Evaluation of microsatellite instability (MSI) status in gastrointestinal (GI) tumor samples tested with comprehensive genomic profiling (CGP).

Abstract

528 Background: PD-1 inhibitor therapy (pembrolizumab) has demonstrated promising activity in MSI-H (MSI-High) colorectal cancer (CRC) and MSI-H non-CRC compared to MSS tumors, supporting MSI as predictive of anti-PD-1/L1 therapy independent of tumor histology. We developed and validated a novel computational method to assess MSI status using next generation sequencing (NGS) data generated from CGP of clinical cases. We then sought to determine the frequency of MSI in a diverse sample of clinical cases of GI tumors previously assayed with CGP (FoundationOne). Methods: To determine MSI status, 114 intronic homopolymer repeat loci (10-20bp long in the human reference genome) with adequate coverage on the CGP panel were analyzed for length variability and compiled into an overall MSI score via principal components analysis. Translation of the MSI score to MSI-H or MSS (MSI-Stable) was established using a training data set. Results: Our methodology was validated in 69 samples with MSI status (20 MSI-H, 49 MSS) previously determined by standard clinical testing, either PCR or immunohistochemistry staining. Our concordance was 97% (65/67). We then applied our method to 2545 GI cancers assayed with CGP in the course of clinical care, with small bowel carcinoma having the highest rate of MSI-H (Table). The 3.5% frequency of MSI-H in CRC is lower than expected, possibly attributed to sampling bias against MSI-H CRC in the cohort. In CRC, we discovered significant differences in mutational profile: histone methyltransferase MLL2/3 mutations were enriched in MSI-H CRC (P<0.0001, Fisher’s Exact test), while TP53mutations were enriched in MSS CRC (P<0.0001, Fisher’s). Conclusions: CGP can be used to detect MSI with high accuracy. In addition, application of this approach to the 2545 GI cancers demonstrates the use of CGP to identify differences in mutational profiles between MSI-H and MSS cancers. Broadened application of these methods to more tumor types may provide target enrichment for emerging immunotherapies. [Table: see text]