Fusion transcript discovery using RNA sequencing in formalin-fixed paraffin-embedded specimen

Chimeric transcripts are critical for diagnosis or prognosis and could constitute effective therapeutic targets. Fresh tissues are the major source for the identification of these fusion transcripts. The quality and quantity of the extracted RNA directly affect fusion transcript discovery. Formalin-fixed paraffin-embedded (FFPE) tissues allow long-time preservation of tumor histology for microscopic evaluation; however, no provision has been made for either the type of fixative or embedding procedure used for preserving RNA. Nonetheless, the widespread use of these FFPE tissues in translational and clinical research prompts to overcome these issues. RNA is, by nature, of reduced quality and amount in these FFPE tissues. Therefore, attempts should be taken to minimize the limitations of FFPE tissues as a widely available source of fusion transcript identification. In this review, we describe approaches allowing fusion transcript identification from FFPE tissues using RNA sequencing techniques.