Abstract 2806: High sensitivity qPCR microsatellite instability detection in FFPE tissue

Abstract

Microsatellite instability (MSI) refers to genetic instability in short nucleotide repeats (e.g., 1-6bp tandem repeats), where a cell comprises a different number of repeats as compared to what was inherited from a progenitor cell. This genetic instability is often observed in tumor cells with impaired mismatch repair (MMR), especially in colorectal cancer (CRC) and endometrial cancer. MSI-high tumors can help identify patients that would benefit from additional genetic testing to diagnose Lynch Syndrome. Additionally, MSI can potentially be used as a biomarker to predict response to treatment with immunotherapy and CRC patients with MSI have a significantly better prognosis compared to those with intact mismatch repair. Here we present the VarTrace® MSI Research qPCR Assay, which enables high sensitivity detection of microsatellite instability. The assay uses NuProbe’s PCR-based Blocker Displacement Amplification (BDA) technology to enable the selective amplification of MSI unstable alleles with 1% analytical limit of detection. The assay is intended for the qualitative detection of mutations in 5 MSI loci (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) without the need of matched normal, and reports MSI-high (MSI-H), MSI-low (MSI-L) and Microsatellite Stable (MSS). Analytical validation of the assay has been completed on Horizon MSI/MSS formalin-fixed, paraffin-embedded (FFPE) DNA reference standard, SeraCare MSI AF5% reference panel mix, and 50 CRC FFPE samples. One FFPE section with as little as 2ng of input DNA is enough for this assay. The high sensitivity potentially allows for the detection of MSI status in liquid biopsy. Citation Format: Yan Helen Yan, Blake Young, Zhiheng Wang, Adam Yaseen, Alessandro Pinto, David Zhang. High sensitivity qPCR microsatellite instability detection in FFPE tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2806.