While widely adopted for comprehensive transcriptome profiling, the methods of poly-A selected or ribodepleted RNA-sequencing may have key limitations, including input mass requirements, inefficient fusion detection, and wasted reads on non-coding transcripts. The detection of fusion transcripts — which are present at low but potentially biologically relevant levels in many tumor types — requires enrichment techniques. However, many on-market fusion panels are unable to profile the entire transcriptome, leading to incomplete gene expression data and limiting insights. 

In this study, Roche demonstrates a new workflow using the new KAPA RNA EvoPrep Kit paired with KAPA HyperExome V2 Probes, which can successfully be used for enrichment of both DNA and RNA libraries. The workflow enables enrichment of protein-coding genes to be used simultaneously in gene expression analysis and detection of fusion and exon-skipping events. The speakers will demonstrate key advancements in RNA library preparation using both high-quality and formalin fixed paraffin embedded (FFPE) samples.

Learning Objectives:

1. Discover the benefit of enriching RNA libraries with an exome panel. 

2. Assess the consistency of the new workflow across input types and mass.

3. Explore detection of clinically relevant fusions and exon skipping events in RNA inputs from formalin fixed paraffin embedded samples.