Infinium Global Diversity Array with Enhanced PGx

Infinium Global Diversity Array (GDA) with Enhanced PGx is the most comprehensive genotyping microarray on the market for pharmacogenomics research.

Overview

The Infinium Global Diversity Array (GDA) with Enhanced PGx-8 v1.0 BeadChip supports pharmacogenomics (PGx) research in diverse populations as well as polygenic risk score development, ancestry determination, and genetic disease research. 

  • The largest genome-wide backbone of any array developed for PGx research

  • > 44K genome-wide PGx markers spanning > 2K PGx targets

  • Automated, scalable 3-day workflow with minimal hands-on time

  • Robust CNV detection and targeted amplification to allow PGx pseudogene disambiguation

  • PGx star allele and variant coverage across 1700+ targets for over 50 genes with optional DRAGEN Array secondary analysis

Comprehensive coverage

The GDA with Enhanced PGx offers coverage of > 6K annotated variants from public PGx databases like PharmGKB1, CPIC2, PharmVar3, and ClinVar4, including hard-to-discern genes like CYP2D6, CYP2B6, and TPMT.  

Exceptional exonic content across populations

The GDA with Enhanced PGx features improved tagging in exonic regions and enriched coverage to map loci from genome-wide association studies (GWAS) with previously identified disease or trait associations. 

QC markers for sample identification

The BeadChip includes quality control (QC) markers for large-scale studies, enabling sample identification, tracking, ancestry determination, stratification, and more. 


Specifications


Required products

Match your chosen kit size to the number of samples you run at a time. Each kit is processed as a single batch and is not designed to be divided across multiple experiments. If you are processing several low-throughput batches, order multiple small kits. The fixed content kits include the interpretation report with star allele calls and metabolizer status.

Custom add-on content is available.

/ Results

Applications

The Infinium Global Diversity Array with Enhanced PGx is designed to support pharmacogenomics (PGx) research, polygenic risk score development, ancestry determination, and genetic disease research.

Example workflow

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Infinium Global Diversity Array with Enhanced PGx

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Infinium Global Diversity Array with Enhanced PGx Infinium Global Diversity Array-8 Kit Infinium Global Screening Array-24 Kit
Assay type Infinium LCG Infinium LCG Infinium HTS
Automation capability Liquid handling robots, Automated array loader Liquid handling robots, Automated array loader Liquid handling robots, Automated array loader
Description

The Infinium Global Diversity Array with Enhanced PGx is built on an 8-sample BeadChip and contains > 1.9M markers. It is the most comprehensive genotyping microarray commercially available for pharmacogenomic (PGx) research, and also supports disease and diversity studies and other applications.  

The 8-sample Infinium Diversity Array provides targeted coverage of more than 4800 key genes across the genome. Approximately 1.8M markers are included on the BeadChip for high exonic coverage in regions of disease relevance, providing highly accurate copy number variation calls, and an average resolution of 1.5Mb.

The Infinium Global Screening Array-24 Kit is an economical genotyping array for population-scale genetics, translational research, variant screening studies, and precision medicine research, combining optimized multiethnic genome-wide content, curated clinical research variants, and QC markers.

Input quantity 200 ng DNA 200 ng DNA 200 ng DNA
Instruments iScan System iScan System iScan System
Method Genome-wide genotyping array Genome-wide genotyping array High-throughput genotyping array, Genome-wide genotyping array
Nucleic acid type DNA DNA DNA
Number of markers 1,933,117 markers in total; custom add-on capacity of 175,000

1,825,277 fixed markers. Custom marker add-on capacity: Up to 175K.

654,027 fixed markers. Custom marker add-on capacity: Up to 100K. 

Number of samples 8 samples per array 8 samples per array 24 samples per array
Sample throughput ~1728 samples per week ~1728 samples per week ~5760 samples per week
Specialized sample types Blood Blood, FFPE Tissue, Buccal Swabs, Saliva Blood, FFPE Tissue, Buccal Swabs, Saliva
Species category Human Human Human
Technology Microarray Microarray Microarray
Variant class Single nucleotide polymorphisms (SNPs), Chromosomal abnormalities, Insertions-deletions (indels), Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Chromosomal abnormalities, Structural variants, Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Structural variants, Copy number variants (CNVs)

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Figures

Infinium Global Diversity Array with Enhanced PGx content

Inner pie shows the proportion of the array selected for genome-wide coverage, clinical research, and quality control (QC). Outer ring shows the weighted reference global allele frequency for unique variants present in 1kGP.5 Variants not in 1kGP are labeled. Counts represent unique variants.

Broad spectrum of pharmacogenomics markers

Clinical research content based on CPIC guidelines and PharmGKB database.1,2 Includes PGx public database variants, variants annotated in PharmGKB, PharmVar,3 CPIC, genome-wide PGx coverage, extended ADME genes, CPIC level A genes, including targeted imputation tag SNPs, and CPIC level A CNV tags.

Disease research content covering diverse populations

The Infinium Global Diversity Array with Enhanced PGx includes extensive coverage of numerous phenotypes and disease classifications based on (A) ClinVar categories and (B) NHGRIGWAS categories.

QC markers

QC variants on the Infinium Global Diversity Array with Enhanced PGx enable various capabilities for sample tracking such as sex determination, continental ancestry, human identification, and more.

Data performance and spacing

Trusted Infinium chemistry delivers the same high-quality, reproducible data that Illumina genotyping arrays have delivered for > 10 years. The high signal-to-noise ratio of the individual genotyping calls from the Infinium assay provides access to genome-wide copy CNV calling.

