Diagnostic primer sets for microsatellite instability optimized for a minimal amount of damaged DNA from colorectal tissue samples

Background: The diagnosis of microsatellite instability from a minimal amount of highly damaged DNA, extracted from formalin-fixed, paraffin-embedded tissue by the microdissection method, is difficult. Therefore, optimized primer sets were newly designed for substitution of documented ones. Methods: DNA was extracted from 15 archival colorectal carcinomas and used as templates for polymerase chain reaction. Nine standard microsatellite markers (BAT-25, BAT-26, BAT-40, D18S69, D2S123, D5S346, D10S197, D17S250, and D18S58) were selected for diagnosis of microsatellite instability in colorectal carcinomas. All polymerase chain reaction conditions for primer sets were unified to save experimental time. Results: The primer sets for the latter five markers documented in the literature were redesigned because of poor efficiency for damaged DNA. As a result, the number of DNA samples, sufficiently amplified at all markers, improved from 0% to 93%. Conclusions: Diagnostic primer sets for microsatellite instability, optimized for a minimal amount of damaged DNA from colorectal tissue samples, were established.