Abstract 421: Improved detection and identification of microsatellite instability features in colorectal cancer: Implications for immunotherapy
Authors: Shin Giwon , Lee HoJoon , Grimes Susan M. , Kubit Matthew A. , Ji Hanlee P. 
Published: August 2018

Abstract
Colorectal cancers with loss of DNA mismatch repair display microsatellite instability (MSI). These tumors have a better prognosis and an improved response rate to immune check point therapies compared to non-MSI tumors. MSI-positive tumors demonstrate a surprising range of somatic alterations in repetitive sequence tracts. For example, elevated microsatellite alterations at selected tetranucleotide repeats (EMAST) that may be related to functional loss of MSH3. Current MSI tests are based on PCR and capillary electrophoresis. This conventional approach is suboptimal because i) only a small number of microsatellite markers are interrogated per assay, and ii) sensitivity is insufficient for low allelic fraction alleles in heterogeneous tumors. Next generation sequencing permits the inclusion of more microsatellite markers, but these NGS method still rely on PCR methods, which is the major source of artifacts that obscure the true somatic alterations.
In this study, we analyzed a series of colorectal cancers using a new sequencing technology that sequences in parallel more than 200 microsatellite regions - we evaluate mono-, di- , tri- and tetranucleotide repeats to provide a broader spectrum of MSI events. This deep sequencing technology provides greater than 2,000X coverage, uses in vitro CRISPR-Cas9 segmentation, and eliminates the need for PCR amplification. Because every read corresponded to a single DNA molecule, we eliminated the artifacts introduced by PCR that obscured true MSI events. Moreover, we improved the sensitivity of detecting minor allele fractions to as low as 0.1% by measuring microsatellite haplotypes. Included in our analysis was new method for somatic copy number changes in 82 cancer genes, by which we can infer chromosomal instability (CIN) status.
Among our cases, 10 cancers had MSI when considering both mononucleotide and tetranucleotide repeats. Interestingly, diagnostic testing of two of these tumors were false negatives and were demonstrated to be MSI-high. There were three major types among the 10 MSI cancers: MSI-high, EMAST, and the cancers having both. However, such types were distinguishable only by microsatellites with intermediate length (10 - 20 bp). MSI-high tumors (n = 3) showed no sign of CIN while all the EMAST tumors (n = 4) also showed CIN phenotype. Our results suggest that the current gold standard MSI diagnostic test may have issues with both false negatives and false positives, indicating that NGS approaches are better suited for evaluating MSI status of tumors and consideration of immunotherapy.
Citation Format: Giwon Shin, HoJoon Lee, Susan M. Grimes, Matthew A. Kubit, Hanlee P. Ji. Improved detection and identification of microsatellite instability features in colorectal cancer: Implications for immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 421.