Sample Submission Guidelines
Introduction to the Infinium Global Diversity Array-8
The Infinium Global Diversity Array-8 v1.0 is an Illumina genotyping backbone built for diverse cohorts. CD Genomics applies the Illumina Infinium Global Diversity Array (GDA-8) to deliver consistent, comparable results across global ancestries. This platform supports population studies, PRS development, and cytogenetics within one integrated workflow.
What sets GDA-8 apart
- Updated multiethnic scaffold optimised for cross-population imputation and fine-mapping.
- Curated clinical research variants from leading databases for translational relevance.
- Optional versions: Infinium Global Diversity Array with Cytogenetics 8 and Enhanced PGx 8.
- Custom add-on content of up to 175k markers for project-specific questions.
- Proven at scale in national precision-medicine initiatives such as All of Us.
Who should use this service
- Researchers running GWAS across multiple ancestries.
- Teams building polygenic risk models for complex traits.
- Cytogenetics groups requiring genome-wide CNV and LOH insight.
Technical Specifications
| Parameter | Specification |
|---|---|
| Assay chemistry | Infinium LCG |
| Platform / instrument | iScan System |
| Samples per BeadChip | 8 |
| Total markers (fixed) | 1,825,277 |
| Custom add-on capacity | Up to 175,000 markers |
| DNA input | 200 ng per sample |
| Max. throughput (single iScan) | ~1,728 samples/week |
| Scan time | ~4.4 min per sample |
| Workflow duration | 3-day Infinium workflow |
| Variant classes reported | SNPs, CNVs, LOH, chromosomal abnormalities, structural variants |
| Specialized sample types | Blood, FFPE tissue, buccal swabs, saliva |
| Nucleic acid type | DNA |
| Technology / method | Microarray; genome-wide genotyping array |
| Gene coverage note | Targeted coverage of >4,800 key genes; avg. resolution ~1.5 Mb |
| Data performance (typical) | Call rate ~99.7%; reproducibility ~99.99% |
| Optional version — Cytogenetics-8 | ~1.8M probes + 160K supplemental across >4,800 genes (adds cytogenetic content) |
| Optional version — Enhanced PGx-8 | >1.9M markers; PGx-enriched while retaining GDA backbone |
| Kit sizes (fixed content) | 16 / 48 / 96 / 384 samples per kit |
| Automation capability | Automated array loader; liquid-handling robots |
Related platform — Infinium Global Screening Array-24 (GSA-24)
For scalable, cost effective population-level genotyping, consider GSA-24, a 24-sample Infinium HTS array that combines multiethnic genome-wide content with clinical research variants. (Research use only)
Learn more → GSA-24 analysis service.
Applications and Research Use Cases
The Infinium Global Diversity Array-8 (GDA-8) enables population-scale projects that need consistent results across ancestries. CD Genomics applies the Illumina Infinium Global Diversity Array to deliver validated genotypes for discovery and translational research.
Population genomics and diversity mapping
Use the multiethnic scaffold for cross-population imputation, ancestry inference, and fine-mapping in global cohorts. This platform replaced Illumina's Multi-Ethnic arrays to improve coverage and portability across studies.
Genome-wide association studies (GWAS)
Run GWAS with ~1.8 M markers to detect trait-associated variants at scale. The array was selected for NIH All of Us, supporting very large cohorts.
Polygenic risk scores (PRS)
Derive PRS using genome-wide content and integrated array analysis software; cloud workflows are supported.
Cytogenetics and structural variation
Choose Infinium Global Diversity Array with Cytogenetics-8 for genome-wide CNV and LOH assessment, with added exonic probes across >4800 genes. Average cytogenetic resolution is reported around the megabase scale.
Pharmacogenomics (PGx)
Select Infinium Global Diversity Array with Enhanced PGx-8 to expand drug-gene content while retaining GDA-8's multiethnic backbone for PRS and disease studies.
Biobank and cohort genotyping
GDA-8 supports high weekly throughput suitable for population programs and longitudinal resources.
Workflow
- Sample Submission – blood, saliva, buccal swabs, FFPE, or genomic DNA.
- DNA Quality Control – concentration, purity, fragment size validation.
