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Medicine

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
HumanCore
(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
HumanOmni5
(Exome chip also available)
5M SNPs, Near complete common and rare variation coverage 4 sample chip, in sets of 16 samples
HumanOmni2.5-8
(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

  • Contact the Core if Illumina Reagents need to be purchased by the Core.
  • Submit all samples in 1.5ml tubes, clearly labeled ON TOPE OF TUBE with sample name and user name/initials (sample name on request form and on tube should match).
  • Larege volume projects may be submitted in FULL SKIRT 96-well plate, clearly labeled on the SIDE WALL with project name, plate number, user name and date. Sample names and well location will be submitted through iLab. 
  • Normalize all samples to the approprate concentration and volume (see chart below).
  • If QC of DNA is not completed prior to submission, additional charges will be applied for the services provided.
  • To begin a request for service please follow the iLab instructions:

The Genomics Core is now transitioning all service requests over to iLab Operations Software, a part of Agilent Technologies’ CrossLab platform. This is an online system to streamline the process of ordering and billing for core service requests. 

In order to gain access to your funds you will need to begin by logging into iLab at the following web address:

https://cwru.corefacilities.org

Once an account is created, the Genomics Core ordering site can be found here:

https://cwru.corefacilities.org/service_center/show_external/4142?name=genomics-core-facility

Simply click on Request Services tab to begin. 

 

Assay TypeConcentrationMinimum VolumeQC
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

Results

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.