Diagnostic whole transcriptome sequencing in a series of 1233 FFPE solid tumor samples

BACKGROUND: Whole Transcriptome Sequencing (WTS) is a comprehensive alternative to targeted panels for detecting gene fusions and splice variants. To integrate WTS into clinical diagnostics, we compared its performance against established fusion assays (Archer FusionPlex and TSO500 RNA). METHODS: WTS was evaluated in an initial cohort of 64 FFPE tumor samples, and quality control (QC) thresholds were defined based on missed fusions correlating with low tumor cell content (TCC < 40%). Key QC metrics included TCC 

• Ball, M.
• Beck, S.
• Wlochowitz, D.
• Fuchs, T.
• Lorenz, K.
• Zgorzelski, C.
• Pallares Robles, A.
• Allgäuer, M.
• Volckmar, A. L.
• Goldschmid, H.
• Ourailidis, I.
• Brandt, R.
• Christopoulos, P.
• Thomas, M.
• Seker-Cin, H.
• Fink, A.
• Schnecko, F.
• Neuman, O.
• Menzel, M.
• Kirchner, M.
• Fioretos, T.
• Schirmacher, P.
• Peters, S.
• Budczies, J.
• Stenzinger, A.
• Kazdal, D.