Data performance Valuea Product specificationb
Call rate 99.7% > 99.0% Avg
Reproducibility 99.99% > 99.90%
Spacing    
Spacing (kb) Mean Median 90th%c
1.53 0.61 3.91

a. Values are derived from genotyping 2228 HapMap reference samples

b. Excudes y chromosome markers for female samples

c. Based on results from Gentrain sample set

Resources

Learn how the Infinium Global Diversity Array with Enhanced PGx-8 v1.0 BeadChip is uniquely suited for pharmacogenomics research applications.

Fixed content (2)

Infinium Global Diversity Array with Enhanced PGx-8 v1.0 Kit (48 Samples)

20044822

Includes six, 8-sample BeadChips and reagents for amplifying, fragmenting, hybridizing, labeling, and detecting 48 DNA samples. Requires 200 ng DNA for input. Each kit is processed as a single batch.

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Infinium Global Diversity Array with Enhanced PGx-8 v1.0 Kit (384 Samples)

20044823

Includes 48, 8-sample BeadChips and reagents for amplifying, fragmenting, hybridizing, labeling, and detecting 384 DNA samples. Requires 200 ng DNA for input. Each kit is processed as a single batch.

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Add-on content (2)

Infinium Global Diversity Array with Enhanced PGx-8+ v1.0 Kit (48 Samples)

20048347

Includes six, 8-sample BeadChips and reagents for amplifying, fragmenting, hybridizing, labeling, and detecting 48 DNA samples. Customize content with an additional ≤ 175K markers using DesignStudio or select from a list of add-on content available as boosters. Requires 200 ng DNA for input. Each kit is processed as a single batch.

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Infinium Global Diversity Array with Enhanced PGx-8+ v1.0 Kit (384 Samples)

20048348

Includes 48, 8-sample BeadChips and reagents for amplifying, fragmenting, hybridizing, labeling, and detecting 384 DNA samples. Customize content with an additional ≤ 175K markers using DesignStudio or select from a list of add-on content available as boosters. Requires 200 ng DNA for input. Each kit is processed as a single batch.

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Software and informatics options (4)

DRAGEN Array Cloud - star allele annotation

20109886

Per sample analysis quota for star allele calling using DRAGEN Array Cloud. One per sample analysis quota is needed per sample analyzed for star allele calling using the analysis type, DRAGEN Array – PGx – star allele calling. DRAGEN Array Cloud provides analysis kickoff using BaseSpace Sequence Hub. The BaseSpace Sequence Hub access is facilitated by an Illumina Connected Analytics (Basic, Professional, or Enterprise) annual subscription. iCredits are used to store data on the cloud platform.

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DRAGEN Array Local - star allele annotation

20109885

Per sample analysis quota for star allele calling using DRAGEN Array Local. One per sample analysis quota is needed per sample analyzed for star allele calling using the star-allele call subcommand. DRAGEN Array Local is a command-line software with no FPGA hardware or specialized server required and is downloadable from the Illumina Support Site. Internet is required for per sample quota check.

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ICA Basic Annual Subscription

20044874

Illumina Connected Analytics (ICA) Basic Annual Subscription. This product includes 1 year of access to ICA Basic, including sequencing instrument connectivity, data management capabilities, and access to pre-packaged analysis tools.

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Illumina Analytics - 1 iCredit

20042038

iCredits are used for data storage and analysis on either BaseSpace Sequence Hub or Illumina Connected Analytics.

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Services (1)

Infinium® Assay: An Introduction – Customer Site

20015273

Three-day, hands-on instruction at customer site to familiarize users with the essential steps in the Infinium protocol. Course provides hands-on training in sample and BeadChip preparation, sample scanning using the iScan System, and primary data evaluation and analysis using array analysis software.

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Selection summary

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FAQ

The GDA with Enhanced PGx is ideal for clinical and translational researchers interested in PGx research, polygenic risk score development, genetic disease research, ancestry determination, and more. PGx research aims to enable physicians to tailor treatment through medication substitution or dosage augmentation and reduce potential risks, resulting in lower medical costs, shorter hospital stays, and improved medication safety and efficacy.

The GDA with Enhanced PGx offers genome-wide coverage of > 44K ADME markers, including critical PGx genes such as CYP2D6, compared with ~31K genome-wide ADME markers on the GDA. It also includes a targeted gene amplification step for accurate genotyping of critical genes such as CYP2D6, CYP2B6, and TPMT. > 6K variants from globally recognized PGx databases including PharmGKB, CPIC, ClinVar, and PharmVar are also included.

The GDA with Enhanced PGx workflow contains an additional step for targeted gene amplification (TGA) to disambiguate pseudogenes. The protocol requires a thermal cycler on day 1. On day 2, the TGA reaction product is added to the whole genome amplification (WGA) reaction product and the remaining workflow steps proceed like the standard GDA, beginning with fragmentation. The overall workflow time is similar for both assays.

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References

1. PharmGKB, The Pharmacogenomics Knowledgebase. pharmgkb.org. Accessed January 23, 2020.

2. Clinical Pharmacogenetics Implementation Consortium (CPIC). cpicpgx.org. Accessed January 23, 2020.

3. PharmVar, Pharmacogene Variation Consortium. pharmvar.org. Accessed January 23, 2020.

4. ClinVar Database. ncbi.nlm.nih.gov/clinvar. Accessed January 23, 2020.

5. European Bioinformatics Institute. 1000 genomes.org. Accessed January 23, 2021.

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