion and reannotation presents enhanced precision of disease annotation, will enable superior HPO-based IEI characterization, and hence benefit both IEI diagnostic and research activities.
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Affiliation(s)
- Matthias Haimel
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Raúl Jiménez Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jasmin Dmytrus
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sevgi Köstel Bal
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Samaneh Zoghi
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Paul van Daele
- Department of Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tracy A Briggs
- NW Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Carine Wouters
- Department of Microbiology and Immunology, Immunobiology, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Pediatric Rheumatology, University Hospitals Leuven, Leuven, Belgium
| | - Brigitte Bader-Meunier
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Florence A Aeschlimann
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker Hospital for Sick Children - AP-HP, Paris, France; Reference Center for Rheumatic, Autoimmune and Systemic Diseases in Children (RAISE), Paris, France
| | - Roberta Caorsi
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Despina Eleftheriou
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Esther Hoppenreijs
- Department of Paediatric Rheumatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Elisabeth Salzer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Shahrzad Bakhtiar
- Department for Children and Adolescents, Division for Stem Cell Transplantation, Immunology and Intensive Care Unit, Goethe University, Frankfurt, Germany
| | - Beata Derfalvi
- Department of Pediatrics, Division of Immunology, Dalhousie University/IWK Health Centre Halifax, Halifax, Nova Scotia, Canada
| | - Francesco Saettini
- Pediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, via Pergolesi 33, Monza, Italy
| | - Maaike A A Kusters
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Reem Elfeky
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron Research Institute, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain; Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mirjam van der Burg
- Department of Immunology, University Medical Center Rotterdam, Rotterdam, The Netherlands; Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiency, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Markus G Seidel
- Research Unit for Pediatric Hematology and Immunology, Division of Pediatric Hemato-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Siobhan Burns
- Department of Immunology, UCL Institute of Immunity & Transplantation, Department of Immunology, Royal Free Hospital NHS Foundation Trust, London, United Kingdom
| | - Klaus Warnatz
- Division of Immunodeficiency, Department of Rheumatology and Clinical Immunology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Munich Centre for Rare Diseases (M-ZSE(LMU)), University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paul Brogan
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kimberly C Gilmour
- Department of Immunology, Great Ormond Street (GOS) Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Catharina Schuetz
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Anna Simon
- Radboudumc Expertise Centre for Immunodeficiency and Autoinflammation (REIA), Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Christoph Bock
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Sophie Hambleton
- Immunity and Inflammation Theme, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Esther de Vries
- Tranzo, Tilburg University, Tilburg, The Netherlands; Laboratory for Medical Microbiology and Immunology, Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands
| | | | - Marielle van Gijn
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands.
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; St Anna Children's Cancer Research Institute (CCRI), Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria; St Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.
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20
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Lai CMB, Setiadi A, Barlas A, Kanani A, Pourshahnazari P, Leitch HA, Metzger DL, Merkeley H, Biggs CM. Targeted treatment of immune thrombocytopenia in CTLA-4 insufficiency: a case report. Br J Haematol 2021; 196:e42-e45. [PMID: 34628649 DOI: 10.1111/bjh.17866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Audi Setiadi
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Angeliki Barlas
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Amin Kanani
- Division of Allergy and Clinical Immunology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Persia Pourshahnazari
- Division of Allergy and Clinical Immunology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Heather A Leitch
- Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | -
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Daniel L Metzger
- Division of Endocrinology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Hayley Merkeley
- Division of Hematology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Catherine M Biggs
- Division of Allergy and Clinical Immunology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,BC Children's and St Paul's Hospitals, Vancouver, BC, Canada
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21
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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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22
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Karimi E, Mahmoudian F, Reyes SOL, Bargir UA, Madkaikar M, Artac H, Sabzevari A, Lu N, Azizi G, Abolhassani H. Approach to genetic diagnosis of inborn errors of immunity through next-generation sequencing. Mol Immunol 2021; 137:57-66. [PMID: 34216999 DOI: 10.1016/j.molimm.2021.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023]
Abstract
Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.
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Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, 85721, USA; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saul O Lugo Reyes
- Immune Deficiencies Lab, National Institute of Pediatrics, Mexico City, Mexico
| | - Umair Ahmed Bargir
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Manisha Madkaikar
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Selcuk University, Konya, Turkey
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden.
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23
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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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24
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Erman B, Çipe F. Genetic Screening of the Patients with Primary Immunodeficiency by Whole-Exome Sequencing. PEDIATRIC ALLERGY IMMUNOLOGY AND PULMONOLOGY 2021; 33:19-24. [PMID: 33406023 DOI: 10.1089/ped.2019.1097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background: Primary immunodeficiencies (PIDs) are a heterogeneous group of congenital disorders characterized by susceptibility to recurrent infections, allergy, malignancies and autoimmunity. The identification of disease-causing genetic defects is critically important for treatment options. In last decade, next-generation sequencing (NGS)-based methods has enabled the rapid genetic screening and the discovery of new genetic defects in PIDs. In this study, we investigated causative mutations in patients with PID by NGS. Methods: We applied whole-exome sequencing in 8 PID patients. Detected mutations by NGS were validated by Sanger sequencing. Results: We made a genetic diagnosis in 5 of 8 (63%) patients, including 3 novel disease-causing variants. The identified mutations were found in RAG1, RAG2, JAK3, RFXANK, and CYBA genes. Conclusions: Our results show that whole-exome sequencing can facilitate the genetic diagnosis of the patients with PID.
