The panel provides deep and uniform coverage of genes associated with functional pathways that are known to be involved in cancer biology and it can be used to identify SNVs, indels, and CNAs in these genes. The ACE Extended Cancer Panel covers a core set of >1,400 cancer-related genes, including clinically-actionable* genes as well as genes that have been identified in the literature as having a role to play in tumorigenesis. This is also complemented by Personalis’ sample sparing protocols for all sample types, including more challenging types such as FFPE, fresh frozen, fine-needle aspirates (FNAs), and peripheral blood mononuclear cells (PBMCs). This exome-capture RNA-Seq protocol ensures that >95% of the bases are mapped within the coding and untranslated regions (UTRs) of the RNA, contributing to enhanced fusion detection and gene expression analysis. This capability is enabled by the use of multiple probes targeting each transcript, which facilitates the capture of transcripts even when the poly-A tail is lost due to RNA degradation making it ideal for FFPE and other problematic sample types.
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 samples. This preservation process makes it difficult to obtain a pure sample and often leads to RNA degradation and/or cross-linking. Many clinical studies depend on tissue archives that have been fixed using formalin-fixed, paraffin-embedded (FFPE) procedures. The same accuracy and coverage enhancements of the ACE Research Exome (see above) are also incorporated into RNA analysis using our unique ACE Research Transcriptome enrichment protocol.