Sample Submission Guidelines
Overview – What Is Infinium GSA-24?
The Infinium Global Screening Array-24 (Infinium GSA-24) is a high-density genotyping platform developed by Illumina for large-scale genetic research. It delivers reliable, reproducible data at a lower cost and faster turnaround compared with sequencing, making it a preferred choice for studies requiring thousands of samples.
Unlike sequencing, which is discovery-driven, the Infinium GSA-24 focuses on known, clinically relevant genetic variants. Each BeadChip processes 24 DNA samples simultaneously and interrogates ~654,000 markers, with the flexibility to add up to 100,000 custom SNPs. This balance of fixed genome-wide coverage and customizable content ensures that the platform can be tailored to diverse study objectives.
Over 15 million samples worldwide have been processed using the Infinium GSA family of arrays, establishing it as one of the most trusted tools in human genetics and translational research.
Specifications
| Parameter | Details |
|---|---|
| Assay Type | Infinium HTS format microarray |
| Automation | Compatible with automated array loader, liquid handling robots |
| DNA Input | 200 ng per sample |
| Instrumentation | iScan System |
| Species | Human DNA |
| Marker Count | ~654,027 fixed markers (plus up to 100K custom add-ons) |
| Sample Capacity | 24 samples per array |
| Throughput | Up to ~5,760 samples per week |
| Variant Types | SNPs, structural variants, CNVs |
Advantages of Infinium GSA-24
High throughput
– 24 samples per BeadChip with weekly capacity up to ~5,760 samples.
Fast turnaround
– streamlined Infinium HTS workflow delivers results in ~3 days.
Robust accuracy
– >99% call rates and 99.9% reproducibility across diverse sample types.
Global relevance
– optimized for high imputation accuracy across 26 populations from the 1000 Genomes Project.
Clinical utility
– curated variants from ClinVar, NHGRI-GWAS, PharmGKB, and ExAC databases.
Pharmacogenomics-ready
– comprehensive coverage of ADME genes and HLA loci.
Broad sample compatibility
– supports DNA from blood, saliva, buccal swabs, and FFPE tissue.
Flexible customization
– option to add up to 100,000 project-specific markers via DesignStudio.
Workflow
Figure: Schematic illustration of the Infinium GSA-24 genotyping workflow. DNA samples are processed through hybridization, scanning, and data analysis in a streamlined process.
The Infinium GSA-24 workflow is based on Illumina’s Infinium HTS chemistry, designed for speed and reproducibility. Each step is optimized to minimize hands-on time and maintain high data quality.
DNA preparation – genomic DNA is amplified and fragmented.
Hybridization – DNA fragments bind to probes on the BeadChip.
Imaging – the iScan system uses dual-laser optics to capture fluorescent signals.
Genotyping – GenomeStudio software converts intensity data into SNP calls with >99% accuracy.
This streamlined process enables large-scale population studies to be completed efficiently, with results ready for downstream association analysis and imputation.
Data Analysis
| Analysis Level | Process & Deliverables |
|---|---|
| Basic QC & Genotyping |
|
| Differential Analysis |
|
| Functional Annotation |
|
| Advanced Genetic Analysis |
|
Delivery Summary
✅ High-confidence genotype data
Expert-curated SNP calls for each sample, ready for downstream analysis.
✅ Quality control summary
Includes overall sample call rates, per-locus cluster metrics, and sample performance assessment.
✅ Allele-frequency visualization
B-allele frequency (BAF) and log R ratio (LRR) plots to reflect genotype distribution and detect CNVs where applicable.
✅ Concordance overview
Summary of concordance against reference datasets or internal validation samples (e.g., rWGS or 1KG standards).
✅ Optional imputed dataset
Genotype data projected onto additional variants via high-accuracy imputation when requested.
Comparison of GSA-24 vs GDA-8
| Feature | Infinium Global Screening Array-24 Kit | Infinium Global Diversity Array-8 Kit |
|---|---|---|
| Assay Type | Infinium HTS format microarray | Infinium LCG (8-sample format) microarray |
| Sample Capacity per Array | 24 samples | 8 samples |
| Marker Count | ~654,027 fixed markers; up to 100K custom markers | ~1.8 million markers, including extensive exonic and clinical content |
| Info Content Focus | Multi-ethnic genome-wide + curated clinical variants (ClinVar, PharmGKB, etc.) | Enhanced clinical coverage including exons, rare variants, phenotype associations |
| CNV Detection & Exonic Coverage | Limited; primarily SNP genotyping | High-resolution CNV detection with exonic emphasis; average resolution ~1.5 Mb |
| Throughput | High; scalable for population-level throughput | Moderate; 8-sample format with high per-variant efficiency |
| Ideal Use Cases | GWAS, pharmacogenomics, disease risk profiling, multi-population studies | Clinical research requiring deep coverage of disease genes, CNVs, and exonic variants |
| Platform Compatibility | Illumina iScan System with automation support | Same iScan System compatible; goal of cost-effective per-variant yield |
Why Offer Both Services
The GSA-24 service excels in high-throughput genotyping with broad, multi-ethnic variant coverage; ideal for large cohort studies.
The GDA-8 service, with its denser marker set and enhanced exonic and clinical content, is better suited for deep, focused investigations—such as detailed variant discovery, CNV analysis, and translational/clinical research.
