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Illumina's BeadStation 500G System

Gene expression

SNP Genotyping

Sentrix Gene Expression

50-mer probes provide better selectivity and sensitivity, high-feature density enables low sample and reagent volumes, high feature redundancy (30X average) delivers high-confidence results

Genome Wide-Expression Arrays

46,000 transcripts per sample for 6 samples or 23,000 transcripts per sample for 8 samples

Focused Expression Arrays

For more information visit www.illumina.com

Sentrix Human-8 Exprsesion Beadchip

(Part No:BD-25-201, Price~ $800/slide)

8 individual/slide: low array-to-array variability
>23,000 transcripts apiece, on the Sentrix
Optimized 50-mer probles:high sensitivity
high data confidence
Redundant feature representation (30X average)
low false rates of differential expression between replicates
100% array QC:
500-100ng total RNA input

The median response for two representative genes are shown. Replicate hybridizations were performed on 18 arrays using labeled human total RNA.

Sentrix Human-8 Expression Beadchip

Part No:BD-25-101, Price~ $960/slide

six individual/slide: low array-to-array variability
>46,000 transcripts apience, on the Sentrix
Optimized 50-mer probes:high sensitivity
high data confidence
Redundant feature representation (30X average)
low false rates of differential expression between replicates
100% array QC
50-100ng total RNA input

The median response for two representative genes are shown. Replicate hybridizations were performed on 18 arrays using labeled human total RNA.

SNP Genotyping

Linkage Panel

>6,000 SNP Markers

Ideal for linkage mapping,, this powerful panel features many thousands of SNP markers evenly distributed at high density across the genome,

Provides an average marker density of less than 1cM - five to ten times greater than common STR maps

Fine Mapping Panels

40,000 SNPs are available in assay panels

Flexible Custom SNP Panels

Candidate gene association or linkage disequilibrium studies

Molecular Biology behind Illumina's Genotyping

Genotyping performed using genomic DNA

Can use whole genome amplified DNA

Phi29 DNA polymerase-based MDA (multiple strand displacement amplification

Each SNP require 3 specific 3-section oligos

2 allele-specific 5' oligos (defined by one of two universal primer complement tags)
1 SNP-specific 3' oligo (defined by the illumiCode complement)

Alleles identified through allele-specific oligo extension, followed by ligation to the illumicode-containing downstream oligo

All SNPs require just 3 universal primers for amplification

After extension and ligation all 3040 (1520 x 2 alleles) products are amplified in multiplex using just 3 primers

GoldenGate" Assay Allele Specific Extension and Ligation

GoldenGate" Assay Amplification

Illumina's Fusion of Biology and Fiber Optics

Illumina Fiber Optic Bundles

There are 49,777 individual fiber strands in each 1.4mm bundle

SEM of an Illumina Fiber Optic Bundle

Bead Preparation and Array Production

Beads individually manufactured and QC'd with full length IllumiCode" oligos Bead type = unique IllumiCode"

Pools produced containing equal mix of all 1520 bead types

Fibers introduced to bead pools and beads self-assemble into pits to form functional array with ~30 copies of each bead type

All elements of the array quality checked for bead presence and type prior to supply

"Optically Wired" Beads in Wells

Hybridization to Universal Illumicode Array

Sentrix" Array Decoding

Traditional arrays are "Ordered"

Each element is manufactured in a known place

BeadArray" matrices are "Random"

Manufactured by self-assembly
Beads are identified by decoding
Every bead on the array is individually QC'd by a functional assay