Specifications

Specifications

HumanExome BeadChip Content Specifications

Marker Categories Values
Total markers > 240,000
Number of unique RefSeq entries covered by at least one probe > 20,000
Nonsynonymous SNPs (NCBI) 219,621
SNPs in splice sites 10,675
Stop variants 5,637
SNPs in promoter regions 7,012
SNPs in extended MHC region 5,158
GWAS tag markers* 4,761
HLA tags 2,061
Ancestry informative markers 3,468
Identity by descent markers 3,369
X / Y / mitochondrial 470 / 101 / 177
Indels 180
% Variation Captured
(r2 > 0.8)
Fraction
MAF > 5.0%  0.10
MAF > 2.5%  0.096
MAF > 1.0% 0.088

* Disease-associated tag markers identified from recent GWAS.

The exome content provides focused coverage of exonic regions and doesnot provide broad genomic coverage outside of coding regions. To see specifications for genome-wide content on the HumanOmniExpressExome or HumanOmni5Exome BeadChips, please see the HumanOmniExpress or HumanOmni5 BeadChip data sheets, respectively 1-2.

HumanOmni5-Quad BeadChip Product Information

BeadChip Content Markers per Sample
Total Fixed Markers 4,301,331
Custom Markers up to 500,000
Feature Description
Number of Samples per BeadChip 4
DNA Requirement 400 ng
Assay Infinium LCG Quad
Instrument Support HiScanSQ or iScan
Sample Throughput* > 460 samples / week
Scan Time / Sample 15 minutes (HiScan)
25 minutes (iScan)

% Variation Captured
(r2 > 0.8)

1 kGP
MAF >5%

1 kGP
MAF >1%

CEU

0.87 0.83

CHB + JPT

0.85 0.76

YRI

0.71 0.58
Data Performance Value/Product Specification
Call Rate 99.9% / > 99% avg
Reproducibility 99.99% / > 99.9%
Log R Dev 0.12 / < 0.30**
Spacing Mean / Median / 90th%
Spacing (kb) 0.68 / 0.36 / 1.57
Marker Categories Number of Markers
Number of SNPs with 10kb of RefSeq genes 2,311,849
Nonsynonymous SNPs
(NCBI annotated)
84,004
MHC / ADME 43,904 / 43,615
Sex Chromosomes
(X / Y / PAR Loci)
113,213 / 2,498 / 511
Mitochondrial 267
Indels / multi-base substitutions 4,722

* Estimate assumes one iScan system, one AutoLoader2, one Tecan Robot, and a five-day work week.

Compared against the June 2011 1kGP data release.

§ Values derived from 454 reference samples.

** Value expected for typical projects using standard Illumina protocols.

Provided by the 1kGP structural variation group.

Note: The 4-sample HumanOmni5Exome BeadChip features > 4.3 milliontag SNPs in addition to > 240,000 exonic markers. This array delivers extensive coverage of common and rare variants (> 1% MAF) across the human genome, along with unprecedented coverage of coding variants within genes, providing the highest likelihood for obtaining new insight to potential disease pathways. The Omni5ExomeBeadChip can be further customized with the addition of up to 200,000 custom markers on the HumanOmni5Exome+ BeadChip.