- Genotyping with GDA-8 – hybridization, staining, scanning on Illumina iScan.
- Data Processing – primary SNP calling, QC.
- Bioinformatics Analysis – GWAS, PRS, CNV, cytogenetic analysis, functional annotation.
- Data Delivery – results delivered securely with report & raw data files.
Data Analysis & Delivery
We process Infinium Global Diversity Array-8 (GDA-8) data end-to-end. Our pipeline converts raw intensities into curated, analysis-ready results for research use only.
Primary processing and QC
- Normalize intensities and perform genotype calling with standard thresholds.
- Report per-sample call rate, heterozygosity, and sex concordance checks.
- Provide per-marker metrics: call rate, Hardy–Weinberg p, duplicate concordance.
- Include representative Illumina Infinium Global Diversity Array cluster plots.
Population structure and imputation
- Compute PCA and relatedness for cohort quality control.
- Generate ancestry projections using established references.
- Prepare imputation-ready files aligned to your reference build.
- Optional phasing and imputation through secure cloud pipelines.
Association and PRS
- Run GWAS with covariate control and multiple-testing reporting.
- Deliver Manhattan and QQ plots plus summary statistics.
- Provide PRS using validated methods with model documentation.
- Supply cohort-level distributions and individual-level scores.
Cytogenetics and PGx options
- infinium global diversity array with cytogenetics 8: CNV and LOH calling.
- Segment files include coordinates, size, confidence, and gene overlap.
- infinium global diversity array with enhanced pgx 8: star-allele calls.
- Output phenotype tables and confidence scores for key pharmacogenes.
Data security and access
- Encrypted transfer via SFTP or secure project portal.
- Data retained on encrypted storage with controlled access.
- Optional long-term archiving under a data retention policy.
Why Choose CD Genomics
CD Genomics delivers reliable Infinium Global Diversity Array-8 (GDA-8) results at scale. Our team is fluent with the Illumina Infinium Global Diversity Array, from sample intake to interpretive reporting.
✅ Depth in multi-ethnic studies
Experienced with diverse cohorts and cross-population imputation.
Consistent pipelines preserve comparability across batches and centres.
✅ Assay craftsmanship and QC
Tight genotype-calling thresholds with documented controls.
Reproducible CNV and LOH calling for cytogenetics options.
✅ Scalable operations
High-throughput scheduling for biobanks and longitudinal projects.
Predictable turnaround with interim QC checkpoints.
✅ Custom content and analysis
Add up to 175k markers for project-specific hypotheses.
PRS, GWAS, and PGx reporting tailored to your endpoints.
✅ Security and compliance
Encrypted transfers, access control, and versioned pipelines.
Clear RUO positioning, audit-ready logs, and data retention options.
✅ Scientific partnership
Study design consultation and power guidance for GDA-8.
Publication-ready figures and method sections upon request.
Sample Requirements
| Category | Requirement | Notes |
|---|---|---|
| Sample types | Tissue, cells, FFPE, genomic DNA | Provide purified DNA where possible |
| DNA purity | OD260/280: 1.7–2.1; clear electrophoresis bands; > 10 kb; no obvious degradation | High-molecular-weight DNA preferred |
| DNA concentration | ≥ 50 ng/µL | Measured by fluorometry or spectrophotometry |
| Total DNA amount | ≥ 1 µg (high-quality samples acceptable down to 500 ng) | Send extra to cover QC/repeats if possible |
| Solvent / buffer | TE or ddH₂O | Nuclease-free, no carriers or detergents |
| Container | 1.5 mL microcentrifuge tube or 96-well plate | Use sealing film; ensure tight caps/heat seals |
| Short-term storage | 2–8 °C | Avoid freeze–thaw cycles |
| Long-term storage | ≤ −20 °C | −80 °C acceptable for archiving |
| Local transport | Cold packs/blue ice, 2–8 °C | Pack to prevent tube damage |
| Long-distance transport | Dry ice, ≤ −20 °C | Include absorbent material and manifest |
Tip: Label tubes or plate wells with unique IDs matching the sample manifest.
Demo
GWAS Manhattan plot from Infinium Global Diversity Array-8 cohort.
