Many clinical studies depend on tissue archives that have been fixed using FFPE procedures. This preservation process makes it difficult to obtain a pure sample and often leads to RNA degradation. To overcome this challenge, Personalis has developed an exome-capture transcriptome protocol based on our ACE Technology that allows us to produce high-quality transcriptome sequencing results from challenging FFPE samples.

Our enrichment protocol directly selects for transcripts using the optimized ACE capture probes, eliminating background and focusing the sequencing on regions of interest. Sequencing using the ACE-enabled transcriptome protocol demonstrated that >90% of the bases mapped within the coding and UTR regions of the RNA (Figure 2).  Thus, the ACE approach results in high quality data and low off-target reads.

Figure 2: ACE-enabled Transcriptome Focuses on Regions of High Interest

Comprehensive characterization of tumor gene expression is an important overlay for interpreting somatic mutations, identifying neoantigens, assessing expression of checkpoint genes in immunotherapy, and identifying prognostic expression signatures. Whether Fresh Frozen or fixed specimens are available for your analysis, the ACE approach produces high quality transcriptome sequencing results.  Using paired FFPE and matched adjacent Fresh Frozen tissues; we found high correlation of normalized (TPM) gene expression (Figure 3.) across various tumor types.  This data demonstrates our ACE-enabled transcriptome for gene expression is an accurate, reliable method for characterizing expression in even challenging materials such as FFPE.

FIGURE 3: Correlation Plots of Log2 Transcripts Per Million (TPM) between matched FF (x-axis) and FFPE (y-axis) pairs in A–D) Colon E) Lung and F) Rectum tumor tissues.