Overview – What Is the Infinium Global Screening Array-24 (GSA-24)?

The Infinium Global Screening Array-24 (GSA-24) is a high-density SNP genotyping platform from Illumina, designed for large-scale genetic and population-based research. It provides highly accurate, reproducible genotyping data with faster turnaround times and lower costs than whole-genome sequencing, making it an ideal solution for studies involving thousands of samples.

Rather than discovering new genetic variants, the GSA-24 is optimized to detect known, clinically and biologically relevant SNPs. Each BeadChip simultaneously analyzes 24 DNA samples and includes approximately 654,000 genome-wide markers, with the option to incorporate up to 100,000 custom SNPs. This combination of comprehensive genome coverage and customizable content enables researchers to tailor the array to specific research objectives.

Trusted by researchers worldwide, the Infinium GSA family of arrays has been used to genotype more than 15 million samples, making it one of the most widely adopted and validated platforms for human genetics, population genomics, clinical research, and translational medicine.

Specifications

Advantages of Infinium Global Screening Array-24 (GSA-24)

• High-Throughput Genotyping -  Process 24 DNA samples per BeadChip with a scalable workflow capable of analyzing up to 5,760 samples per week, making it ideal for large population studies.

• Rapid Turnaround Time -  The optimized Infinium HTS workflow delivers high-quality genotyping results in approximately 3 days, accelerating project completion.

• Exceptional Data Quality -  Achieve >99% call rates and >99.9% reproducibility, ensuring reliable and consistent results across a wide range of sample types.

• Comprehensive Multi-Ethnic Coverage -  Designed for high imputation accuracy across 26 global populations, enabling robust analyses in diverse genetic cohorts.

• Clinically Relevant Variant Content -  Includes carefully curated markers from leading resources such as ClinVar, NHGRI-EBI GWAS Catalog, PharmGKB, and ExAC, supporting translational and clinical research.

• Optimized for Pharmacogenomics -  Provides extensive coverage of ADME genes and HLA loci, making it well suited for pharmacogenomic and precision medicine applications.

• Wide Sample Compatibility -  Compatible with DNA extracted from whole blood, saliva, buccal swabs, and FFPE tissue, offering flexibility for various study designs.

• Customizable Marker Content -  Enhance your study by adding up to 100,000 custom SNP markers using Illumina DesignStudio, enabling targeted analysis tailored to your research objectives.

Infinium GSA-24 Workflow

The Infinium Global Screening Array-24 (GSA-24) utilizes Illumina's proven Infinium HTS chemistry, delivering a streamlined workflow optimized for high throughput, reproducibility, and exceptional data quality. Each stage is carefully designed to reduce hands-on time while ensuring accurate and consistent genotyping results.

1. DNA Preparation -  High-quality genomic DNA is amplified, enzymatically fragmented, and prepared for hybridization.

2. BeadChip Hybridization -  The processed DNA is hybridized to sequence-specific probes on the Infinium GSA-24 BeadChip, enabling precise detection of targeted SNP markers.

3. High-Resolution Imaging -  Following single-base extension and staining, the Illumina iScan System captures fluorescent signals using advanced dual-laser optics to generate high-resolution image data.

4. Genotype Calling & Quality Analysis -  Fluorescence intensity data are analyzed using GenomeStudio™ Software, which accurately converts signal intensities into SNP genotype calls, consistently achieving >99% call rates with outstanding reproducibility.

This efficient end-to-end workflow enables rapid processing of large sample cohorts, delivering high-quality genotyping data ready for genome-wide association studies (GWAS), population genetics, imputation, pharmacogenomics, and other downstream genomic analyses.

Figure: Schematic illustration of the Infinium GSA-24 genotyping workflow. DNA samples are processed through hybridization, scanning, and data analysis in a streamlined process.

Data Analysis

Project Deliverables

✅ High-Quality Genotype Data

Receive expert-validated SNP genotype calls for every sample, formatted and ready for downstream genomic and statistical analyses.

✅ Comprehensive Quality Control Report

A detailed QC summary including sample call rates, marker performance, cluster quality metrics, and overall data quality assessment to ensure confidence in the generated results.

✅ Allelic Signal Visualization

Includes B-Allele Frequency (BAF) and Log R Ratio (LRR) plots for genotype visualization, copy number variation (CNV) assessment, and quality evaluation where applicable.

✅ Concordance & Validation Summary

A comprehensive concordance report comparing results against reference datasets or internal validation samples (such as rWGS or 1000 Genomes Project standards) to verify genotyping accuracy.

✅ Optional High-Accuracy Imputed Dataset

Upon request, genotype data can be expanded through high-accuracy imputation, providing additional variant information to support genome-wide association studies (GWAS), fine mapping, and other advanced analyses.

Comparison of GSA-24 vs GDA-8

Why We Offer Both GSA-24 and GDA-8 Services

At N2Jenomics Lab Pvt. Ltd., we offer both Infinium Global Screening Array-24 (GSA-24) and Infinium Global Diversity Array-8 (GDA-8) to meet the diverse requirements of modern genomics research.

