Illumina BeadArray SNP genotyping

As a leading provider of genomic research services, we offer the Illumina BeadArray technology for SNP genotyping.  The Illumina BeadArray platform, and more recently the Illumina iScan which utilises the same BeadArray technology unique to Illumina, offers a highly reproducible, efficient and cost-effective option for expression studies. 


There are multiplex capabilities which is great for high throughput projects but yet still suitable for smaller sample numbers too.  The Illumina platform offers an average call rate of 99.9% which helps with downstream analyses since there are less likelihood of false positives and negatives due to the higher sample call rates.  We offer services using the Illumina BeadStation/iScan using Goldengate, iSelect, Infinium II and Infinium HD assays.

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 processes.

Assay technology

Illumina assay technologies for SNP genotyping include the GoldenGate, iSelect, Infinium II and Infinium HD assays.

  • The GoldenGate assay is used to interrogate 384 - 1536 SNPs simultaneously by using allele specific extension and ligation. The high level of multiplexing minimises the time and reagents required for processing. Researchers can select SNP loci of choice to form customer panels for targeted genotyping or an expanding selection of standard panels is also available
  • The Infinium II assay, coupled with BeadChips, allows large scale interrogation of variations in the human genome at unlimited levels of loci multiplexing. Whole genome BeadChips covering SNP content ranging from 240,000 to 1 million and iSelect Infinium Custom Genotyping Panels are available through Source BioScience LifeSciences. The SNPs contained on the whole genome BeadChip range of products are derived from Phase I HapMap data, and contain mainly tag SNPs. The use of tag SNPs greatly improves the power of association studies.

Genotyping options

  • Whole Genome (up to 1 million SNPs)
  • Focused content including standard panel and custom content through GoldenGate and iSelect
  • CNV/LOH analysis


  • Whole-genome association studies
  • Fine-mapping studies
  • Whole genome LOH / copy number variation analysis
  • Disease-associated copy number variation analysis


  • 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.
  • New bead pools are easily synthesised, allowing fast turnaround for custom panels
  • Powerful assay technologies allow high levels of multiplexing, allowing a very large number of variations to be interrogated in parallel


  • MATRIX PlateMatePlus and Tecan for high throughput liquid handling
  • Illumina Beadstation 500
  • Illumina Infinium II and Goldengate assays
  • Illumina BeadChip and Array Matrix formats
  • Beadstudio data analysis software

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


If you would like more information please contact us