Design Markers | Process BeadChip | Analyze Data

Infinium™ Global Screening Array-24 v3.0
BeadChipA powerful, high-quality, cost-effective array for population-scale genetic studies.

Highlights• Optimized global content
Includes a multiethnic genome-wide backbone, clinicalresearch variants, QC markers, and custom add-on content• Broad clinical research applications
Enables genotyping for complex disease studies,
pharmacogenomics research, lifestyle and wellness
characterization, and more
• High-throughput workflow
Supports high-throughput processing of thousands ofsamples per week for population-scale studies• Robust, high-quality assay
Maintains the same data quality of Illumina genotyping arrayswith call rates > 99% and reproducibility > 99.9%
Figure 1: Infinium Global Screening Array-24 v3.0 BeadChip—Built on thetrusted 24-sample Infinium HTS platform.

Introduction
The Infinium Global Screening Array-24 v3.0 BeadChip is anadvanced genotyping array that provides a high-value, scalable, andcost-effective solution for population-scale genetic studies, variant
screening, and precision medicine research (Table 1). Using the iScan™
System, integrated analysis software, and the Infinium high-throughput
screening (HTS) assay, this high-density, 24-sample BeadChip(Figure 1) provides optimized content (Figure 2) for a broad range ofapplications, delivered with the same high-quality, reproducible datathat Illumina genotyping arrays have provided for over a decade. The
Global Screening Array Kit includes convenient packaging containing
BeadChips and reagents for amplifying, fragmenting, hybridizing,labeling, and detecting genetic variants using the high-throughput,streamlined Infinium workflow.
Table 1: Product informationa

Low–Frequency = 96,420

Not in 1000G = 3053
Rare = 7275
Not in 1000G = 36,986

Rare = 68,431
Common = 78,548

118,826
Low–Frequency = 11,477
QC = 9735

513,547

Common = 294,578

FeatureDescription

Species

Human

Total number of markersb

654,027

Capacity for custom bead types

100,000

Number of samples per BeadChip

24

DNA input requirement

200 ng genomic DNA

Assay chemistry

Infinium HTS

Instrument support

iScan System

Maximum iScan System sample
throughputa~5760 samples/week

Scan time per sample

1.3 minutes

Genome-Wide Backbone

Clinical Research

QC

Figure 2: Summary of content— Genome-wide content enables a broad
range of clinical research and genetic variant screening applications. Plotted in
the inner pie is the proportion of the array selected for genome-wide coverage,
clinical research, and quality control (QC). The outer ring summarizes theweighted reference global allele frequency for unique variants present in the 1000
Genomes Project (1000G).1 Variants not in 1000G are labeled. Counts represent
unique variants.

a. Approximate values, scan times, and maximum throughput may vary depending onlaboratory and system configurations.

For Research Use Only. Not for use in diagnostic procedures.

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Design Markers | Process BeadChip | Analyze Data

Table 2: High-value content
Content

No. ofmarkersa

Content

No. ofmarkers

Research application/note

ACMG2 59 2016 genecoverage

21,730GO9 CVS genes

105,219

Cardiovascular conditions

ACMG 59 all annotations

15,208

Database of
Genomic Variants10

507,399

Genomic structural variation

ACMG 59 pathogenic

7023

eQTLs11

2704

Genomic loci regulating mRNA expression levels

566

Human identification

Research application/note

Variants with known clinicalsignificance identified from clinical
WGS and WES samples

ACMG 59 likely
pathogenic

3039

ACMG 59 benign

567

gnomAD13 exome

64,575

WES and WGS results from unrelated individuals
from various studies

ACMG 59 likely benign

932

HLA genes14

455

Disease defense, transplant rejection, andautoimmune disorders

ACMG 59 VUS

2205

Extended MHC14c

8367

Disease defense, transplant rejection, andautoimmune disorders

ADME3 core andextended + CPIC genes

14,608Drug absorption, distribution,
metabolism, and excretion

KIR genes4

27

Autoimmune disorders and disease defense

ADME core andextended + CPIC genes+/- 10 kb

17,551

Includes regulatory regions

Neanderthal
SNPs151528

Neanderthal ancestry and human population
migration

AIMsb

2923

Ancestry-informative markers

Newborn/carrier
screening genecoverage

25,827

Genes associated childhood diseases includedin the TruSight™ Inherited Disease Sequencing
Panel19

