Is SNV/indel calling supported in (RNA-based) FUSIONPlex™ panels?

Yes, hotspot SNV/indel targets are included in many of our FUSIONPlex panel designs. The hotspot mutations listed in Archer™ product inserts are intentionally targeted by the assay designs. Note that for SNV/indel targets which do not appear in our product inserts, coverage will occasionally be generated by gene specific primers (GSP) designed to cover fusion breakpoints, therefore, we flag all GSP2s with both the “FUSION” and “SNV” function flags in our GTFs. Version 6.2.8 and earlier of Archer Analysis may not support RNA SNV/indel variant calling at exon junctions depending on the sequence context (SNVs ≤5bp, indels ≤30bp). RNA SNV/indel mutation detection is not formally supported on the Ion Torrent™ Sequencing Platform, but labs are not prevented from performing SNV/indel calling on Ion Torrent libraries. Users are currently allowed to perform targeted variant detection using a targeted mutation file (TMF).

Additional considerations:

• FUSIONPlex assays can only be used to interrogate variants that are expressed in the sample.
• Archer Analysis reports expressed allele frequencies.
• Inactivating mutations in RNA can increase instability of transcripts via nonsense mediated decay. This can lead to a higher rate of false negative calls when using RNA input. 
• DNA is a better input to interrogate for certain variants. For detection of those variants, VARIANTPlex™ panels can be ran in parallel with FUSIONPlex for comprehensive genomic profiling.