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Bing N, Zhou H, Chen X, Hirose T, Kochi Y, Tsuchida Y, Ishigaki K, Sumitomo S, Fujio K, Zhang B, Valdez H, Vincent MS, Martin D, Clark JD. Contribution of a European-Prevalent Variant near CD83 and an East Asian-Prevalent Variant near IL17RB to Herpes Zoster Risk in Tofacitinib Treatment: Results of Genome-Wide Association Study Meta-Analyses. Arthritis Rheumatol 2021; 73:1155-1166. [PMID: 33455090 PMCID: PMC8361995 DOI: 10.1002/art.41655] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/12/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Tofacitinib is an oral JAK inhibitor for the treatment of rheumatoid arthritis (RA), psoriatic arthritis, and ulcerative colitis, and has been previously investigated for psoriasis (PsO). This meta-analysis of genome-wide association studies (GWAS) was performed to identify genetic factors associated with increased risk/faster onset of herpes zoster (HZ) in subjects with RA or PsO receiving tofacitinib treatment, and to determine potential mechanisms that could be attributed to the varying rates of HZ across ethnicities. METHODS In an ethnicity/indication-specific, trans-ethnic, trans-population meta-analysis of GWAS in subjects with RA or PsO from phase II, phase III, and long-term extension studies of tofacitinib, 8 million genetic variants were evaluated for their potential association with time to an HZ event and incidence of an HZ event (case versus control) with tofacitinib treatment, using Cox proportional hazard and logistic regression analyses, respectively. RESULTS In total, 5,246 subjects were included (3,168 with RA and 2,078 with PsO). After adjustment for age, baseline absolute lymphocyte count, genetically defined ethnicity, and concomitant methotrexate use (in RA subjects only), 4 loci were significantly associated with faster onset of HZ in European subjects (P < 5 × 10-8 ), including a single-nucleotide polymorphism (SNP) near CD83 (frequency of risk allele ~2% in European subjects versus ~0.1% in East Asian subjects). In the trans-ethnic, trans-population meta-analysis, the CD83 SNP remained significant. Four additional significant loci were identified in the meta-analysis, among which a SNP near IL17RB was associated with faster onset of HZ (meta-analysis hazard ratio 3.6 [95% confidence interval 2.40-5.44], P = 7.6 × 10-10 ; frequency of risk allele ~12% in East Asian subjects versus <0.2% in European subjects). CONCLUSION Genetic analysis of tofacitinib-treated subjects with RA or PsO identified multiple loci associated with increased HZ risk. Prevalent variants near the immune-relevant genes CD83 and IL17RB in European and East Asian populations, respectively, may contribute to risk of HZ in tofacitinib-treated subjects.
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Affiliation(s)
| | | | | | | | - Yuta Kochi
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan, and Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | - Yumi Tsuchida
- University of Tokyo Graduate School of MedicineTokyoJapan
| | | | - Shuji Sumitomo
- University of Tokyo Graduate School of MedicineTokyoJapan
| | - Keishi Fujio
- University of Tokyo Graduate School of MedicineTokyoJapan
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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: 57] [Impact Index Per Article: 14.3] [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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3
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Suratannon N, van Wijck RTA, Broer L, Xue L, van Meurs JBJ, Barendregt BH, van der Burg M, Dik WA, Chatchatee P, Langerak AW, Swagemakers SMA, Goos JAC, Mathijssen IMJ, Dalm VASH, Suphapeetiporn K, Heezen KC, Drabwell J, Uitterlinden AG, van der Spek PJ, van Hagen PM. Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency. Front Immunol 2020; 11:614. [PMID: 32373116 PMCID: PMC7179678 DOI: 10.3389/fimmu.2020.00614] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Genetic tests for primary immunodeficiency disorders (PIDs) are expensive, time-consuming, and not easily accessible in developing countries. Therefore, we studied the feasibility of a customized single nucleotide variant (SNV) microarray that we developed to detect disease-causing variants and copy number variation (CNV) in patients with PIDs for only 40 Euros. Methods: Probes were custom-designed to genotype 9,415 variants of 277 PID-related genes, and were added to the genome-wide Illumina Global Screening Array (GSA). Data analysis of GSA was performed using Illumina GenomeStudio 2.0, Biodiscovery Nexus 10.0, and R-3.4.4 software. Validation of genotype calling was performed by comparing the GSA with whole-genome sequencing (WGS) data of 56 non-PID controls. DNA samples of 95 clinically diagnosed PID patients, of which 60 patients (63%) had a genetically established diagnosis (by Next-Generation Sequencing (NGS) PID panels or Sanger sequencing), were analyzed to test the performance of the GSA. The additional SNVs detected by GSA were validated by Sanger sequencing. Results: Genotype calling of the customized array had an accuracy rate of 99.7%. The sensitivity for detecting rare PID variants was high (87%). The single sample replication in two runs was high (94.9%). The customized GSA was able to generate a genetic diagnosis in 37 out of 95 patients (39%). These 37 patients included 29 patients in whom the genetic variants were confirmed by conventional methods (26 patients by SNV and 3 by CNV analysis), while in 8 patients a new genetic diagnosis was established (6 patients by SNV and 2 patients suspected for leukemia by CNV analysis). Twenty-eight patients could not be detected due to the limited coverage of the custom probes. However, the diagnostic yield can potentially be increased when newly updated variants are added. Conclusion: Our robust customized GSA seems to be a promising first-line rapid screening tool for PIDs at an affordable price, which opens opportunities for low-cost genetic testing in developing countries. The technique is scalable, allows numerous new genetic variants to be added, and offers the potential for genetic testing not only in PIDs, but also in many other genetic diseases.
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Affiliation(s)
- Narissara Suratannon
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Rogier T A van Wijck
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Linda Broer
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Laixi Xue
- Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Joyce B J van Meurs
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Barbara H Barendregt
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - Willem A Dik
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Pantipa Chatchatee
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Sigrid M A Swagemakers
- Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Pathology & Clinical Bioinformatics, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jacqueline A C Goos
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Kim C Heezen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Jose Drabwell
- International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United Kingdom
| | - André G Uitterlinden
- Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Peter J van der Spek
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
| | - P Martin van Hagen
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand.,Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Heimall JR, Hagin D, Hajjar J, Henrickson SE, Hernandez-Trujillo HS, Tan Y, Kobrynski L, Paris K, Torgerson TR, Verbsky JW, Wasserman RL, Hsieh EWY, Blessing JJ, Chou JS, Lawrence MG, Marsh RA, Rosenzweig SD, Orange JS, Abraham RS. Use of Genetic Testing for Primary Immunodeficiency Patients. J Clin Immunol 2018; 38:320-329. [PMID: 29675737 DOI: 10.1007/s10875-018-0489-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/16/2018] [Indexed: 12/11/2022]
Abstract
Genetic testing plays a critical role in diagnosis for many primary immunodeficiency diseases. The goals of this report are to outline some of the challenges that clinical immunologists face routinely in the use of genetic testing for patient care. In addition, we provide a review of the types of genetic testing used in the diagnosis of PID, including their strengths and limitations. We describe the strengths and limitations of different genetic testing approaches for specific clinical contexts that raise concern for specific PID disorders in light of the challenges reported by the clinical immunologist members of the CIS in a recent membership survey. Finally, we delineate the CIS's recommendations for the use of genetic testing in light of these issues.
