PGxAnalysis plugin
The PGxAnalysis plugin is designed to be used with the Ion AmpliSeq™ Pharmacogenomics Research Panel, a targeted gene panel that allows the interrogation of Pharmacogenomics variants in samples for genotyping and CYP2D6 copy number detection. The plugin analysis incorporates optimized variant calling for the Ion AmpliSeq™ Pharmacogenomics Research Panel, export of results that are compatible with downstream reporting software, and detection of gene and exon-level CNV for CYP2D6.
Analysis by the PGxAnalysis plugin requires two other Torrent Suite™ Software plugins: the variantCaller plugin for genotyping and coverageAnalysis plugin for CYP2D6 copy number detection.
The figure shows a summary of the analysis pipeline.
The run plan template that is used with the Ion AmpliSeq™ Pharmacogenomics Research Panel must be imported from AmpliSeq.com. The template includes optimized TVC parameters. The variantCaller plugin that includes pharmocogenomics parameters settings musbe be run before the PGxAnalysis plugin to complete the analysis. For details about how to set up Torrent Suite™ Software Planned Runs that incorporate the Ion AmpliSeq™ Pharmacogenomics Research Panel Planned Run template and the PGxAnalysis plugin, see the following documents at the Thermo Fisher Scientific website (thermofisher.com):