Library preparation and next generation sequencing (NGS)

Library preparation for the SalvGlandDx panel and the Archer FusionPlexSarcoma panel was performed according to the protocol of the Archer FusionPlex technology (ArcherDX, Boulder, CO, USA), using 250 ng input RNA. Libraries were sequenced with 150bp paired-end on a NextSeq550. Library preparation for the custom-extended Archer FusionPlexSarcoma panel was performed according to the manufacturer's protocol (ArcherDX, Boulder, CO, USA), using 250 ng input RNA. Libraries were sequenced on the Ion S5 system (ThermoFisher Scientific, Waltham, MA, USA).

Library preparation for the Oncomine Focus Assay and Oncomine Comprehensive Assay v3 was performed according to the manufacturer's manual (ThermoFisher Scientific, Waltham, MA, USA), using 10 ng or 20 ng of input material. Libraries were templated on Ion 540 chips using the Ion Chef Instrument and sequenced on the Ion S5 system (ThermoFisher Scientific, Waltham, MA, USA).