Illumina BeadArray Analysis

The Genomics Core offers a variety of microarray analysis options for DNA and epigenetic studies. The Illumina BeadArray technology combined with the Illumina iScan Array Scanner allows for analysis of genome-wide association studies and detection of mutations, copy number variants, and chromosome aberrations. Sample type, the size of the project, and how many markers will be investigated can help determine which Illumina microarray is best to use. With Illumina methylation arrays, researchers can analyze multiple samples in parallel while examining methylation sites across the genome at single-nucleotide resolution. All chips and kits are purchased directly through Illumina on a per-project basis.


Popular BeadArrays (not all inclusive)

Array Type Description of Chip Kit size
highly informative genome-wide tag SNPs found across diverse world populations, add up to 300,000 semi-custom SNPs 24 sample chip, in sets of 48 samples
HumanOmni5 5M SNPs, Near complete common and rare variation coverage. Exome chip also available. 4 sample chip, in sets of 16 samples
Global Diversity Array Targeted coverage of more than 4800 key genes across the genome. Approximately 1.8M markers are included for high exonic coverage.  8 sample chip, in sets of 16 samples
Methylation EPIC  Enhancer and Promoter Informed Content (EPIC). Coverage of >850K CpG islands, genes, and enhancers. 8 sample chip, in sets of 16 samples


DNA Prep (completed by User prior to submission)

  • Quantify DNA samples using either Qubit Fluorometer or PicoGreen assay. Do NOT use NanoDrop as it routinely overestimates the actual DNA concentration.
  • Check quality/purity of DNA samples by UV spectrophotometric measurements (260:280 / 260:230) and agarose gel electrophoresis.
  • For best results, submit DNA samples of only high quality. However, FFPE options are available for some arrays.
  • If DNA QC is not completed prior to submission, additional charges will be applied for the services provided.


Sample Submission

  1. Contact the Core to determine the best kit for your project and secure a quote for the Illumina Reagents.
  2. Normalize all samples to the appropriate concentration and volume, given in the DNA Requirement chart below.
  3. Submit all samples in 1.5ml eppendorf tubes, clearly labeled on TOP of tube with sample name and user initials, and label SIDE of tube with the date. Sample names on tube and iLab request form should match.
  4. Large volume projects may be submitted in FULL SKIRT 96-well plates, with at least one SIDE WALL clearly labeled with project name, plate number, user name, and date. Sample names and well location will be submitted through iLab.  


DNA Requirements

Assay Type Concentration Minimum Volume QC
Illumina Genotyping Assay 50 – 100ng/ul 30ul 260/280: 1.8-2.0
Illumina Methylation Assay 20 – 50ng/ul 30ul 260/280: 1.8-2.0

Submit a Request



For all data generated using the Illumina HiScan Array Scanner, a User Computer with the latest Illumina Genome Studio Software is available for analysis. Illumina Genome Studio Software is now also available for FREE download from the Illumina website. The Genomics Core staff is available to help with the initial analysis of data. Please contact the Core for further details.