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Related Concept Videos

Genetic Screens02:46

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...
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Rapid Low-Cost Microarray-Based Genotyping for Genetic Screening in Primary Immunodeficiency.

Narissara Suratannon1,2, Rogier T A van Wijck3, Linda Broer4

  • 1Department of Immunology, Laboratory Medical Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands.

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Summary

A new, affordable microarray accurately screens for primary immunodeficiency disorders (PIDs), offering a cost-effective genetic testing solution for developing countries. This tool aids in rapid diagnosis and potential identification of new genetic variants.

Keywords:
SNP microarraycopy number variants (CNV) callingmicroarray-based genotypingprimary immunodeficienciessingle nucleotide variants (SNV) calling

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Area of Science:

  • Genetics
  • Immunology
  • Bioinformatics

Background:

  • Genetic testing for primary immunodeficiency disorders (PIDs) is often inaccessible and costly in developing nations.
  • A custom single nucleotide variant (SNV) microarray was developed to address these limitations for PID diagnosis.
  • The microarray aims to detect disease-causing variants and copy number variations (CNVs) affordably.

Purpose of the Study:

  • To evaluate the feasibility and performance of a custom-designed SNV microarray for diagnosing PIDs.
  • To assess the cost-effectiveness of the microarray for genetic testing in resource-limited settings.
  • To determine the diagnostic yield of the microarray in clinically diagnosed PID patients.

Main Methods:

  • Custom probes for 9,415 variants across 277 PID-related genes were integrated into the Illumina Global Screening Array (GSA).
  • Genomic data analysis utilized Illumina GenomeStudio, Biodiscovery Nexus, and R software.
  • The GSA's genotype calling accuracy was validated against whole-genome sequencing (WGS) and Sanger sequencing for 95 PID patients.

Main Results:

  • The custom GSA demonstrated high accuracy (99.7%) and sensitivity (87%) for detecting rare PID variants.
  • The microarray successfully provided a genetic diagnosis for 39% (37/95) of PID patients, including new diagnoses.
  • The cost-effective nature of the test was highlighted at approximately 40 Euros per sample.

Conclusions:

  • The customized GSA is a robust, affordable, and rapid first-line screening tool for PIDs.
  • This technology offers significant potential for low-cost genetic testing in developing countries.
  • The scalable platform can be expanded to include new variants and applied to other genetic diseases.