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Affiliation(s)
- Jennifer R Heimall
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, University of Pennsylvania, Wood Building 3rd Floor, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - David Hagin
- Allergy and Immunology Division, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - Joud Hajjar
- Department of Pediatrics, Section of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX, USA
| | - Sarah E Henrickson
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, University of Pennsylvania, Wood Building 3rd Floor, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Wherry Lab, University of Pennsylvania, Philadelphia, PA, USA
| | - Hillary S Hernandez-Trujillo
- Division of Infectious Disease & Immunology, Connecticut Children's Medical Center, Hartford, CT, USA
- CT Asthma and Allergy Center, West Hartford, CT, USA
| | - Yuval Tan
- The Charles Bronfman Institute of Personalized Medicine, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kenneth Paris
- Division of Allergy-Immunology, LSU Health Sciences Center, Children's Hospital, New Orleans, LA, USA
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James W Verbsky
- Pediatrics and Microbiology and Molecular Genetics Section of Pediatric Rheumatology, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Elena W Y Hsieh
- Department of Immunology and Microbiology, Department of Pediatrics, Division of Allergy and Immunology, University of Colorado, School of Medicine, Aurora, CO, USA
| | - Jack J Blessing
- Division of Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Janet S Chou
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Monica G Lawrence
- Division of Asthma, Allergy and Clinical Immunology, University of Virginia Health System, Charlottesville, VA, USA
| | - Rebecca A Marsh
- Bone Marrow Transplantation and Immune Deficiency, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Jordan S Orange
- Center for Human Immunobiology, Texas Children's Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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5
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Bradshaw G, Lualhati RR, Albury CL, Maksemous N, Roos-Araujo D, Smith RA, Benton MC, Eccles DA, Lea RA, Sutherland HG, Haupt LM, Griffiths LR. Exome Sequencing Diagnoses X-Linked Moesin-Associated Immunodeficiency in a Primary Immunodeficiency Case. Front Immunol 2018; 9:420. [PMID: 29556235 PMCID: PMC5845094 DOI: 10.3389/fimmu.2018.00420] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/15/2018] [Indexed: 12/21/2022] Open
Abstract
Background We investigated the molecular etiology of a young male proband with confirmed immunodeficiency of unknown cause, presenting with recurrent bacterial and Varicella zoster viral infections in childhood and persistent lymphopenia into early adulthood. Aim To identify causative functional genetic variants related to an undiagnosed primary immunodeficiency. Method Whole genome microarray copy number variant (CNV) analysis was performed on the proband followed by whole exome sequencing (WES) and trio analysis of the proband and family members. A >4 kbp deletion identified by repeated CNV analysis of exome sequencing data along with three damaging missense single nucleotide variants were validated by Sanger sequencing in all family members. Confirmation of the causative role of the candidate gene was performed by qPCR and Western Blot analyses on the proband, family members and a healthy control. Results CNV identified our previously reported interleukin 25 amplification in the proband; however, the variant was not validated to be a candidate gene for immunodeficiency. WES trio analysis, data filtering and in silico prediction identified a novel, damaging (SIFT: 0; Polyphen 1; Grantham score: 101) and disease-causing (MutationTaster) single base mutation in the X chromosome (c.511C > T p.Arg171Trp) MSN gene not identified in the UCSC Genome Browser database. The mutation was validated by Sanger sequencing, confirming the proband was hemizygous X-linked recessive (–/T) at this locus and inherited the affected T allele from his non-symptomatic carrier mother (C/T), with other family members (father, sister) confirmed to be wild type (C/C). Western Blot analysis demonstrated an absence of moesin protein in lymphocytes derived from the proband, compared with normal expression in lymphocytes derived from the healthy control, father and mother. qPCR identified significantly lower MSN mRNA transcript expression in the proband compared to an age- and sex-matched healthy control subject in whole blood (p = 0.02), and lymphocytes (p = 0.01). These results confirmed moesin deficiency in the proband, directly causative of his immunodeficient phenotype. Conclusion These findings confirm X-linked moesin-associated immunodeficiency in a proband previously undiagnosed up to 24 years of age. This study also highlights the utility of WES for the diagnosis of rare or novel forms of primary immunodeficiency disease.
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Affiliation(s)
- Gabrielle Bradshaw
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robbie R Lualhati
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Cassie L Albury
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Neven Maksemous
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Deidre Roos-Araujo
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Robert A Smith
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Miles C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - David A Eccles
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rod A Lea
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi G Sutherland
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
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