Comparison of RNA-sequencing from Fresh Frozen or Formalin-fixed paraffin-embedded tissue in glioblastoma

We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. By performing several quality control measurements, we found that FFPE’s RNA was highly degraded but kept transcriptomic similarities with RNA from FF samples. Certain caveats regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data to be used in molecular studies of GBM.