Briefly, for each case scrolls (3–4 at 10 microns) were cut from formalin-fixed paraffin-embedded tissue into Eppendorf tubes. RNA was extracted using the ExpressArt FFPE Clear RNA Ready kit (Amsbio, Cambridge, MA). RNA-seq libraries were prepared using 20-100 ng total RNA with the TruSight RNA Fusion Panel (Illumina, San Diego, CA), an enrichment-based assay that targets 507 known fusion-associated genes. Each sample was sequenced 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 the STAR aligner and Manta fusion caller as well as the JAFFA fusion caller utilizing BOWTIE2 aligner.(15 (link), 16 (link))
The mRNA expression levels of NUTM1, and the respective fusion partners, were evaluated and compared to those of other samples analyzed on the same targeted RNA sequencing platform.
The mRNA expression levels of NUTM1, and the respective fusion partners, were evaluated and compared to those of other samples analyzed on the same targeted RNA sequencing platform.