Offering both enables CD Genomics to flexibly guide clients to the appropriate array based on their sample size, variant resolution needs, and study goals.
Sample Requirements
| Parameter | Requirement |
|---|---|
| DNA Input Quantity | ≥200 ng genomic DNA per sample |
| DNA Concentration | >50 ng/µL recommended |
| Purity (OD260/280) | 1.7–2.1, with clear electrophoresis bands |
| DNA Integrity | High molecular weight DNA >10 kb, minimal degradation |
| Accepted Sample Types | Blood, saliva, buccal swabs, fresh/frozen tissue, FFPE tissue |
| Buffer/Storage | TE buffer or nuclease-free water (ddH₂O) |
| Container | 1.5 mL microcentrifuge tube or 96-well plate, sealed with film |
| Storage Conditions | –20°C or below for long-term storage |
| Transport Conditions | 2–8°C with ice packs for local delivery; dry ice shipping (< –20°C) for long distance |
Applications of Infinium GSA-24 Genotyping
The Infinium Global Screening Array-24 (Infinium GSA-24) is a versatile platform that supports a wide range of research applications:
Population genetics & ancestry analysis
Leverages multi-ethnic genome-wide markers for robust population structure studies and ancestry mapping
Genome-Wide Association Studies (GWAS)
Ideal for large-scale variant discovery linking genetic markers to complex traits and diseases
Disease risk profiling & biomarker discovery
Includes curated variants from ClinVar, NHGRI-GWAS catalog, and more for targeted risk analysis
Pharmacogenomics & drug response research
Features ADME-related markers and HLA/KIR content relevant to drug metabolism and personalized medicine
Lifestyle and wellness characterization
Supports trait mapping, wellness panels, and consumer genomics use cases with customizable boosters
Translational and precision medicine initiatives
Employed in clinical research for population stratification and therapeutic target validation
High-throughput variant screening
Enables flexible loading of large sample cohorts with an efficient 3-day workflow and automated processing
FAQs – Infinium GSA-24 Genotyping Service
Q1: How accurate is the Infinium Global Screening Array-24?
The Infinium GSA 24 demonstrates >99% concordance with reference whole-genome sequencing (rWGS) and benchmark datasets, with over 82% of assays achieving a Positive Predictive Value (PPV) of 100%—a standard aligned with clinical screening needs.
Q2: Can the GSA-24 handle low-quality or low DNA input samples?
Yes. The array maintains excellent performance even with low DNA inputs, preserving high call rates and reproducibility across sample types—a key advantage for studies using degraded or limited clinical samples.
Q3: What types of research benefit most from the Infinium GSA-24?
This platform supports a wide range of applications including SNP-based GWAS, disease risk profiling, pharmacogenomics (ADME/HLA), ancestry mapping, and translational studies—all powered by dense multi-ethnic coverage and curated clinical variants.
Q4: What data do I receive after the run?
We deliver high-density SNP genotype calls, QC metrics, optional imputed datasets, and detailed reliability assessments—ready for association studies or clinical-genomics pipelines.
Q5: What is Positive Predictive Agreement (PPA), and why does it matter?
PPA is the proportion of positive array results confirmed by gold-standard sequencing. Achieving PPV = 100% in over 82% of assays means the GSA-24 reliably identifies true positives—critical for confidence in variant interpretation.
Q6: How many SNPs does Infinium GSA-24 include?
The Infinium Global Screening Array-24 (GSA-24) features approximately 654,027 fixed markers, with the option to incorporate up to 100,000 customizable SNPs for tailored study needs.
Q7: Is the GSA-24 accurate for pharmacogenomic markers?
Yes. The GSA-24 includes curated pharmacogenomic (PGx) markers sourced from databases like PharmGKB and ClinVar, ensuring clinically relevant coverage for ADME, HLA, and immune-related genes.
Case Study
Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories, bioRxiv , 2022.
1. Background
The study aimed to validate the Infinium Global Screening Array-24 v3.0 (GSA-24) for forensic applications, following SWGDAM and FBI Quality Assurance Standards (QAS). The goal was to test precision, sensitivity, reproducibility, and suitability for degraded or low-input DNA samples.
2. Methods
- The validation used DNA standards (NA12878, NA24385, NA24631) with inputs ranging from 200 ng down to 0.2 ng.
- Evaluations included sensitivity, accuracy, repeatability, reproducibility, degradation, species specificity, contamination, and mixtures.
- Genotype concordance was measured against NIST/Genome-in-a-Bottle (GIAB) reference data.
3. Results
- Call rates exceeded 99% for inputs ≥ 1 ng, and remained >95% at 0.2 ng.
- Concordance rates versus GIAB references were consistently high (99.2% average). Within-sample replicates showed >99.8% reproducibility.
- In mixture tests, profiles with a 3:1 ratio achieved 98.85% concordance and at 9:1 reached >99.99% concordance.
- The array demonstrated robust performance even with challenging or degraded samples.
Figure caption: "Call rate and concordance across DNA input levels, demonstrating high performance of the GSA-24 v3.0 at inputs as low as 0.2 ng."
4. Conclusions
The validation confirms that Infinium GSA-24 v3.0 delivers high accuracy (>95% call rate at 0.2 ng), exceptional reproducibility (>99.8%), and robustness across degraded or mixed samples. These findings underscore its reliability for high-throughput research, forensics, precision medicine, and population-genetics applications.
Demo
