Assessment of microsatellite instability in very small microdissected samples and in tumor samples that are contaminated with normal DNA.

Microsatellite instability (MSI) testing is important for the management of young patients with colonic adenocarcinoma. Biopsies can be small and can be contaminated by normal cells. It is not known how sample size or contamination by non-neoplastic cell populations affects the interpretation of MSI assays. Serial microdissection targets (0.75 to 5.5 mm) were obtained from cases with high-level MSI. Polymerase chain reaction was performed for the standard National Cancer Institute recommended markers and products were analyzed by capillary electrophoresis. DNA from a patient with a BAT25 polymorphism was used to determine the sensitivity of detecting an aberrant allele in otherwise normal DNA. In small targets, MSI was seen sporadically in the setting of low DNA concentration. The results for small targets ranged from 1/4 to 5/5 loci with MSI, secondary to allelic dropout. In the sensitivity study, the aberrant allele was detected only when present at a concentration of above 10%. Allelic dropout can lead to under-estimation of the presence of MSI in small tissue samples or samples with low DNA concentration. Contaminating normal cell DNA can mask the presence of MSI. MSI testing on tissue fragments that are <5.5 mm can lead to a false-negative MSI test.