APOE4

18

Cardiovascular disease, Alzheimer's
disease, and cognition

NHGRI-EBI GWAS
catalog16

16,160Markers from published GWAS

Blood phenotype genes5

1931

Blood phenotypes

PharmGKB17,18 all

4125
30

Fingerprint SNPs

12

ClinVar variants

45,998

PharmGKB level 1A

ClinVar pathogenic

15,213

PharmGKB level 1B

2

ClinVar likely pathogenic

6584

PharmGKB level 2A

17

ClinVar benign

7820

PharmGKB level 2B

60

ClinVar likely benign

4668

PharmGKB level 3

1300

ClinVar VUS

5548

PharmGKB level 4

154

COSMIC7 genes

301,888

RefSeq20 3' UTRs

14,313

3' untranslated regionsd

6

Relationships among variation,
phenotypes, and human healthSomatic mutations in cancer

Human genetic variation associated with drug
responses

CPIC8 all231

RefSeq 5' UTRs

6519

5' untranslated regionsd

CPIC-A

114

RefSeq All UTRs

20,214

Untranslated regionsd

RefSeq336,086

All known genes

RefSeq +/- 10 kb

392,003

Regulatory regionsd

RefSeq Promoters

14,976

2 kb upstream to include promoter regionsd

RefSeq Splice
Regions

3536

Variants at splice sitesd

CPIC-A/B

1

CPIC-B

17

CPIC-C

14

CPIC-C/D

15

CPIC-D

70

Variants with potential guidelines tooptimize drug therapy

a. The number of markers for each category may be subject to change
b. Based on internal calculations
c. Extended MHC is a 8 Mb regiond. Of all known genes
Abbreviations: ACMG: American College of Medical Genetics; ADME: absorption, distribution, metabolism, and excretion; AIM: ancestry-informative marker; APOE: apolipoprotein E; COSMIC:
catalog of somatic mutations in cancer; CPIC: Clinical Pharmacogenetics Implementation Consortium; EBI: European Bioinformatics Institute; eQTL: expression quantitative trait loci; gnomAD:
Genome Aggregation Database; GO CVS: gene ontology annotation of the cardiovascular system; GWAS: genome-wide association study; HLA: human leukocyte antigen; KIR: killer cell
immunoglobulin-like receptor; MHC: major histocompatibility complex; NHGRI: national human genome research institute; PharmGKB: Pharmacogenomics Knowledgebase; RefSeq: NCBI
Reference Sequence Database; UTR: untranslated region; VUS, variant of unknown significance; WES, whole-exome sequencing; WGS, whole-genome sequencing

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For Research Use Only. Not for use in diagnostic procedures.

Design Markers | Process BeadChip | Analyze Data

Table 3: Marker information
Marker categories

No. of markers

Exonic markersa

85,342Intronic markersa

262,173

Nonsense markersb

5904

Missense markersb

51,188

Synonymous markersb

9273

MItochondrial markersb

1138

Indelsc

10,118Sex chromosomesc

X

Y

PAR/homologous

27,1764138

879

a. RefSeq - NCBI Reference Sequence Database.20 Accessed May 2020.
b. Compared against the UCSC Genome Broswer.4 Accessed May 2020.
c. NCBI Genome Reference Consortium, Version GRCh37.21 Accessed May 2020.
Abbreviations: indel, insertion/deletion; PAR, pseudoautosomal region.

Widespread adoption
The Infinium Global Screening Array-24 v3.0 BeadChip builds on
the success of the consortium version of the product that has been
widely adopted by a community of human disease researchers, healthcare networks, consumer genomics companies, andgenomic service
providers. Over 15 million samples of the Global Screening Array havebeen ordered by a global community of users powering discovery
through collaboration and data sharing.