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Affiliation(s)
- Baran Erman
- Department of Molecular Biology and Genetics, Istınye University, Istanbul, Turkey.,Institute of Child Health, Hacettepe University, Ankara, Turkey
| | - Funda Çipe
- Department of Pediatrics, Medical School, Istinye University, Istanbul, Turkey
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25
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Tavakol M, Jamee M, Azizi G, Sadri H, Bagheri Y, Zaki-Dizaji M, Mahdavi FS, Jadidi-Niaragh F, Tajfirooz S, Kamali AN, Aghamahdi F, Noorian S, Kojidi HT, Mosavian M, Matani R, Dolatshahi E, Porrostami K, Elahimehr N, Fatemi-Abhari M, Sharifi L, Arjmand R, Haghi S, Zainaldain H, Yazdani R, Shaghaghi M, Abolhassani H, Aghamohammadi A. Diagnostic Approach to the Patients with Suspected Primary Immunodeficiency. Endocr Metab Immune Disord Drug Targets 2020; 20:157-171. [PMID: 31456526 DOI: 10.2174/1871530319666190828125316] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 06/16/2019] [Accepted: 08/04/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Primary immunodeficiency diseases (PIDs) are a group of more than 350 disorders affecting distinct components of the innate and adaptive immune systems. In this review, the classic and advanced stepwise approach towards the diagnosis of PIDs are simplified and explained in detail. RESULTS Susceptibility to recurrent infections is the main hallmark of almost all PIDs. However, noninfectious complications attributable to immune dysregulation presenting with lymphoproliferative and/or autoimmune disorders are not uncommon. Moreover, PIDs could be associated with misleading presentations including allergic manifestations, enteropathies, and malignancies. CONCLUSION Timely diagnosis is the most essential element in improving outcome and reducing the morbidity and mortality in PIDs. This wouldn't be possible unless the physicians keep the diagnosis of PID in mind and be sufficiently aware of the approach to these patients.
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Affiliation(s)
- Marzieh Tavakol
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Allergy and Clinical Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahnaz Jamee
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Homa Sadri
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Allergy and Clinical Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Yasser Bagheri
- Clinical Research Development Unit (CRDU), 5 azar Hospital, Golestan University of Medical Sciences, Gorgan, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | | | | | - Sanaz Tajfirooz
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Ali N Kamali
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Fatemeh Aghamahdi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Shahab Noorian
- Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Habibeh Taghavi Kojidi
- Department of Pediatric Endocrinology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Mosavian
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.,Department of Gastroenterology and Hepatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Rahman Matani
- Department of Gastroenterology and Hepatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Elahe Dolatshahi
- Department of Rheumatology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Kumars Porrostami
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nasrin Elahimehr
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Marzie Fatemi-Abhari
- Department of Pediatrics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Laleh Sharifi
- Uro- Oncology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Arjmand
- Department of Infectious Disease, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sabahat Haghi
- Department of Hematology & Oncology, School of Medicine, Alborz university of medical sciences, Karaj, Iran
| | - Hamed Zainaldain
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Shaghaghi
- Russell H. Morgan Department of Radiology and Radiological Sciences, Johns Hopkins Hospital, Baltimore, MD, United States
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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26
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A Novel DSP Truncating Variant in a Family with Episodic Myocardial Injury in the Course of Arrhythmogenic Cardiomyopathy-A Possible Role of a Low Penetrance NLRP3 Variant. Diagnostics (Basel) 2020; 10:diagnostics10110955. [PMID: 33207704 PMCID: PMC7697544 DOI: 10.3390/diagnostics10110955] [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: 10/14/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 02/06/2023] Open
Abstract
Mono-allelic dominant mutations in the desmoplakin gene (DSP) have been linked to known cardiac disorders, such as arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy. During the course of DSP cardiomyopathy, episodes of acute myocardial injury may occur. While their mechanisms remain unclear, myocarditis has been postulated as an underlying cause. We report on an adolescent girl with arrhythmogenic biventricular cardiomyopathy and three acute myocarditis-like episodes in whom we found a novel truncating DSP variant accompanied by a known low penetrance R490K variant in the NLRP3. Upon family screening, other carriers of the DSP variant have been identified in whom only mild cardiac abnormalities were found. We hypothesized that the uncommon course of cardiomyopathy in the proband as well as striking discrepancies in the phenotype observed in her family may be explained by the co-existence of her low penetrance genetic autoinflammatory predisposition.