CNV and LOH tracks from infinium global diversity array with cytogenetics 8.
Representative SNP cluster plot from Illumina Infinium Global Diversity Array.
Polygenic risk score summary from infinium global diversity array-8 cohort.
FAQ
What is the Infinium Global Diversity Array-8 Kit?
A high-density, multiethnic genotyping BeadChip with ~1.83 M markers for genome-wide screening and diversity studies. It replaces Illumina's Multi-Ethnic arrays.
How does GDA-8 differ from the Infinium Global Diversity Array with Enhanced PGx-8?
Enhanced PGx-8 adds expanded pharmacogenomics content (>1.9 M markers) while retaining the GDA backbone for disease and diversity research. Choose it when drug-gene questions are in scope.
When should I choose the Infinium Global Diversity Array with Cytogenetics-8?
Select Cytogenetics-8 when genome-wide CNV/LOH assessment is required alongside SNP genotyping; it packages Infinium chemistry with cytogenetics-oriented content and documentation.
What is the role of microarray in cytogenetics?
Microarrays provide genome-wide detection of copy-number changes and allelic imbalance, enabling high-resolution cytogenetic screening and genotype–phenotype interpretation.
Does GDA-8 support PRS development and imputation?
Yes. The array was designed as a multiethnic scaffold for cross-population tagging; workflows also support array-based PRS in standard toolchains.
What deliverables can your team provide?
We return raw intensities and manifests (e.g., IDAT/GTC, product files), plus analysis-ready outputs per your scope.
Can I customise content?
Illumina provides add-on and "+" kit options to extend loci while using the same 8-sample format. We map these to your study endpoints.
Is this suitable for large cohorts and biobanks?
Yes. GDA-8 is positioned for population-scale studies and is widely used in multi-ancestry research programs.
Is the Global Diversity Array the successor to the Multi-Ethnic Global array?
Yes. Illumina lists GDA-8 as the recommended replacement.
How many markers are on the Global Diversity Array?
Approximately 1,825,277 fixed markers on the v1.0 BeadChip.
What is the difference between Cytogenetics-8 and Enhanced PGx-8?
Cytogenetics-8 emphasises CNV/LOH analysis; Enhanced PGx-8 expands pharmacogenomic loci while keeping the GDA backbone.
What files are available for downstream analysis?
Illumina provides support files (manifests, cluster files, demo data); we add genotype and CNV deliverables per scope.
Case Study: Analytical Validation of the Illumina Global Screening Array (GSA)
Cherukuri et al., Establishing analytical validity of BeadChip array genotype data by comparison to whole genome sequence and standard benchmark datasets, BMC Medical Genomics (2022)
1. Background
The study aimed to analytically validate the Illumina Global Screening Array (GSA) for clinical screening applications. Researchers sought to assess genotyping accuracy, positive predictive value (PPV), and overall platform reliability by comparing GSA calls to high-confidence reference datasets (whole-genome sequencing (rWGS) and 1000 Genomes Phase 3).
2. Methods
Samples: 263 Coriell samples genotyped in triplicate using the GSA and compared to rWGS and 1KG benchmarks.
Assessments:
Accuracy: Concordance with rWGS and 1KG.
Positive Predictive Value: Fraction of GSA assays with perfect PPV.
Evaluations also included performance across variant types (transitions vs. transversions), genomic complexity, and allele frequencies.
Figure 1. Analytical validation framework for the Global Screening Array, comparing triplicate GSA genotypes to rWGS and benchmark datasets (1KG, GIAB).
3. Results
High accuracy: GSA genotypes aligned with rWGS/1KG benchmarks at >99% concordance overall.
Robust PPV: Over 82% of GSA assays displayed perfect predictive value (PPV = 1).
Variant-type performance: Common variants and transitions performed particularly well. Performance dipped slightly for rare variants, transversions, and low-complexity regions—but still maintained >99% accuracy in most cases.
4. Conclusions
This validation confirms the GSA's analytical strength for clinical and research screening:
- Proven high accuracy and reliability across many variant types;
- Exceptional concordance with "gold standard" sequencing benchmarks;
- Suitable for genomic screening workflows, with known limitations for certain variant classes.
