Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency
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 varia...
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Frontiers Media S.A.
2020-04-01
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Series: | Frontiers in Immunology |
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Online Access: | https://www.frontiersin.org/article/10.3389/fimmu.2020.00614/full |
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English |
format |
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author |
Narissara Suratannon Narissara Suratannon Rogier T. A. van Wijck Linda Broer Laixi Xue Joyce B. J. van Meurs Barbara H. Barendregt Barbara H. Barendregt Mirjam van der Burg Willem A. Dik Willem A. Dik Willem A. Dik Pantipa Chatchatee Anton W. Langerak Anton W. Langerak Sigrid M. A. Swagemakers Sigrid M. A. Swagemakers Jacqueline A. C. Goos Irene M. J. Mathijssen Virgil A. S. H. Dalm Virgil A. S. H. Dalm Virgil A. S. H. Dalm Kanya Suphapeetiporn Kanya Suphapeetiporn Kim C. Heezen Jose Drabwell André G. Uitterlinden Peter J. van der Spek Peter J. van der Spek Peter J. van der Spek P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen The South East Asia Primary Immunodeficiencies (SEAPID) Consortium |
spellingShingle |
Narissara Suratannon Narissara Suratannon Rogier T. A. van Wijck Linda Broer Laixi Xue Joyce B. J. van Meurs Barbara H. Barendregt Barbara H. Barendregt Mirjam van der Burg Willem A. Dik Willem A. Dik Willem A. Dik Pantipa Chatchatee Anton W. Langerak Anton W. Langerak Sigrid M. A. Swagemakers Sigrid M. A. Swagemakers Jacqueline A. C. Goos Irene M. J. Mathijssen Virgil A. S. H. Dalm Virgil A. S. H. Dalm Virgil A. S. H. Dalm Kanya Suphapeetiporn Kanya Suphapeetiporn Kim C. Heezen Jose Drabwell André G. Uitterlinden Peter J. van der Spek Peter J. van der Spek Peter J. van der Spek P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen The South East Asia Primary Immunodeficiencies (SEAPID) Consortium Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency Frontiers in Immunology primary immunodeficiencies microarray-based genotyping SNP microarray single nucleotide variants (SNV) calling copy number variants (CNV) calling |
author_facet |
Narissara Suratannon Narissara Suratannon Rogier T. A. van Wijck Linda Broer Laixi Xue Joyce B. J. van Meurs Barbara H. Barendregt Barbara H. Barendregt Mirjam van der Burg Willem A. Dik Willem A. Dik Willem A. Dik Pantipa Chatchatee Anton W. Langerak Anton W. Langerak Sigrid M. A. Swagemakers Sigrid M. A. Swagemakers Jacqueline A. C. Goos Irene M. J. Mathijssen Virgil A. S. H. Dalm Virgil A. S. H. Dalm Virgil A. S. H. Dalm Kanya Suphapeetiporn Kanya Suphapeetiporn Kim C. Heezen Jose Drabwell André G. Uitterlinden Peter J. van der Spek Peter J. van der Spek Peter J. van der Spek P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen P. Martin van Hagen The South East Asia Primary Immunodeficiencies (SEAPID) Consortium |
author_sort |
Narissara Suratannon |
title |
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency |
title_short |
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency |
title_full |
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency |
title_fullStr |
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency |
title_full_unstemmed |
Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency |
title_sort |
rapid low-cost microarray-based genotyping for genetic screening in primary immunodeficiency |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Immunology |
issn |
1664-3224 |
publishDate |
2020-04-01 |
description |
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. |
topic |
primary immunodeficiencies microarray-based genotyping SNP microarray single nucleotide variants (SNV) calling copy number variants (CNV) calling |
url |
https://www.frontiersin.org/article/10.3389/fimmu.2020.00614/full |
work_keys_str_mv |
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doaj-2b37dbfc533b442aad705ee9c4ba4dda2020-11-25T03:25:35ZengFrontiers Media S.A.Frontiers in Immunology1664-32242020-04-011110.3389/fimmu.2020.00614497722Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary ImmunodeficiencyNarissara Suratannon0Narissara Suratannon1Rogier T. A. van Wijck2Linda Broer3Laixi Xue4Joyce B. J. van Meurs5Barbara H. Barendregt6Barbara H. Barendregt7Mirjam van der Burg8Willem A. Dik9Willem A. Dik10Willem A. Dik11Pantipa Chatchatee12Anton W. Langerak13Anton W. Langerak14Sigrid M. A. Swagemakers15Sigrid M. A. Swagemakers16Jacqueline A. C. Goos17Irene M. J. Mathijssen18Virgil A. S. H. Dalm19Virgil A. S. H. Dalm20Virgil A. S. H. Dalm21Kanya Suphapeetiporn22Kanya Suphapeetiporn23Kim C. Heezen24Jose Drabwell25André G. Uitterlinden26Peter J. van der Spek27Peter J. van der Spek28Peter J. van der Spek29P. Martin van Hagen30P. Martin van Hagen31P. Martin van Hagen32P. Martin van Hagen33The South East Asia Primary Immunodeficiencies (SEAPID) ConsortiumDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsPediatric 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, ThailandDepartment Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsGenetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsGenetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsLaboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsPediatric 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, ThailandDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment of Pathology & Clinical Bioinformatics, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment of Plastic and Reconstructive Surgery, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsDepartment Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsCenter of Excellence for Medical Genomics, Division of Medical Genetics and Metabolism, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand0Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, ThailandDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands1International Patient Organization for Primary Immunodeficiencies (IPOPI), Downderry, United KingdomGenetic Laboratory and Human Genomics Facility HuGeF, Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, NetherlandsPediatric 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, ThailandAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsLaboratory for Immunology, Department of Pediatrics, Leiden University Medical Centre, Leiden, NetherlandsDepartment of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsPediatric 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, ThailandDepartment Internal Medicine, Division of Clinical Immunology, Erasmus MC, University Medical Center, Rotterdam, NetherlandsAcademic Center for Rare Immunological Diseases (Rare Immunological Disease Center, RIDC), Erasmus MC, University Medical Center, Rotterdam, NetherlandsBackground: 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.https://www.frontiersin.org/article/10.3389/fimmu.2020.00614/fullprimary immunodeficienciesmicroarray-based genotypingSNP microarraysingle nucleotide variants (SNV) callingcopy number variants (CNV) calling |