Microarray analysis using Illumina iScan

The TCGA can offer microarray analysis using the Illumina iScan high-throughput microarray scanner for genome wide or targeted genotyping, cytogenomics and methylation analysis. Pre-developed arrays are available for a range of organisms including human, mouse, canine, bovine, ovine, porcine, maize and potatoes. For analysis of human samples arrays have been designed to interrogate clinically relevant regions across the whole exome, genome, DNA methylome or more targeted regions such as those associated with autoimmune disorders, or a predisposition to cancer or psychiatric conditions. In addition there is the option to develop custom genotyping arrays or to add additional targets to off-the-shelf arrays.

Microarray analysis is a robust process, which can tolerate sub-optimal DNA quality such as that derived from formalin fixed paraffin embedded (FFPE) samples. All bead arrays include multiple quality control markers to ensure the successful analysis of each sample. The TCGA microarray service includes all steps from isolated DNA or RNA though to array scanning including quality control of DNA, sample preparation, hybridisation, scanning and primary quality control of the data.

Example applications

  • The Global Screening Array includes approximately 640,000 variants including those with established disease associations; relevant pharmacogenomics markers and curated exonic content based on ClinVar, NHGRI, PharmGKB and ExAC databases. This analysis can cost as little as £50 per sample (based on testing 24 samples in a batch).
  • The Infinium MethylationEPIC array interrogates over 850,000 methylation sites within the human genome including CpG sites outside of CpG islands, non-CpG methylated sites, differentially methylated sites identified in tumour versus normal, FANTOM5 enhancers, ENCODE open chromatin and enhancers, DNase hypersensitive sites and miRNA promoter regions. This analysis can cost as little as £254 per sample (based on testing 8 samples in a batch).

If you are interested in microarray analysis using the Illumina iScan please contact us.