Optimized global and high-value content
The Infinium Global Screening Array-24 v3.0 BeadChip combines
highly optimized multiethnic genome-wide content, curated clinicalresearch variants, and QC markers for a broad range of clinicalresearch and variant screening applications (Table 2 and Table 3).
These applications include disease association and risk profilingstudies, pharmacogenomics research, disease characterization,
lifestyle and wellness characterization, and marker discovery incomplex disease research.

Expertly selected content empowering clinicalresearch applications
The clinical research content of the Infinium Global Screening Array-24
v3.0 BeadChip was designed through collaboration with medical
genomics experts using multiple annotation databases6-21 to create an
informative, cost-effective panel for clinical research applications (Table
2 and Figure 3).
Variants included on the array consist of markers with known
disease association based on ClinVar,6 the Pharmacogenomics
Knowledgebase (PharmGKB),17 and the National Human Genome
Research Institute (NHGRI)-EBI database. In addition to diseaseassociated markers, the Infinium Global Screening Array-24 v3.0
BeadChip contains imputation-based tagSNPs for HLA alleles,
extended MHC region, the KIR gene, and exonic content from thegnomAD database.13

For Research Use Only. Not for use in diagnostic procedures.

gnomAD | 64,575

NHGRI-EBI-GWAS-Catalog | 16,160

ClinVar | 45,998

MHC-HLA-KIR Coverage | 8454
PGx-PharmGKB | 4125

Figure 3: Clinical research content—Content was expertly selected fromscientifically recognized databases to create a highly informative array for clinicalresearch applications. Variant counts may be subject to change.

Broad spectrum of pharmacogenomics markers
and exonic content
The Infinium Global Screening Array-24 v3.0 BeadChip provides
coverage of pharmacogenomics variants associated with absorption,
distribution, metabolism, and excretion (ADME) phenotypes basedon PharmGKB17 and Clinical Pharmacogenetics Implementation
Consortium (CPIC) guidelines8 (Figure 4). It also features diverse exonic
content from the ExAC database,13 including both cross populationand population specific markers (Table 4) with either functionality orstrong evidence for association.

132
CPIC A-B

231
CPIC all4317
PGx public database variants

14,608
Genome-wide PGx coverage
Figure 5: Broad spectrum of pharmacogenomics markers—Clinical researchcontent features an extensive list of pharmacogenomics markers selected basedon CPIC guidelines and the PharmGKB database.16 PGx public databasevariants, variants annotated in PharmGKB, PharmVar, CPIC; Genome-wide
PGx coverage, includes markers located in an extended ADME genes or CPIC
level A genes including targeted imputation tag SNPs and CPIC level A copy
number variation (CNV) tags.

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Table 4: Global exonic content
Population(s)aBlood phenotype (1541)

No. of markers

EUR

52,980EAS31,375AMR

45,977

AFR

43,122SAS

Fingerprinting (420)
Sex determination (2354)

QC markers

Pseudo autosomal regions (879)
Ancestry informative (2867)
Mitochondrial (1138)

40,298Human linkage (919)

a. www.internationalgenome.org/category/population

Forensic sequencing (6)Extensive range of disease categories covered
Clinical research content on the Infinium Global Screening Array-24
v3.0 BeadChip enables validation of disease associations, risk
profiling, preemptive screening research, and pharmacogenomics
studies. Variant selection includes a range of pathology classifications
based on ClinVar and American College of Medical Genetics (ACMG)
annotations (Figure 5A).2 The BeadChip contains extensive coverageof phenotypes and disease classifications based on ClinVar (Figure 5B)
and the NHGRI-EBI GWAS catalog (Figure 6).
Biological process

441 462

Body measurement
CancerCardiovascular disease or measurement
Digestive system disorder
Hematological measurement
Immune system disorder
Inflammatory measurement

1282
902
825

5147

786

Lipid or lipoprotein measurement
Liver enzyme measurement
Metabolic disorder843

Neurological disorder
Other disease, measurement, or trait
Response to drug

703
1365

425

613
44

75

Figure 7: QC markers—QC variants on the array enable various capabilities forsample tracking such as sex determination, continental ancestry, and humanidentifcation and more.

