Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency
Frontiers in Immunology, vol. 11, pp. 614
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.
Authors 20
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Narissara Suratannon corresponding
Thai Red Cross Society · Chulalongkorn University · Erasmus MC · King Chulalongkorn Memorial Hospital
Affiliation as printed
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
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Rogier T. A. van Wijck corresponding
Affiliation as printed
Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Mirjam van der Burg Aachen Laboratory for Immunology Department of Pediatrics, Leiden University Medical Centre
Leiden University · Leiden University Medical Center
Affiliation as printed
Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, Netherlands
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Affiliation as printed
Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Thai Red Cross Society · Chulalongkorn University · King Chulalongkorn Memorial Hospital
Affiliation as printed
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
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Affiliation as printed
Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
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
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Affiliation as printed
Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Department of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Affiliation as printed
Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Thai Red Cross Society · Chulalongkorn University · King Chulalongkorn Memorial Hospital
Affiliation as printed
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
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Affiliation as printed
Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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International Patient Organisation for Primary Immunodeficiencies
Affiliation as printed
International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United Kingdom
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Affiliation as printed
Genetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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Peter J. van der Spek Aachen Laboratory for Immunology Department of Pediatrics, Leiden University Medical Centre
Leiden University · Thai Red Cross Society · Chulalongkorn University · Leiden University Medical Center · Erasmus MC · King Chulalongkorn Memorial Hospital
Affiliation as printed
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
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
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Thai Red Cross Society · Chulalongkorn University · Erasmus MC · King Chulalongkorn Memorial Hospital
Affiliation as printed
Academic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, Netherlands
Department Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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
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