Data Sheet: Genotyping

Infinium Multi-Ethnic EUR/EAS/SAS BeadChip®

A cost-effective array for understanding complex disease in European, East Asian, and South
Asian populations.
Introduction
The Infinium Multi-Ethnic EUR/EAS/SAS BeadChip harnesses content
from Phase 3 of the 1000 Genomes Project (1kGP)1, Consortium
on Asthma among African-ancestry Populations in the Americas(CAAPA), Population Architecture using Genomics and Epidemiology(PAGE), T2D-Genes Consortium, OMIM, ClinVar, ACMG, carrier
screening panels, and other resources to create a multipurpose,
multiethnic array. With > 1.4 million expertly selected markers, theInfinium Multi-Ethnic EUR/EAS/SAS BeadChip enables identificationof genetic associations with both common and rare traits providing
insight across European, East Asian, and South Asian populations toepidemiologists, health care researchers, population geneticists, andgenomic researchers (Table 1–5).

Maximized Imputation Accuracy
Consortium partners developed content for the Infinium Multi-Ethnic
EUR/EAS/SAS BeadChip using tagging strategies with the power toperform more effective association studies in European, East Asian,and South Asian populations. The novel algorithm selects populationspecific and transethnic tag SNPs that maximize imputation accuracy,
as imputation has become a standard practice in the interpretation ofgenotyping data and allows for more accurate statistical inference ofgenotypes not directly genotyped.

Table 1: Multi-Ethnic EUR/EAS/SAS BeadChip Product
Information
FeatureDescription

Total No. of Markers

1,475,140

Capacity for Custom Markers

245,000

No. Samples per BeadChip

8DNA Input

200 ngAssay Chemistry

Infinium® LCG
iScan® or HiScan® System

Instrument Support
Sample Throughput~ 1067 samples/week

Scan Time per Sample

iScan System
11.3 min

Data Performance

Valueb

Product Specification

Call Rate

99.87%> 99% avg.

Reproducibility

99.99%> 99.9%0.10< 0.30aLog R Deviation

HiScan System
6.5 minSpacing

MeanMedian90th %c

Spacing (kb)

1.98

0.92

4.94

a. Estimated sample throughput based on use of 1 HiScan System, 1 AutoLoader 2.x, 1Tecan robot, and a 5-day work week.
b. Values are derived from genotyping 708 HapMap reference samples.
c. Value expected for typical projects using standard Illumina protocols. Tumor samples
and samples prepared by methods other than standard Illumina protocols are excluded.

Expert-Selected Content
The Infinium Multi-Ethnic EUR/EAS/SAS BeadChip combines
expertly selected markers and content from the most popular Illuminacommercial arrays with the most current genomic information.
Researchers can detect both common and rare variants acrossEuropean, East Asian, and South Asian populations and imputevariants in a vast number of subpopulations.
The Infinium Multi-Ethnic EUR/EAS/SAS BeadChip contains thefollowing content:••••Highly informative European, East Asian, and South Asian genomewide tag SNPs from the Infinium HumanCore-24 BeadChip
Genome-wide coverage for diverse populations selected by PAGE
using a new cross-population tagging strategy
Total exonic content of > 380,000 markers including the Infinium
Exome-24 BeadChip content and Multiethnic exome content
designed by PAGE
Over 17,000 variants chosen to be relevant to clinical andpharmacogenetic studies and 23,000 hand-curated variants
picked for functional, immunological, oncological, ancestry, andforensic applications

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

Table 2: Imputation Accuracy for European, East Asian,and South Asian Populations from 1kGP at Different MAFThresholds
Minor Allele Frequency (MAF) Threshold
Population

0.5–1%

1–5%

≥ 5%

EAS

57.3%

82.4%

96.3%

EUR

70.2%

87.9%

97.1%

SAS

61.5%

84.7%

96.5%

ba. EAS: East Asian; EUR: European; SAS: South Asian.1

Table 3: LD Mean r2 for European, East Asian, and South Asian
Populations from 1kGP at Different MAF Thresholds
Minor Allele Frequency (MAF) Threshold
Populationa