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27
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Targeting NF-κB pathway for the therapy of diseases: mechanism and clinical study. Signal Transduct Target Ther 2020; 5:209. [PMID: 32958760 PMCID: PMC7506548 DOI: 10.1038/s41392-020-00312-6] [Citation(s) in RCA: 707] [Impact Index Per Article: 176.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023] Open
Abstract
NF-κB pathway consists of canonical and non-canonical pathways. The canonical NF-κB is activated by various stimuli, transducing a quick but transient transcriptional activity, to regulate the expression of various proinflammatory genes and also serve as the critical mediator for inflammatory response. Meanwhile, the activation of the non-canonical NF-κB pathway occurs through a handful of TNF receptor superfamily members. Since the activation of this pathway involves protein synthesis, the kinetics of non-canonical NF-κB activation is slow but persistent, in concordance with its biological functions in the development of immune cell and lymphoid organ, immune homeostasis and immune response. The activation of the canonical and non-canonical NF-κB pathway is tightly controlled, highlighting the vital roles of ubiquitination in these pathways. Emerging studies indicate that dysregulated NF-κB activity causes inflammation-related diseases as well as cancers, and NF-κB has been long proposed as the potential target for therapy of diseases. This review attempts to summarize our current knowledge and updates on the mechanisms of NF-κB pathway regulation and the potential therapeutic application of inhibition of NF-κB signaling in cancer and inflammatory diseases.
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28
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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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29
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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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30
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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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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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32
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Gruber C, Bogunovic D. Incomplete penetrance in primary immunodeficiency: a skeleton in the closet. Hum Genet 2020; 139:745-757. [PMID: 32067110 PMCID: PMC7275875 DOI: 10.1007/s00439-020-02131-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/02/2020] [Indexed: 12/11/2022]
Abstract
Primary immunodeficiencies (PIDs) comprise a diverse group of over 400 genetic disorders that result in clinically apparent immune dysfunction. Although PIDs are classically considered as Mendelian disorders with complete penetrance, we now understand that absent or partial clinical disease is often noted in individuals harboring disease-causing genotypes. Despite the frequency of incomplete penetrance in PID, no conceptual framework exists to categorize and explain these occurrences. Here, by reviewing decades of reports on incomplete penetrance in PID we identify four recurrent themes of incomplete penetrance, namely genotype quality, (epi)genetic modification, environmental influence, and mosaicism. For each of these principles, we review what is known, underscore what remains unknown, and propose future experimental approaches to fill the gaps in our understanding. Although the content herein relates specifically to inborn errors of immunity, the concepts are generalizable across genetic diseases.
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Affiliation(s)
- Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Department of Pediatrics, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Precision Immunology Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, 10029, USA.
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33
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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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34
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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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35
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Viñas-Giménez L, Padilla N, Batlle-Masó L, Casals F, Rivière JG, Martínez-Gallo M, de la Cruz X, Colobran R. FHLdb: A Comprehensive Database on the Molecular Basis of Familial Hemophagocytic Lymphohistiocytosis. Front Immunol 2020; 11:107. [PMID: 32076423 PMCID: PMC7006814 DOI: 10.3389/fimmu.2020.00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background: Primary immunodeficiencies (PIDs) are a heterogeneous group of disorders. The lack of comprehensive disease-specific mutation databases may hinder or delay classification of the genetic variants found in samples from these patients. This is especially true for familial hemophagocytic lymphohistiocytosis (FHL), a life-threatening PID classically considered an autosomal recessive condition, but with increasingly demonstrated genetic heterogeneity. Objective: The aim of this study was to build an open-access repository to collect detailed information on the known genetic variants reported in FHL. Methods: We manually reviewed more than 120 articles to identify all reported variants related to FHL. We retrieved relevant information about the allelic status, the number of patients with the same variant, and whether functional assays were done. We stored all the data retrieved in a PostgreSQL database and then built a website on top of it, using the Django framework. Results: The database designed (FHLdb) (https://www.biotoclin.org/FHLdb) contains comprehensive information on reported variants in the 4 genes related to FHL (PRF1, UNC13D, STXBP2, STX11). It comprises 240 missense, 69 frameshift, 51 nonsense, 51 splicing, 10 in-frame indel, 7 deep intronic, and 5 large rearrangement variants together with their allelic status, carrier(s) information, and functional evidence. All genetic variants have been classified as pathogenic, likely pathogenic, uncertain significance, likely benign or benign, according to the American College of Medical Genetics guidelines. Additionally, it integrates information from other relevant databases: clinical evidence from ClinVar and UniProt, population allele frequency from ExAC and gnomAD, and pathogenicity predictions from well-recognized tools (e.g., PolyPhen-2, SIFT). Finally, a diagram depicts the location of the variant relative to the gene exon and protein domain structures. Conclusion: FHLdb includes a broad range of data on the reported genetic variants in familial HLH genes. It is a free-access and easy-to-use resource that will facilitate the interpretation of molecular results of FHL patients, and it illustrates the potential value of disease-specific databases for other PIDs.
