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Genomics Core

MicroArray Analysis

MicroArray Analysis

Microarray Analysis Options

The Genomics Core offers a variety of microarray analysis options for DNA and epigenetic studies. The Illumina BeadArray technology combined with the Illumina HiScan 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.

The Illumina HiScan array scanner, sitting on a lab desk, is used to analyze the high-multiplex HumanOmni BeadChip arrays and other  Illumina arrays available.

Illumina MicroArrays (not all inclusive)

Array TypeDescription of ChipKit size
(Exome chip also available)
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
(Exome chip also available)
5M SNPs, Near complete common and rare variation coverage 4 sample chip, in sets of 16 samples
(Exome chip also available)
2.5M SNPs, Comprehensive common and rare variation coverage 8 sample chip, in sets of 16 samples
HumanOmniExpress HAPMAP, Highest throughput, common variation coverage, lowest per-sample pricing 24 sample chip, in sets of 48 samples
iSelect HD (custom) 3,072 – 90,000 SNPs, Fully custom, any SNP, any species 24 sample chip
iSelect HD (custom) 90,000 – 250,000 SNPs, fully custom, any SNP, any species 12 sample chip
iSelect HD (custom) 250,001 – 1 million SNPs, fully custom, any SNP, any species 4 sample chip
Infinium Methylation EPIC kit 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 or PicoGreen assay, NOT NanoDrop as it routinely overestimates the actual 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.

Sample Submission

If QC of DNA is not completed prior to submission, additional charges will be applied for the services provided.
Email a plate map of sample name, well position, volume and quantity (ng/ul) to the Core.

Assay TypeConcentrationVolumeQC
Illumina Genotyping Assay 50 – 100ng/ul 20ul 260/280: 1.8-2.0
Illumina Methylation Assay 20 – 50ng/ul 20ul 260/280: 1.8-2.0


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