Gene Expression Profiling using Illumina BeadArray and Assay technologies

Description

As a leading provider of genomic research service in the UK, Geneservice has recently added the Illumina BeadArray technology to the range of platforms available for Gene Expression Profiling.

BeadArray Technology

In the heart of the BeadArray technology is the use of 3μM beads that randomly assemble in either a fibre optic bundle substrate or a silica slide substrate. These two substrates form the basis of the two different array formats available: the 96-sample array matrix format based on fibre optic bundle and the BeadChip format based on the silica slide. Each bead contains a large number of a specific oligonucleotide and a 23 base address code. The randomly assembled beads are then decoded through a series of sequential hybridisation process.

Assay Technology

Illumina assay technologies for gene expression profiling include the Direct Hybridisation assay and the cDNA-mediated Annealing, Selection, Extension and Ligation (DASL) assay.

• Illumina direct hybridisation assay is compatible with the standard techniques used widely in the gene expression community. The direct hybridisation assay is used in the Whole Genome Expression BeadChip range of products.


• Illumina DASL assay allows RNA profiling of up to 1536 targets using partially degraded RNA samples, frequently found in formalin-fixed, paraffin embedded samples. The DASL leverages the GoldenGate Assay protocol and is used in the Sentrix® Array Matrix (to process 96 RNA samples in a single experiment) and the Sentrix® BeadChip (to process 16 samples in a single experiment). At present Illumina offers one standard DASL assay oligonucleotide panel, the human cancer panel which can measure the expression levels of 502 known human cancer genes. In addition to this cancer panel customers can design their own unique DASL panel of between 512 and 1536 genes.

Highlights

BeadArray

• Each bead type is represented more than 20 times on the substrate. This strategy provides the statistical accuracy of multiple measurements and results in providing high quality, highly reproducible data.
• The decoding process means that each bead has gone through a functional validation process, allowing Quality Control of every feature of every array to ensure that each array element is present and functional.

Direct Hybridisation assay

• High reproducibility possible due to 50mer probes and 100% array QC
• Requires low sample input at 50-100ng of total RNA

DASL assay

• Profile partially degraded RNA samples frequently found in formalin-fixed, paraffin embedded samples, allowing analysis of previously collected preserved samples
• Sensitivity to detect low-abundance transcripts
• Requires low sample input of 100-200ng total RNA

Expression Profiling Options

• Genome wide expression for Human, Mouse and Rat BeadChip
• Focused array with standard or custom probe content
• DASL gene expression for degraded RNA samples with standard human cancel panel or custom set
• MicroRNA expression

Platforms

• Illumina Beadstation 500
• Illumina Beadstudio analysis software
• Quantum Appligene Template-Tamer™ PCR workstation provides a nuclease-free environment
• Agilent 2100 Bioanalyzer estimates RNA sample integrity

Bioinformatics - Analysis Support

Our Bioinformatics scientists provide a complete analysis package that can also be customised to your specific research needs using:

• Illumina BeadStudio data analysis software
• Partek Genomics Suite
• Open source tools

Contact