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Affiliation(s)
- Laura Viñas-Giménez
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Laura Batlle-Masó
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases and Immunodeficiencies Unit (UPIIP), Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Institut Catala per la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona (UAB), Barcelona, Spain.,Jeffrey Model Foundation Excellence Center, Barcelona, Spain.,Genetics Department, Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
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36
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Kwon WK, Choi S, Kim HJ, Huh HJ, Kang JM, Kim YJ, Yoo KH, Ahn K, Cho HK, Peck KR, Jang JH, Ki CS, Kang ES. Flow Cytometry for the Diagnosis of Primary Immunodeficiency Diseases: A Single Center Experience. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2020; 12:292-305. [PMID: 32009323 PMCID: PMC6997278 DOI: 10.4168/aair.2020.12.2.292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 12/03/2019] [Accepted: 12/03/2019] [Indexed: 12/19/2022]
Abstract
Purpose While there is an urgent need for diagnosis and therapeutic intervention in patients with primary immunodeficiency diseases (PIDs), current genetic tests have drawbacks. We retrospectively reviewed the usefulness of flow cytometry (FCM) as a quick tool for immunophenotyping and functional assays in patients suspected to have PIDs at a single tertiary care institute. Methods Between January 2001 and June 2018, patients suspected of having PIDs were subjected to FCM tests, including lymphocyte subset analysis, detection of surface- or intracellular-target proteins, and functional analysis of immune cells, at Samsung Medical Center, Seoul, Korea. The genetic diagnosis was performed using Sanger or diagnostic exome sequencing. Results Of 60 patients diagnosed with definite or probable PID according to the European Society of Immune Deficiencies criteria, 24 patients were provided with useful information about immunological dysfunction after initial FCM testing. In 10 patients, the PID diagnosis was based on abnormal findings in FCM testing without genetic tests. The FCM findings provided strong evidence for the diagnosis of severe combined immunodeficiency (n = 6), X-linked chronic granulomatous diseases (CGD) (n = 6), leukocyte adhesion deficiency type 1 (n = 3), X-linked agammaglobulinemia (n = 11), autoimmune lymphoproliferative syndrome-FASLG (n = 1), and familial hemophagocytic lymphohistiocytosis type 2 (n = 1), and probable evidence for autosomal recessive-CGD (n = 2), autosomal dominant-hyper-immunoglobulin E (IgE)-syndrome (n = 1), and STAT1 gain-of-function mutation (n = 1). In PIDs derived from PIK3CD (n = 2), LRBA (n = 2), and CTLA4 mutations (n = 3), the FCM test provided useful evidence of immune abnormalities and a tool for treatment monitoring. Conclusions The initial application of FCM, particularly with known protein targets on immune cells, would facilitate the timely diagnosis of PIDs and thus would support clinical decisions and improve the clinical outcome.
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Affiliation(s)
- Won Kyung Kwon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - SooIn Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Soonchunhyang University Hospital, Cheonan, Korea
| | - Hee Jin Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ji Man Kang
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yae Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Keon Hee Yoo
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kangmo Ahn
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Kyung Cho
- Department of Pediatrics, Gachon University Gil Medical Center, Incheon, Korea
| | - Kyong Ran Peck
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ja Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Green Cross Genome, Yongin, Korea
| | | | - Eun Suk Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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37
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Lye JJ, Williams A, Baralle D. Exploring the RNA Gap for Improving Diagnostic Yield in Primary Immunodeficiencies. Front Genet 2019; 10:1204. [PMID: 31921280 PMCID: PMC6917654 DOI: 10.3389/fgene.2019.01204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Challenges in diagnosing primary immunodeficiency are numerous and diverse, with current whole-exome and whole-genome sequencing approaches only able to reach a molecular diagnosis in 25–60% of cases. We assess these problems and discuss how RNA-focused analysis has expanded and improved in recent years and may now be utilized to gain an unparalleled insight into cellular immunology. We review how investigation into RNA biology can give information regarding the differential expression, monoallelic expression, and alternative splicing—which have important roles in immune regulation and function. We show how this information can inform bioinformatic analysis pipelines and aid in the variant filtering process, expediting the identification of causal variants—especially those affecting splicing—and enhance overall diagnostic ability. We also demonstrate the challenges, which remain in the design of this type of investigation, regarding technological limitation and biological considerations and suggest potential directions for the clinical applications.
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Affiliation(s)
- Jed J Lye
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom
| | - Anthony Williams
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Wessex Investigational Sciences Hub Laboratory (WISH Lab), Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Diana Baralle
- University of Southampton Medical School, University of Southampton, Southampton, United Kingdom.,Faculty of Medicine, Highfield Campus, University of Southampton, Southampton, United Kingdom
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38
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Chang CC, Levitz SM. Fungal immunology in clinical practice: Magical realism or practical reality? Med Mycol 2019; 57:S294-S306. [PMID: 31292656 DOI: 10.1093/mmy/myy165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/15/2022] Open
Abstract
Invasive fungal infections (IFIs) occur predominantly in immunocompromised individuals but can also be seen in previously well persons. The human innate immune system recognizes key components of the fungal cell wall as foreign resulting in a myriad of signaling cascades. This triggers release of antifungal molecules as well as adaptive immune responses, which kill or at least contain the invading fungi. However, these defences may fail in hosts with primary or secondary immunodeficiencies resulting in IFIs. Knowledge of a patient's immune status enables the clinician to predict the fungal infections most likely to occur. Moreover, the occurrence of an opportunistic mycosis in a patient without known immunocompromise usually should prompt a search for an occult immune defect. A rapidly expanding number of primary and secondary immunodeficiencies associated with mycoses has been identified. An investigative approach to determining the nature of these immunodeficiencies is suggested to help guide clinicians encountering patients with IFI. Finally, promising adjunctive immunotherapy measures are currently being investigated in IFI.
