Targeted Cancer Next Generation Sequencing as a Primary Screening Tool for Microsatellite Instability and Lynch Syndrome in Upper Gastrointestinal Tract Cancers

Background: No consensus guideline has been established for microsatellite instability testing in upper gastrointestinal tract cancers. This study aims to determine whether targeted cancer next generation sequencing can accurately detect microsatellite instability in upper gastrointestinal tract cancers and screen for patients with Lynch syndrome. Methods: In a cohort of 645 upper gastrointestinal tract cancers, targeted next generation sequencing assessed microsatellite instability by identifying characteristic insertion and deletion mutations. Sequencing classification was compared to mismatch repair protein immunohistochemistry. Cancers with microsatellite instability by sequencing were analyzed using a testing protocol to identify patients with Lynch syndrome. Results: Sequencing identified microsatellite instability in 3.6% (23 of 645) of upper gastrointestinal tract cancers, including 28% (8 of 29) of small intestinal and 9% (9 of 97) of gastric carcinomas. In 20 cancers classified as having microsatellite instability, 19 demonstrated loss of expression of MLH1, PMS2, MSH2, or MSH6, and one cancer was indeterminate by immunohistochemistry. In contrast, 52 control cancers demonstrated retained expression of all mismatch repair proteins. Using targeted sequencing as the initial screening test, 1.1% (7 of 645) of patients were identified to have pathogenic germline variants confirming a diagnosis of Lynch syndrome. Conclusions: Targeted cancer next generation sequencing is an accurate first-line test to detect microsatellite instability in upper gastrointestinal tract cancers. Impact: This study provides a proof of concept for the use of targeted next generation sequencing to detect microsatellite instability and screen for Lynch syndrome.