EXaCT-2: An augmented and customizable oncology-focused whole exome sequencing platform

Abstract

With the rapid advances in cancer research, the list of variants and genes that drive human diseases is constantly expanding. Moreover, the FDA has approved more cancer therapies that incorporate a broader set of genomic features than simple gene variants such as Tumor Mutation Burden (TMB), microsatellite instability status (MSI), and fusion events in gene families such as the NTRK receptors. These features currently require multiple testing methods (IHC/FISH/etc.). With the cost of NGS testing dropping, it is now possible to envision an NGS assay capable of reliably detecting these features without the need for additional testing. The EIPM multidisciplinary team has developed EXaCT-2: a whole exome sequencing (WES) assay that gives the coverage of a targeted assay on cancer genes and the breadth to detect copy number events, cancer-related fusions, and viruses, which can facilitate diagnostic and therapeutic decisions for cancer patients. We evaluated EXaCT-2 on 250 matched tumor/normal pairs and compared its performance with orthogonally validated results. We show the assay achieves the expected coverage of critical cancer genes, provides a better characterization of somatic copy number alterations, detects common cancer rearrangements and viruses, and enables the accurate estimation of global molecular metrics, such as tumor mutational burden and microsatellite instability. Further, we demonstrate the sensitivity of the assay to identify sub-clonal mutations that standard whole-exome assays are incapable of detecting, including the presence of KRAS mutations in samples previously believed to only contain wild-type KRAS, as well aging-related, somatic mosaicism in a phenotypically benign sample that is proximal to endometrial cancer.