The GSA-24 is optimized for high-throughput, cost-effective SNP genotyping, making it an excellent choice for large population studies, genome-wide association studies (GWAS), biobank projects, pharmacogenomics, and precision medicine research. Its broad multi-ethnic genome coverage and scalable workflow are ideal for projects involving thousands of samples.

The GDA-8 provides higher marker density with expanded exonic, clinically relevant, and functional variant content, making it well suited for high-resolution genetic studies, detailed variant analysis, copy number variation (CNV) detection, and translational or clinical research where deeper genomic coverage is required.

By offering both platforms, N2Jenomics Lab Pvt. Ltd. helps researchers select the most suitable genotyping solution based on sample size, study objectives, required genomic resolution, budget, and turnaround time, ensuring optimal performance and cost efficiency for every project.

Sample Requirements

Applications of Infinium Global Screening Array-24 (GSA-24) Genotyping

The Infinium Global Screening Array-24 (GSA-24) is a powerful, high-throughput SNP genotyping platform designed to support a broad range of genomic research and clinical applications.

• Population Genetics & Ancestry Studies

Utilize comprehensive multi-ethnic genome-wide marker coverage to investigate population structure, genetic diversity, ancestry inference, and evolutionary relationships across diverse populations.

• Genome-Wide Association Studies (GWAS)

Identify genetic variants associated with complex traits and diseases through large-scale, cost-effective genome-wide association studies involving thousands of samples.

• Disease Risk Assessment & Biomarker Discovery

Analyze clinically relevant genetic variants curated from resources such as ClinVar, the NHGRI-EBI GWAS Catalog, and other public databases to support biomarker discovery, disease susceptibility studies, and translational research.

• Pharmacogenomics & Precision Therapeutics

Comprehensive coverage of ADME genes, HLA, and other pharmacogenomic markers enables research into drug metabolism, treatment response, adverse drug reactions, and personalized medicine.

• Lifestyle, Wellness & Consumer Genomics

Support genetic studies related to health, wellness, nutrition, fitness, ancestry, and inherited traits, with the flexibility to incorporate custom SNP content for specialized applications.

• Translational & Precision Medicine Research

Facilitate clinical and translational research by enabling patient stratification, genetic risk analysis, therapeutic target validation, and precision medicine initiatives.

• Large-Scale High-Throughput Genotyping

Process thousands of samples efficiently using the streamlined Infinium HTS workflow, delivering reliable, high-quality genotyping data with rapid turnaround times for large cohort studies.

Q1. How accurate is the Infinium Global Screening Array-24 (GSA-24)?

The Infinium GSA-24 delivers exceptional genotyping accuracy, demonstrating >99% concordance with reference whole-genome sequencing (rWGS) and other benchmark datasets. More than 82% of assays achieve a Positive Predictive Value (PPV) of 100%, providing highly reliable results suitable for research and clinical screening applications.

Q2. Can the GSA-24 analyze low-quality or low-input DNA samples?

Yes. The GSA-24 is optimized to perform reliably with low DNA input and challenging sample types while maintaining high call rates, excellent reproducibility, and consistent data quality. This makes it well suited for clinical, biobank, and archived sample collections.

Q3. What research applications is the GSA-24 best suited for?

The Infinium GSA-24 supports a wide range of genomic studies, including:

• • Genome-Wide Association Studies (GWAS)

• • Population genetics and ancestry analysis
• • Disease risk profiling and biomarker discovery
• • Pharmacogenomics and precision medicine research
• • Translational and clinical genomics
• • Large-scale population screening

• Its multi-ethnic genome coverage and clinically curated variant content make it a versatile platform for diverse research programs.

Q4. What deliverables are included with the GSA-24 genotyping service?

Our service provides a comprehensive set of deliverables, including:

• • High-confidence SNP genotype data
• • Quality control (QC) reports and performance metrics
• • B-Allele Frequency (BAF) and Log R Ratio (LRR) plots
• • Concordance and validation summaries
• • Optional high-accuracy imputed genotype datasets upon request

• These outputs are ready for downstream statistical, association, and genomic analyses.

Q5. What is Positive Predictive Value (PPV), and why is it important?

Positive Predictive Value (PPV) measures how accurately positive genotype calls represent true genetic variants when compared with a gold-standard reference. A PPV of 100% for the majority of assays demonstrates the GSA-24's ability to deliver highly reliable variant calls, increasing confidence in downstream analyses and clinical research.

Q6. How many genetic markers are included in the Infinium GSA-24?

The Infinium Global Screening Array-24 (GSA-24) contains approximately 654,000 fixed genome-wide markers and supports the addition of up to 100,000 custom SNP markers, allowing researchers to tailor the array to specific study requirements.

Q7. Is the GSA-24 suitable for pharmacogenomics research?

Yes. The GSA-24 includes a comprehensive set of pharmacogenomic (PGx) markers, including variants in ADME genes, HLA loci, and immune-related genes curated from resources such as PharmGKB and ClinVar. This makes it an excellent platform for studies investigating drug response, drug metabolism, adverse drug reactions, and precision medicine.