Flexible content options
The Infinium Global Screening Array-24 v3.0 BeadChip can becustomized to incorporate up to 100,000 custom bead types or apredesigned content panel (Table 5). The DesignStudio™ Microarray
Assay Designer can be used to design targets such as SNPs, copy
number variants (CNVs), and indels.
Table 5: Flexible content options
Compatible content

No. ofmarkers

Custom content

Custom design virtually any target (eg,~100,000 SNP, CNV, indel) using the DesignStudio
Microarray Assay Designera

Multi-disease drop-in
panel~50,000

Fine-mapping content derived fromexome sequencing and meta analysisof phenotypespecific consortia focusedon the following traits: psychiatric,
neurological, cancer, cardiometabolic,autoimmune, anthropometric~30,000

Markers from the Infinium PsychArray-24
BeadChipb associated with common
psychiatric disorders including,schizophrenia, bipolar disorder, autism
spectrum disorders, attention deficit
hyperactivity disorder, major depressive
disorders, obsessive compulsive disorder,anorexia, Tourette’s syndrome

Figure 4: NHGRI disease categories—Global Diversity Array clinical researchcontent features markers across a broad range of disease coategories based on
the NHGRI database.

QC markers for sample identification, tracking,and stratification
The Infinium Global Screening Array-24 v3.0 BeadChip includes
quality control (QC) markers for large-scale studies, enabling sample
identification, tracking, ancestry determination, and stratification(Figure 7).

A
VUS
Likely Benign
BenignLikely Pathogenic
Pathogenic

Infinium PsychArray-24
focused content panel

Description

a. www.illumina.com/informatics/sample-experiment-management/custom-assay-design.
html
b. www.illumina.com/products/by-type/microarray-kits/infinium-psycharray.html

B

2205
5548

166

ClinVar/ACMG 59 gene list
ClinVar full database

1020

932

Endocrine/metabolic

2574

892

CancerNewborn
Health risk factors

4668
567

Neurological diseases

7829

Cardiovascular andhemtological diseases
Other

2282

3039
6584

2825

7023
15,21302000 4000 6000 8000 10000 12000 14000

2389

Number of variants

Figure 6: Broad coverage of disease catogories—(A) Variants sorted by range of pathology classifications according to ClinVar American College of Medical Genetics(ACMG) annotations. (B) Global Diversity Array clinical research content by category within the ClinVar database. Variant counts may be subject to change.

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For Research Use Only. Not for use in diagnostic procedures.

Design Markers | Process BeadChip | Analyze Data

High-throughput workflow

Day 1

The Infinium Global Screening Array-24 v3.0 BeadChip uses the highly
scalable Infinium 24-sample Infinium HTS format, which enables
laboratories to efficiently scale as needed. For flexible throughput
processing, the Infinium HTS assay provides the capability to run
hundreds to thousands of samples per week. The Infinium HTS assay
provides a rapid, three-day workflow that allows users to gather andreport data quickly (Figure 8). For labs interested in quickly scaling or
increasing efficiency and operational excellence, the Illumina ArrayLab
Consulting Service offers customized solutions.

Day 2

Call rate

99.5%> 99.0% avg

Reproducibility

99.99%> 99.90%

Log R deviation

0.15c< 0.30 avgd

Mean

Median90th%c

4.4

2.3

10.7

a. Values are derived from genotyping 1725 HapMap reference samples.
b. Excudes Y chromosome markers for female samples.
c. Based on results from GenTrain sample set.
d. Value expected for typical projects using standard Illumina protocols. Tumor samples
and samples prepared by methods other than standard Illumina protocols are excluded.

