Assessing microsatellite instability with semiautomated fluorescent technology: Application to the analysis of primary brain tumors

The replication error phenotype, revealed by the observation of widespread microsatellite instability (MIN), has been identified as a new mechanism of cancer susceptibility, and the comparison of the allele sizes of polymorph ic microsatellite repeats between normal and tumor DNA is now frequently un dertaken in colorectal and other human neoplasias. The lack of precise char acterization of the electrophoretic profiles of microsatellites is one of t he main sources of discord between the rate of MIN reported for the same ty pe of tumor by different investigators. The recent introduction of fluoresc ent-based semiautomated microsatellite analysis allows a more accurate size comparison, but one or more artificial peaks, generated during polymerase chain reaction (PCR) and/or electrophoresis, are frequently detected along with the true allele peaks. The aim of this study was to characterize the m ost frequent artificial extra peaks in the short tandem repeats (STRs) used by us to assess MIN in human cancers. We analyzed eight microsatellite loc i in 113 primary brain tumors. HumFibra/FGA exhibited the most frequent ext ra peak formation. For each microsatellite there is a characteristic patter n of artifact formation which must be recognized to avoid a false-positive diagnosis of MIN.