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Targeted Gene Panel Sequencing

The ATG facility provides targeted sequencing of >400 cancer-relevant genes using the Ion Ampliseq Comprehensive Cancer Panel, a multiplexed PCR-based assay that results in the sequencing of all of the protein-coding regions for nearly all oncogenes, tumor suppressors and other genes important in cancer biology. These assays are usually barcoded and run four at a time on a single P1 chip on the Ion Proton sequencer, which typically produces about 80 million "reads" and produces >750x average read depth across the targeted regions. That makes these assays ideal for detecting rare variants (e.g. in <5% of the tumor cells) or for studying tumor heterogeneity (subclones within the tumor). The CCP assay is very robust and works well with DNA from FFPE material or fresh or frozen tissue.

The ATG facility uses some standard bioinformatics tools to detect variants (SNVs) identified by the CCP assay, and has developed customized scripts in R/Bioconductor to analyze other features such as tumor heterogeneity, loss of heterozygosity (LOH), copy number variants, etc. However, these assays also require analysis of normal tissue for comparison. An excellent combination is to use the CCP targeted assay for the tumor tissue, combined with the Ion Ampliseq Exome assay for normal tissue to detect germline (inherited) variants and markers linked to ethnicity.