High imputation accuracy for global
populations
High imputation accuracy provides increased power to support
population-scale disease research and population-specific causal
variant detection. Leveraging available whole-genome reference datafrom over 26 global populations in 1000G Phase 3,1 the genome-wide
content on the Infinium Global Screening Array-24 v3.0 BeadChip has
been selected to generate high imputation accuracy for low-frequency
and common variants—minor allele frequencies (MAF) of > 1% (Table
7, Table 8).

Imputation calculation methodology
Imputation performance is measured by simulating Global Screening
Array-24 v3.0 genotyped variants on 1000G samples (Table 7, Table
8). A random sample from all 26 1000G global populations wereselected, stratified by super population, and tested against variants on
the array. The remaining 1000G samples were treated as the reference(1000G data is already phased using BEAGLE). Minimac3 was used
to perform imputation and imputation quality was measured using thecorrelation r2 from the info file produced by minimac3.

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3

Precipitation

4

Resuspension5

Hybridization

6

Extension and staining

7

Imaging8

Analysis and genotyping

Overnight incubation

Day 3

Spacing
Spacing (kb)Fragmentation

DNA is amplified andincubated overnight.

DNA is enzymaticallyfragmented.

DNA is alcohol precipitated.

Safe stopping point*

Table 6: Data performance and spacing
Product specificationb

2

Safe stopping point*

The Infinium Global Screening Array-24 v3.0 BeadChip uses trusted
Infinium assay chemistry to deliver the same high-quality, reproducible
data (Table 6) that Illumina genotyping arrays have provided for overa decade. The Infinium product line provides high call rates and highreproducibility for numerous sample types including, saliva, blood,solid tumors, fresh frozen, and buccal swabs. It is compatible with theInfinium FFPE QC and DNA Restoration Kits, enabling genotyping offormalin-fixed, paraffinembedded (FFPE) samples. In addition, the highsignal-to-noise ratio of the individual genotyping calls from the Infinium
assay provides access to genome-wide copy CNV calling.

ValueaAmplification

Overnight incubation

Robust and trusted, high-quality assay

Data performance1*If needed, users can stop at
this point and resume theworkflow on the next day.

DNA is resuspended.

Samples are hybridized
to BeadChip.

Samples undergo enzymaticbase extension andfluorescent staining.

BeadChips are imaged
by iScan System.

Illumina software automatically
performs analysis andgenotype calling.

Figure 8: The Infinium 24-sample format workflow—The Infinium HTS format
provides a rapid three-day workflow with minimal hands-on time.

Table 7: Imputation accuracy from 1000G at various MAF
thresholds
Population

Imputation accuracy
MAF ≥ 5%

MAF ≥ 1%

MAF 1–5%

AFR

0.86

0.84

0.80

AMR

0.90

0.83

0.70

EAS

0.84

0.81

0.72

EUR

0.88

0.86

0.79

SAS

0.91

0.87

0.77

a. Compared against Phase 3, version 5 of the 1000G. www. www.internationalgenome.
org. Accessed May 20. 2020. Imputed using minimac3.
b. www.internationalgenome.org/category/population

Table 8: Number of markers imputed at r2 ≥ 0.80 from 1000Ga
Populationb

No. of imputed markers
MAF ≥ 5%

MAF ≥ 1%

MAF 1–5%

AFR

7,186,582

12,181,676

4,995,094

AMR

5,911,729

8,411,902

2,500,173

EAS

4,464,253

5,768,496

1,304,243

EUR

5,512,064

7,542,581

2,030,517

SAS

6,005,008

8,179,336

2,174,328

a. Compared against Phase 3, version 5 of the 1000G. www. www.internationalgenome.
org. Accessed May 20. 2020. Imputed using minimac3.
b. www.internationalgenome.org/category/population

For Research Use Only. Not for use in diagnostic procedures.

Design Markers | Process BeadChip | Analyze Data

Summary

References

The Infinium Global Screening Array-24 v3.0 BeadChip provides a
cost-effective solution for population-scale genetic studies, variant
screening, and precision medicine research. It builds on the successof the consortium version of the product and has been widely adopted
with over 15 million samples ordered worldwide. Using the proveniScan System, Infinium HTS Assay, and integrated analysis software,
the high-density, 24-sample Infinium Global Screening Array-24 v3.0
BeadChip provides optimized content for a broad range of clinicalresearch applications.

