SUPR
RNA seq of clinical synovial sarcoma
Dnr:

sens2019015

Type:

SNIC SENS

Principal Investigator:

Felix Haglund

Affiliation:

Karolinska Institutet

Start Date:

2019-06-03

End Date:

2024-10-01

Primary Classification:

30203: Cancer and Oncology

Webpage:

Allocation

  • Castor /proj/nobackup at UPPMAX: 12000 GiB
  • Cygnus /proj/nobackup at UPPMAX: 12000 GiB
  • Castor /proj at UPPMAX: 200 GiB
  • Cygnus /proj at UPPMAX: 200 GiB
  • Bianca at UPPMAX: 10 x 1000 core-h/month

Abstract

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.