دورية أكاديمية
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency.
| العنوان: | Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency. |
|---|---|
| المؤلفون: | Suratannon N; 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., van Wijck RTA; Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Broer L; Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Xue L; Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands., van Meurs JBJ; Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Barendregt BH; 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., van der Burg M; Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands., Dik WA; 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., Chatchatee P; 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., Langerak AW; 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., Swagemakers SMA; 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., Goos JAC; Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Mathijssen IMJ; Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Dalm VASH; 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., Suphapeetiporn K; 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., Heezen KC; Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands., Drabwell J; International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United Kingdom., Uitterlinden AG; Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands., van der Spek PJ; 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., van Hagen PM; 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. |
| مؤلفون مشاركون: | South East Asia Primary Immunodeficiencies (SEAPID) Consortium |
| المصدر: | Frontiers in immunology [Front Immunol] 2020 Apr 15; Vol. 11, pp. 614. Date of Electronic Publication: 2020 Apr 15 (Print Publication: 2020). |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Frontiers Research Foundation] Country of Publication: Switzerland NLM ID: 101560960 Publication Model: eCollection Cited Medium: Internet ISSN: 1664-3224 (Electronic) Linking ISSN: 16643224 NLM ISO Abbreviation: Front Immunol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [Lausanne : Frontiers Research Foundation] |
| مواضيع طبية MeSH: | Genetic Testing/*methods , Genotyping Techniques/*methods , High-Throughput Nucleotide Sequencing/*methods , Primary Immunodeficiency Diseases/*genetics, Costs and Cost Analysis ; DNA Copy Number Variations ; Genotyping Techniques/economics ; Humans ; Polymorphism, Single Nucleotide ; Reproducibility of Results |
| مستخلص: | 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. (Copyright © 2020 Suratannon, van Wijck, Broer, Xue, van Meurs, Barendregt, van der Burg, Dik, Chatchatee, Langerak, Swagemakers, Goos, Mathijssen, Dalm, Suphapeetiporn, Heezen, Drabwell, Uitterlinden, van der Spek, van Hagen and the South East Asia Primary Immunodeficiencies (SEAPID) Consortium.) |
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| فهرسة مساهمة: | Keywords: SNP microarray; copy number variants (CNV) calling; microarray-based genotyping; primary immunodeficiencies; single nucleotide variants (SNV) calling |
| تواريخ الأحداث: | Date Created: 20200507 Date Completed: 20210325 Latest Revision: 20210325 |
| رمز التحديث: | 20231215 |
| مُعرف محوري في PubMed: | PMC7179678 |
| DOI: | 10.3389/fimmu.2020.00614 |
| PMID: | 32373116 |
| قاعدة البيانات: | MEDLINE |
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