1.

Ordering Information
Order Illumina Infinium products online at www.illumina.com
Infinium Global Screening Array-24 v3.0 BeadChip Kit

Catalog no.

48 samples

20030770

288 samples

20030771

1152 samples

20030772

Infinium Global Screening Array-24+ v3.0 BeadChip Kita

Catalog no.

48 samples

20030773

288 samples

20030774

1152 samples

20030775

a. Enabled for custom content

Learn more
Learn more about the Infinium Global Screening Array-24 v3.0
BeadChip and other Illumina genotyping products and services atwww.illumina.com/techniques/microarrays.html.
For labs interested in higher throughput processing with the Infinium
Global Screening Array-24 v3.0, contact your local account manager
for more information about Infinium HTS Extra high-throughput
kit configurations.

The 1000 Genomes Project. www.1000genomes.org. Accessed May 20,
2020.
2. ACMG Recommendations for Reporting of Incidental Findings in Clinical
Exome and Genome Sequencing. www.ncbi.nlm.nih.gov/clinvar/docs/
acmg/. Accessed May 20, 2020.
3. PharmaADME Gene List. www.pharmaadme.org. Accessed May 20, 2020.
4. University of California, Santa Cruz (UCSC) Genome Browser. genome.ucsc.
edu. Accessed May 20, 2020.
5. NCBI Reference Sequence Blood Group Antigen Gene Mutation Database.
www.ncbi.nlm.nih.gov/projects/gv/rbc/xslcgi.fcgi?cmd=bgmut/systems.
Accessed May 20, 2020.
6. ClinVar Database. www.ncbi.nlm.nih.gov/clinvar. Accessed May 20, 2020.
7. Catalog of somatic mutations in cancer. cancer.sanger.uk/cosmic. Accessed
May 20, 2020.
8. Clinical Pharmacogenetics Implementation Consortium (CPIC). cpicpgx.org.
Accessed May 20, 2020.
9. Gene Ontology Consortium. www.geneontology.org. Accessed May 20,
2020.
10. Database of Genomic Variants. dgv.tcag.ca/dgv/app/home. Accessed May
20, 2020.
11. NCBI eQTL Database. www.ncbi.nlm.nih.gov/projects/gap/eqtl/index.cgi.
Accessed May 20, 2020.
12. The Allele Frequency Database. alfred.med.yale.edu/alfred/snpSets.asp.
Accessed May 20, 2020.
13. gnomAD, Genome Aggregation Database. gnomad.broadinstitute.org.
Accessed May 20, 2020.
14. de Bakker PIW, McVean G, Sabeti PC, et al. A high-resolution HLA and
SNP haplotype map for disease association studies in the extended human
MHC. Nat Genet. 2006;38:1166–1172.
15. Neanderthal Genome Browser. neandertal.ensemblgenomes.org/index.html.
Accessed May 20, 2020.
16. National Human Genome Research Institute. www.genome.gov/. Accessed
May 20, 2020.
17. PharmGKB, The Pharmacogenomics Knowledgebase. www.pharmgkb.org.
Accessed May 20, 2020.
18. PharmGKB, Clinical Annotation Levels of Evidence. www.pharmgkb.org/
page/clinAnnLevels. Accessed May 20, 2020.
19. Illumina (2017). TruSight Inherited Disease Sequencing Panel Data Sheet.
Accessed May 20, 2020.
20. RefSeq - NCBI Reference Sequence Database. www.ncbi.nlm.nih.gov/
refseq. Accessed May 20, 2020.
21. NCBI Genome Reference Consortium. Version GRCh37. www.ncbi.nlm.nih.
gov/grc/human. Accessed May 20, 2020.
22. Illumina (2012) Infinium FFPE QC and DNA Restoration Kit. Accessed May
20, 2020.

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