Abstract 3735: Detection of microsatellite instable colorectal cancers from routine NGS panel sequencing data

Abstract

Abstract Introduction In about 15% of all colorectal cancers, microsatellite instability (MSI) caused by defects in the DNA mismatch repair machinery can be detected. MSI driven tumors have a better prognosis compared to microsatellite stable (MSS) tumors and show good response to drugs targeting the PD-1-PD-L1 axis. Current molecular diagnostic procedures for colorectal cancer are primarily focused on the detection of oncogenic mutations in RAS family genes by either classical Sanger sequencing or next-generation sequencing. Routine testingof MSI status for therapeutic purposes is still rare and usually carried out by a different array of methods including PCR and immunohistochemistry. Experimental procedures In our routine diagnostic CRC screening, we sequenced more than 600 colorectal tumors with an entity specific customized 180 amplicon NGS panel encompassing HotSpot regions of 31 genes. This panel includes several homopolymeric regions of genes that are known to be affected by MSI. We retrospectively analysed this data set for MSI signatures, including deletion/insertion mutations in 20 different homopolymeric regions (>7) and mutations/deletions of MLH1, MSH3, MSH6 and TGFBR2. Cases with an MSI signature detected by panel sequencing were reevaluated by PCR-based screening (Bethesda panel). Results From the 20 homopolymeric regions analyzed, several loci showed deletion/insertion mutations in MSI-positive patients. The highest discriminatory power presented a homopolymeric region within the ACVR2A gene showing a high analytical sensitivity and specificity towards MSI prediction. In combination with the readout of additional homopolymeric regions and the mutation status of MLH1, MSH3, MSH6 and TGFBR2, a sensitive and specific detection algorithm for MSI can be obtained from routine panel sequencing data. In conclusion, using only one assay, this approach facilitates simultaneous detection of mutations in RAS genes (and other druggable targets) and the MSI status in CRC As the assay is tissue sparing and time saving it may be advantageous over classic test approaches that are currently being employed in routine diagnostics. Note: This abstract was not presented at the meeting. Citation Format: Volker Endris, Martina Kirchner, Matthias Kloor, Anna-Lena Volckmar, Magnus von Knebel Doeberitz, Roland Penzel, Peter Schirmacher, Albrecht Stenzinger. Detection of microsatellite instable colorectal cancers from routine NGS panel sequencing data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3735. doi:10.1158/1538-7445.AM2017-3735