We have sequenced (RNA-seq) 106 clinical cases of synovial sarcomas using the NovaSeq platform (SciLifelabs Stockholm). All data is collected. The study is sponsored by Barncancerfonden.
We will upload the data manually from our local server.
We will use FusionCatcher and STARFusion to identify fusion gene breakpoints and visualization in IGV. We will try mutational calling using Variant Detection in RNA(VaDiR). Basic Differential expression will be done in R / DESeq2 package.
Identified pathways / genes of interest will be validated in in vitro and in vivo models.