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Affiliation(s)
- Christina C Chang
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia
| | - Stuart M Levitz
- Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
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39
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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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40
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Abstract
Primary immunodeficiency diseases are a heterogeneous group of rare inherited disorders of innate or adaptive immune system function. Patients with primary immunodeficiencies typically present with recurrent and severe infections in infancy or young adulthood. More recently, the co-occurrence of autoimmune, benign lymphoproliferative, atopic, and malignant complications has been described. The diagnosis of a primary immunodeficiency disorder requires a thorough assessment of a patient's underlying immune system function. Historically, this has been accomplished at the time of symptomatic presentation by measuring immunoglobulins, complement components, protective antibody titers, or immune cell counts in the peripheral blood. Although these data can be used to critically assess the degree of immune dysregulation in the patient, this approach fall short in at least 2 regards. First, this assessment often occurs after the patient has suffered life-threatening infectious or autoinflammatory complications. Second, these data fail to uncover an underlying molecular cause of the patient's primary immune dysfunction, prohibiting the use of molecularly targeted therapeutic interventions. Within the last decade, the field of primary immunodeficiency diagnostics has been revolutionized by 2 major molecular advancements: (1) the onset of newborn screening in 2008, and (2) the onset of next-generation sequencing in 2010. In this article, the techniques of newborn screening and next-generation sequencing are reviewed and their respective impacts on the field of primary immunodeficiency disorders are discussed with a specific emphasis on severe combined immune deficiency and common variable immune deficiency.
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Affiliation(s)
- Jocelyn R Farmer
- Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA.
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Center for Advanced Molecular Diagnostics, Brigham and Women's Hospital, Boston, MA, USA
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41
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Yska HAF, Elsink K, Kuijpers TW, Frederix GWJ, van Gijn ME, van Montfrans JM. Diagnostic Yield of Next Generation Sequencing in Genetically Undiagnosed Patients with Primary Immunodeficiencies: a Systematic Review. J Clin Immunol 2019; 39:577-591. [PMID: 31250335 PMCID: PMC6697711 DOI: 10.1007/s10875-019-00656-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND As the application of next generation sequencing (NGS) is moving to earlier stages in the diagnostic pipeline for primary immunodeficiencies (PIDs), re-evaluation of its effectiveness is required. The aim of this study is to systematically review the diagnostic yield of NGS in PIDs. METHODS PubMed and Embase databases were searched for relevant studies. Studies were eligible when describing the use of NGS in patients that had previously been diagnosed with PID on clinical and/or laboratory findings. Relevant data on study characteristics, technological performance and diagnostic yield were extracted. RESULTS Fourteen studies were eligible for data extraction. Six studies described patient populations from specific PID subcategories. The remaining studies included patients with unsorted PIDs. The studies were based on populations from Italy, Iran, Turkey, Thailand, the Netherlands, Norway, Saudi Arabia, Sweden, the UK, and the USA. Eight studies used an array-based targeted gene panel, four used WES in combination with a PID filter, and two used both techniques. The mean reported reading depth ranged from 98 to 1337 times. Five studies described the sensitivity of the applied techniques, ranging from 83 to 100%, whereas specificity ranged from 45 to 99.9%. The percentage of patients who were genetically diagnosed ranged from 15 to 79%. Several studies described clinical implications of the genetic findings. DISCUSSION NGS has the ability to contribute significantly to the identification of molecular mechanisms in PID patients. The diagnostic yield highly depends on population and on the technical circumstances under which NGS is employed. Further research is needed to determine the exact diagnostic yield and clinical implications of NGS in patients with PID.
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Affiliation(s)
- Hemmo A F Yska
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Kim Elsink
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mariëlle E van Gijn
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Joris M van Montfrans
- Department of Pediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands.
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42
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Siggs OM, Russell A, Singh-Grewal D, Wong M, Chan P, Craig ME, O'Loughlin T, Stormon M, Goodnow CC. Preponderance of CTLA4 Variation Associated With Autosomal Dominant Immune Dysregulation in the MYPPPY Motif. Front Immunol 2019; 10:1544. [PMID: 31396201 PMCID: PMC6664875 DOI: 10.3389/fimmu.2019.01544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/20/2019] [Indexed: 01/05/2023] Open
Abstract
One of the primary targets of immune checkpoint inhibition is the negative immune regulatory molecule CTLA-4. Immune-related adverse events are commonly observed following CTLA-4 inhibition in melanoma treatment, and a spectrum of these conditions are also observed in individuals with germline haploinsufficiency of CTLA4. Here we describe a heterozygous de novo missense variant of CTLA4 in a young girl with childhood-onset autoimmune hepatitis and polyarthritis, the latter responding to treatment with CTLA-4-Ig fusion protein. This variant lay within the highly conserved MYPPPY motif of CTLA-4: a critical structural determinant of ligand binding, which is also bound by the anti-CTLA-4 monoclonal antibody ipilimumab. Within the spectrum of CTLA4 variants reported, missense variants in the MYPPPY motif were overrepresented when compared to variants within a control population, highlighting the physiological importance of this motif in both the genetic and pharmacological regulation of autoimmunity and anti-tumor immunity.