0.5–1%

1–5%

≥ 5%

EAS

0.300

0.636

0.873

EUR0.307

0.616`

0.870

SAS0.302

0.609

0.854

a. EAS: East Asian; EUR: European; SAS: South Asian.1

Data Sheet: Genotyping
Table 4: Multi-Ethnic EUR/EAS/SAS BeadChip MarkerInformation

Table 5: Multi-Ethnic EUR/EAS/SAS BeadChip High-Value
ContentContent

No. ofMarkers

Research Application / Note

ADME Core andExtended Genesa

14,342

Drug metabolism and excretion

ADME Core andExtended Genesa+/- 10 kb

17,598Drug metabolism and excretion(+ regulatory regions)

APOE

73

Cardiovascular disease,
Alzheimer's disease,immunoregulation, and cognition

Blood Phenotype
Genes2754

Blood phenotypes

COSMIC Genesa

774,774

Somatic mutations in cancer

GO CVS Genesa

231,232

Cardiovascular conditions

Database of
Genomic Variants

1,155,179

Genomic structural variation

eQTLs

6091

Genomic loci regulating mRNA
expression levels

Fingerprint SNPs

475

Human identification

HLA Genes

846

Disease defense, transplant
rejection, and autoimmune
disorders

Extended MHCa

16,499Disease defense, transplant
rejection, and autoimmune
disorders

KIRa

120

Autoimmune disorders anddisease defense

Neanderthal SNPs

1816

Neanderthal ancestry and humanpopulation migration

NHGRI GWASCataloga

10,024Markers from published genomewide association studies

RefSeq 3’ UTRs

34,396

3' untranslated regions of known
genes

RefSeq 5’ UTRs

23,9125' untranslated regions of known
genes

References

RefSeq All UTRs

56,624

All untranslated regions of known
genes

1.
2.

RefSeq852,999

All known genes

RefSeq +/-10 kb

959,082

All known genes +/- 10 kb toinclude regulatory regions

RefSeq Promoters

33,940

2 kb 5' of all known genes toinclude promoter regions

RefSeq SpliceRegions

5087

Variants at splice sites in allknown genes

Marker Category

No. of Markers

Exonic Markers

381,752

Intronic Markers

522,294

Nonsense Markers

10,826

Missense Markers

318,990

Synonymous Markers

18,228

Mitochondrial Markers

645

Indels11,871Sex ChromosomesX
39,507Y
1598

PAR / Homologous
265

Ordering Information
Infinium Multi-Ethnic EUR/EAS/SAS-8 v1.0 Kit

Catalog No.

16 samples

2000110048 samples

20001101

96 samples

20001102384 samples

20001103

Infinium Multi-Ethnic EUR/EAS/SAS-8+ v1.0 Kit

Catalog No.

16 samples

20001104

48 samples

20001105

96 samples

20001106384 samples

20001107

aa. Enabled for additional custom content.

Learn More
To learn more about the Infinium Multi-Ethnic EUR/EAS/SAS v1.0
BeadChip, visit
www.illumina.com/techniques/popular-applications/genotyping.html

3.

1000 Genomes (www.1000genomes.org). Accessed July 21, 2015.
COSMIC: Catalogue of somatic mutations in cancer (http://cancer.sanger.
ac.uk/cosmic). Accessed July 21, 2015.
Gene Ontology Consortium (www.geneontology.org). Accessed July 21,
2015.

a. ADME: absorption, distribution, metabolism, and excretion; COSMIC: catalog of somaticmutations in cancer2; GO CVS: Gene Ontology annotation of the cardiovascular system3;
eQTL: expression quantitative trait loci; HLA: human leukocyte antigen; KIR: killer cell
Ig-like receptor; MHC: major histocompatibility complex; NHGRI: national human genome
research institute.

Illumina • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
For Research Use Only. Not for use in diagnostic procedures.
© 2016 Illumina, Inc. All rights reserved. Illumina, HiScan, Infinium, iScan, and the pumpkin orange color are trademarks of Illumina, Inc. and/or its affiliate(s) in the U.S. and/or other countries. Pub. No. 370-2015-005 Current as of 25 January 2016