Formalin-fixed paraffin-embedded tissue sections (either scrolls [3–4 at 10 microns] or tissue scraped from glass slides [4–5 at 4 microns] were obtained from each case. RNA extraction was performed with the ExpressArt FFPE Clear RNA Ready kit (Amsbio, Cambridge, MA). Libraries were prepared using 20–100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA), an enrichment-based assay targeting 507 fusion-associated genes. RNA sequencing (RNA-seq) was performed with 76 base-pair paired-end reads on an Illumina MiSeq at 8 samples per flow cell (~3 million reads per sample). The results were analyzed using both the STAR aligner and Manta fusion caller, and the BOWTIE2 aligner and JAFFA fusion caller (10 (link), 11 (link)).
Archer™ FusionPlex™ technology was used to develop the MSK-Solid Fusion assay, which is a clinical molecular diagnostic essay performed in a CLIA-accredited laboratory utilizing multiplex polymerase chain reaction (PCR) to detect oncogenic fusion transcripts involving 62 genes as described previously (12 (link)).
Archer™ FusionPlex™ technology was used to develop the MSK-Solid Fusion assay, which is a clinical molecular diagnostic essay performed in a CLIA-accredited laboratory utilizing multiplex polymerase chain reaction (PCR) to detect oncogenic fusion transcripts involving 62 genes as described previously (12 (link)).