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Affiliation(s)
- Owen M Siggs
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Amanda Russell
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Davinder Singh-Grewal
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Pearl Chan
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Maria E Craig
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Ted O'Loughlin
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Stormon
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, Australia
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43
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Siggs OM, Russell A, Singh-Grewal D, Wong M, Chan P, Craig ME, O'Loughlin T, Stormon M, Goodnow CC. Preponderance of CTLA4 Variation Associated With Autosomal Dominant Immune Dysregulation in the MYPPPY Motif. Front Immunol 2019. [PMID: 31396201 DOI: 10.3389/fimmu.2019.01544/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
One of the primary targets of immune checkpoint inhibition is the negative immune regulatory molecule CTLA-4. Immune-related adverse events are commonly observed following CTLA-4 inhibition in melanoma treatment, and a spectrum of these conditions are also observed in individuals with germline haploinsufficiency of CTLA4. Here we describe a heterozygous de novo missense variant of CTLA4 in a young girl with childhood-onset autoimmune hepatitis and polyarthritis, the latter responding to treatment with CTLA-4-Ig fusion protein. This variant lay within the highly conserved MYPPPY motif of CTLA-4: a critical structural determinant of ligand binding, which is also bound by the anti-CTLA-4 monoclonal antibody ipilimumab. Within the spectrum of CTLA4 variants reported, missense variants in the MYPPPY motif were overrepresented when compared to variants within a control population, highlighting the physiological importance of this motif in both the genetic and pharmacological regulation of autoimmunity and anti-tumor immunity.
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Affiliation(s)
- Owen M Siggs
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Department of Ophthalmology, Flinders University, Adelaide, SA, Australia
| | - Amanda Russell
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Davinder Singh-Grewal
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Melanie Wong
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Pearl Chan
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Maria E Craig
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Ted O'Loughlin
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Michael Stormon
- The Children's Hospitals Network, The University of New South Wales, Sydney, NSW, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, The University of New South Wales, Sydney, NSW, Australia
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van Dongen JJM, van der Burg M, Kalina T, Perez-Andres M, Mejstrikova E, Vlkova M, Lopez-Granados E, Wentink M, Kienzler AK, Philippé J, Sousa AE, van Zelm MC, Blanco E, Orfao A. EuroFlow-Based Flowcytometric Diagnostic Screening and Classification of Primary Immunodeficiencies of the Lymphoid System. Front Immunol 2019; 10:1271. [PMID: 31263462 PMCID: PMC6585843 DOI: 10.3389/fimmu.2019.01271] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/17/2019] [Indexed: 12/16/2022] Open
Abstract
Guidelines for screening for primary immunodeficiencies (PID) are well-defined and several consensus diagnostic strategies have been proposed. These consensus proposals have only partially been implemented due to lack of standardization in laboratory procedures, particularly in flow cytometry. The main objectives of the EuroFlow Consortium were to innovate and thoroughly standardize the flowcytometric techniques and strategies for reliable and reproducible diagnosis and classification of PID of the lymphoid system. The proposed EuroFlow antibody panels comprise one orientation tube and seven classification tubes and corresponding databases of normal and PID samples. The 8-color 12-antibody PID Orientation tube (PIDOT) aims at identification and enumeration of the main lymphocyte and leukocyte subsets; this includes naïve pre-germinal center (GC) and antigen-experienced post-GC memory B-cells and plasmablasts. The seven additional 8(-12)-color tubes can be used according to the EuroFlow PID algorithm in parallel or subsequently to the PIDOT for more detailed analysis of B-cell and T-cell subsets to further classify PID of the lymphoid system. The Pre-GC, Post-GC, and immunoglobulin heavy chain (IgH)-isotype B-cell tubes aim at identification and enumeration of B-cell subsets for evaluation of B-cell maturation blocks and specific defects in IgH-subclass production. The severe combined immunodeficiency (SCID) tube and T-cell memory/effector subset tube aim at identification and enumeration of T-cell subsets for assessment of T-cell defects, such as SCID. In case of suspicion of antibody deficiency, PIDOT is preferably directly combined with the IgH isotype tube(s) and in case of SCID suspicion (e.g., in newborn screening programs) the PIDOT is preferably directly combined with the SCID T-cell tube. The proposed ≥8-color antibody panels and corresponding reference databases combined with the EuroFlow PID algorithm are designed to provide fast, sensitive and cost-effective flowcytometric diagnosis of PID of the lymphoid system, easily applicable in multicenter diagnostic settings world-wide.
