Data Sheet: Genotyping

Infinium Multi-Ethnic AMR/AFR BeadChip®

A cost-effective array for understanding complex disease in Hispanic and African American
populations.
Introduction
The Infinium Multi-Ethnic AMR/AFR 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, multiethnicarray. With > 1.4 million expertly selected markers, the Infinium
Multi-Ethnic AMR/AFR BeadChip enables identification of genetic
associations with common and rare traits, providing insight acrossHispanic and African American populations to epidemiologists, healthcare researchers, population geneticists, and genomic researchers(Table 1–5).

Maximized Imputation Accuracy
Consortium partners developed content for the Infinium Multi-Ethnic
AMR/AFR BeadChip using tagging strategies with the power toperform more effective association studies in Hispanic and African
American populations. The novel algorithm selects population-specificand transethnic tag SNPs that maximize imputation accuracy, asimputation 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 AMR/AFR BeadChip Product Information
FeatureDescription

Total No. of Markers

1,430,141

Capacity for Custom BeadTypes

245,000

No. Samples per BeadChip

8DNA Input Requirement

200 ngAssay Chemistry

Infinium® LCGiScan® or HiScan® System

Instrument SupportSample Throughput~ 1067 samples/weekaiScan System
11.3 minScan Time per Sample

HiScan System
6.5 min

Data PerformanceValueb

Product Specification

Call Rate

99.87%> 99% avg.

Reproducibility

99.99%> 99.9%Log R Deviation

0.10< 0.30SpacingMeanMedian90th %cSpacing (kb)

2.05

0.89

5.17

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
prepared by methods other than standard Illumina protocols are excluded.

Expert-Selected Content
The Infinium Multi-Ethnic AMR/AFR 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 acrossHispanic and African American populations and impute variants in avast number of subpopulations.
The Infinium Multi-Ethnic AMR/AFR BeadChip contains thefollowing content:
••
•
•

•

Highly informative Hispanic and African American genome-wide tagSNPs from the Infinium HumanCore-24 BeadChip
African Diaspora Consortium Power Chip content identified
through sequencing of 692 individuals by CAAPA
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 Hispanic and African
Populations from 1kGP at Different MAF Thresholds
Minor Allele Frequency (MAF) Threshold
Populationa

0.5–1%

1–5%

≥ 5%

AFR

77.1%

89.0%

95.7%

AMR

81.3%

89.1%

96.8%

a. AFR: African; AMR: Ad-mixed American.1

Table 3: LD Mean r2 for Hispanic and African Populations from1kGP at Different MAF Thresholds
Minor Allele Frequency (MAF) Threshold
Population

0.5–1%

1–5%

≥ 5%

AFR

0.162

0.406

0.664

AMR

0.414

0.593

0.830

aa. AFR: African; AMR: Ad-mixed American.1Data Sheet: Genotyping
Table 4: Multi-Ethnic AMR/AFR BeadChip Marker Information

Table 5: Multi-Ethnic AMR/AFR BeadChip High-Value ContentContent

No. ofMarkers

Research Application / Note

ADME Core andExtended Genesa

14,981Drug metabolism and excretion

ADME Core andExtended Genesa+/- 10 kb

18,114

Drug metabolism and excretion(+ regulatory regions)

APOE

75

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

Blood Phenotype
Genes

2667

Blood phenotypes

COSMIC Genesa

754,633

Somatic mutations in cancer

GO CVS Genesa

200,973

Cardiovascular conditions

Database of
Genomic Variants

1,120,149

Genomic structural variation

eQTLs

6025

Genomic loci regulating mRNA
expression levels

Fingerprint SNPs

474

Human identification

HLA Genes

833

Disease defense, transplant
rejection, and autoimmune
disorders

Extended MHCa

16,050

Disease defense, transplant
rejection, and autoimmune
disorders

KIRa

117

Autoimmune disorders anddisease defense

Neanderthal SNPs

1705

Neanderthal ancestry andhuman population migration

NHGRI GWASCataloga

10,053Markers from published genomewide association studies

RefSeq 3’ UTRs

34,3983' untranslated regions of knowngenes

RefSeq 5’ UTRs

23,8185' untranslated regions of knowngenes

References

RefSeq All UTRs

56,579All untranslated regions ofknown genes

1.
2.

RefSeq830,329

All known genes

RefSeq +/-10 kb

933,485

All known genes +/- 10 kb toinclude regulatory regions

RefSeq Promoters

33,503

2 kb 5' of all known genes toinclude promoter regions

RefSeq Splice
Regions

4947

Variants at splice sites in all
known genes

Marker Category

No. of Markers

Exonic Markers

381,196

Intronic Markers

499,952Nonsense Markers

10,587

Missense Markers

318,693

Synonymous Markers

18,163

Mitochondrial Markers

645

Indels

11,779Sex ChromosomesX
39,165

Y2360

PAR / Homologous
3753

Ordering Information
Infinium Multi-Ethnic AMR/AFR-8 v1.0 Kit

Catalog No.

16 samples

20001090

48 samples

20001091

96 samples

20001092

384 samples

20001093

Infinium Multi-Ethnic AMR/AFR-8+ v1.0 Kita

Catalog No.

16 samples

20001094

48 samples

20001095

96 samples

20001096

384 samples

20001097

a. Enabled for additional custom content.

Learn More
To learn more about the Infinium Multi-Ethnic AMR/AFR v1.0
BeadChip and other Illumina genotyping products and services, 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 somatic
mutations 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. 370-2015-006 Current as of 29 February 2016