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Affiliation(s)
- Jacques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, Rotterdam, Netherlands.,Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Tomas Kalina
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Charles University, Prague, Czechia
| | - Martin Perez-Andres
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
| | - Ester Mejstrikova
- Department of Pediatric Hematology and Oncology, University Hospital Motol, Charles University, Prague, Czechia
| | - Marcela Vlkova
- Institute of Clinical Immunology and Allergology, St. Anne's University Hospital Brno, Masaryk University, Brno, Czechia
| | | | | | - Anne-Kathrin Kienzler
- Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jan Philippé
- Department of Laboratory Medicine, University Hospital Ghent, Ghent, Belgium
| | - Ana E Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Lisbon, Portugal
| | - Menno C van Zelm
- Department of Immunology, Erasmus MC, Rotterdam, Netherlands.,Department of Immunology and Pathology, Central Clinical School, Alfred Hospital, Monash University, Melbourne, VIC, Australia
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
| | - Alberto Orfao
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), University of Salamanca (USAL), Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.,Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), CB/16/12/00233, Instituto Carlos III, Madrid, Spain
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45
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RNAseq Supports the Molecular Genetic Diagnosis of Late-Onset ADA Deficiency. J Clin Immunol 2019; 39:270-273. [PMID: 30989467 DOI: 10.1007/s10875-019-00625-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/02/2019] [Indexed: 10/27/2022]
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46
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Cifaldi C, Brigida I, Barzaghi F, Zoccolillo M, Ferradini V, Petricone D, Cicalese MP, Lazarevic D, Cittaro D, Omrani M, Attardi E, Conti F, Scarselli A, Chiriaco M, Di Cesare S, Licciardi F, Davide M, Ferrua F, Canessa C, Pignata C, Giliani S, Ferrari S, Fousteri G, Barera G, Merli P, Palma P, Cesaro S, Gattorno M, Trizzino A, Moschese V, Chini L, Villa A, Azzari C, Finocchi A, Locatelli F, Rossi P, Sangiuolo F, Aiuti A, Cancrini C, Di Matteo G. Targeted NGS Platforms for Genetic Screening and Gene Discovery in Primary Immunodeficiencies. Front Immunol 2019; 10:316. [PMID: 31031743 PMCID: PMC6470723 DOI: 10.3389/fimmu.2019.00316] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/06/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Primary Immunodeficiencies (PIDs) are a heterogeneous group of genetic immune disorders. While some PIDs can manifest with more than one phenotype, signs, and symptoms of various PIDs overlap considerably. Recently, novel defects in immune-related genes and additional variants in previously reported genes responsible for PIDs have been successfully identified by Next Generation Sequencing (NGS), allowing the recognition of a broad spectrum of disorders. Objective: To evaluate the strength and weakness of targeted NGS sequencing using custom-made Ion Torrent and Haloplex (Agilent) panels for diagnostics and research purposes. Methods: Five different panels including known and candidate genes were used to screen 105 patients with distinct PID features divided in three main PID categories: T cell defects, Humoral defects and Other PIDs. The Ion Torrent sequencing platform was used in 73 patients. Among these, 18 selected patients without a molecular diagnosis and 32 additional patients were analyzed by Haloplex enrichment technology. Results: The complementary use of the two custom-made targeted sequencing approaches allowed the identification of causative variants in 28.6% (n = 30) of patients. Twenty-two out of 73 (34.6%) patients were diagnosed by Ion Torrent. In this group 20 were included in the SCID/CID category. Eight out of 50 (16%) patients were diagnosed by Haloplex workflow. Ion Torrent method was highly successful for those cases with well-defined phenotypes for immunological and clinical presentation. The Haloplex approach was able to diagnose 4 SCID/CID patients and 4 additional patients with complex and extended phenotypes, embracing all three PID categories in which this approach was more efficient. Both technologies showed good gene coverage. Conclusions: NGS technology represents a powerful approach in the complex field of rare disorders but its different application should be weighted. A relatively small NGS target panel can be successfully applied for a robust diagnostic suspicion, while when the spectrum of clinical phenotypes overlaps more than one PID an in-depth NGS analysis is required, including also whole exome/genome sequencing to identify the causative gene.
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Affiliation(s)
- Cristina Cifaldi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Immacolata Brigida
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Matteo Zoccolillo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Valentina Ferradini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Davide Petricone
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria Pia Cicalese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Dejan Lazarevic
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and BioInformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Maryam Omrani
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Attardi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesca Conti
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Alessia Scarselli
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Maria Chiriaco
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Silvia Di Cesare
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Francesco Licciardi
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Montin Davide
- Division of Immunology and Rheumatology, Department of Paediatric Infectious Diseases, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Clementina Canessa
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Claudio Pignata
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Silvia Giliani
- Department of Molecular and Translational Medicine, A. Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia, Italy
| | - Simona Ferrari
- Unit of Medical Genetics, St. Orsola-Malpighi University Hospital, University of Bologna, Bologna, Italy
| | - Georgia Fousteri
- Division of Immunology Transplantation and Infectious Diseases (DITID), Diabetes Research Institute (DRI) IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Graziano Barera
- Pediatric Department, San Raffaele Scientific Institute, Milan, Italy
| | - Pietro Merli
- Department of Onco-Hematology and Cell and Gene Therapy, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Paolo Palma
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
| | - Simone Cesaro
- Paediatric Hematology-Oncology, “Ospedale della Donna e del Bambino”, Verona, Italy
| | - Marco Gattorno
- Center for Autoinflammatory Diseases and Immunodeficiencies, IRCCS Giannina Gaslini, Genoa, Italy
| | - Antonio Trizzino
- Department of Pediatric Hematology and Oncology, “ARNAS Civico Di Cristina Benfratelli” Hospital, Palermo, Italy
| | - Viviana Moschese
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Loredana Chini
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Pediatric Immunopathology and Allergology Unit, University of Rome Tor Vergata Policlinico Tor Vergata, Rome, Italy
| | - Anna Villa
- Milan Unit, National Research Council (CNR) Institute for Genetic and Biomedical Research (IRGB), Milan, Italy
- Humanitas Clinical and Research Institute, Rozzano, Italy
| | - Chiara Azzari
- Pediatric Immunology, Department of Health Sciences, University of Florence, Florence, Italy
- Meyer Children's Hospital, Florence, Italy
| | - Andrea Finocchi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, University of Rome La Sapienza, Rome, Italy
| | - Paolo Rossi
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, Scientific Institute for Research and Healthcare (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita Salute San Raffaele University, Milan, Italy
| | - Caterina Cancrini
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Gigliola Di Matteo
- Unit of Immune and Infectious Diseases, University Department of Pediatrics (DPUO), Scientific Institute for Research and Healthcare (IRCCS) Childrens' Hospital Bambino Gesù, Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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Ponsford MJ, Klocperk A, Pulvirenti F, Dalm VASH, Milota T, Cinetto F, Chovancova Z, Rial MJ, Sediva A, Litzman J, Agostini C, van Hagen M, Quinti I, Jolles S. Hyper-IgE in the allergy clinic--when is it primary immunodeficiency? Allergy 2018; 73:2122-2136. [PMID: 30043993 DOI: 10.1111/all.13578] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/22/2018] [Accepted: 07/05/2018] [Indexed: 12/29/2022]
Abstract
The 2017 International Union of Immunological Societies (IUIS) classification recognizes 3 hyper-IgE syndromes (HIES), including the prototypic Job's syndrome (autosomal dominant STAT3-loss of function) and autosomal recessive PGM3 and SPINK5 syndromes. Early diagnosis of PID can direct life-saving or transformational interventions; however, it remains challenging owing to the rarity of these conditions. This can result in diagnostic delay and worsen prognosis. Within increasing access to "clinical-exome" testing, clinicians need to be aware of the implication and rationale for genetic testing, including the benefits and limitations of current therapies. Extreme elevation of serum IgE has been associated with a growing number of PID syndromes including the novel CARD11 and ZNF341 deficiencies. Variable elevations in IgE are associated with defects in innate, humoral, cellular and combined immunodeficiency syndromes. Barrier compromise can closely phenocopy these conditions. The aim of this article was to update readers on recent developments at this important interface between allergy and immunodeficiency, highlighting key clinical scenarios which should draw attention to possible immunodeficiency associated with extreme elevation of IgE, and outline initial laboratory assessment and management.
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Affiliation(s)
| | - Adam Klocperk
- Department of Immunology; 2nd Faculty of Medicine; Charles University and Motol University Hospital; Prague Czech Republic
| | | | - Virgil A. S. H. Dalm
- Department of Internal Medicine; Division of Clinical Immunology and Department of Immunology; Erasmus MC; Rotterdam The Netherlands
| | - Tomas Milota
- Department of Immunology; 2nd Faculty of Medicine; Charles University and Motol University Hospital; Prague Czech Republic
| | - Francesco Cinetto
- Department of Medicine; Treviso Hospital; University of Padova; Padova Italy
| | - Zita Chovancova
- Department of Clinical Immunology and Allergology; St. Anne's University Hospital in Brno; Czech Republic
- Faculty of Medicine; Masaryk University; Brno Czech Republic
| | - Manuel J. Rial
- Department of Allergy; University Hospital Jiménez Díaz Foundation; Madrid Spain
| | - Anna Sediva
- Department of Immunology; 2nd Faculty of Medicine; Charles University and Motol University Hospital; Prague Czech Republic
| | - Jiri Litzman
- Department of Clinical Immunology and Allergology; St. Anne's University Hospital in Brno; Czech Republic
- Faculty of Medicine; Masaryk University; Brno Czech Republic
| | - Carlo Agostini
- Department of Medicine; Treviso Hospital; University of Padova; Padova Italy
| | - Martin van Hagen
- Department of Internal Medicine; Division of Clinical Immunology and Department of Immunology; Erasmus MC; Rotterdam The Netherlands
| | - Isabella Quinti
- Department of Molecular Medicine; Sapienza University of Rome; Rome Italy
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The Utility of Next-Generation Sequencing for Primary Immunodeficiency Disorders: Experience from a Clinical Diagnostic Laboratory. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9647253. [PMID: 29888287 PMCID: PMC5977064 DOI: 10.1155/2018/9647253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/06/2018] [Accepted: 04/01/2018] [Indexed: 01/09/2023]
Abstract
Introduction Primary immune deficiency disorders (PIDs) are a group of diseases with profound defects in immune cells. The traditional diagnostics have evolved from clinical evaluation, flow cytometry, western blotting, and Sanger sequencing to focusing on small groups of genes. However, this is not sufficient to confirm the suspicion of certain PIDs. Our innovative approach to diagnostics outlines the algorithm for PIDs and the clinical utility of immunophenotyping with a custom-designed multigene panel. Materials and Methods We have designed a diagnostic algorithm based on flow cytometry studies to classify the patients; then the selected multigene panel was sequenced. In silico analysis for mutations was carried out using SIFT, Polyphen-2, and MutationTaster. Results and Discussion The causative mutation was identified in 46% of PIDs. Based on these results, this new algorithm including immune phenotyping and NGS for PIDs was suggested for the clinical use. Conclusions This study provides a thorough validation of diagnostic algorithm and indicates that still the traditional methods can be used to collect significant information related to design of most current diagnostics. The benefits of such testing are for diagnosis and prevention including the prenatal and preimplantation diagnosis, prognosis, treatment, and research.
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