Detection of microsatellite instability in cancers by arbitrarily primed PCR fingerprinting using a fluorescently labeled primer (FAP-PCR)

The microsatellite mutator phenotype (MMP), detected as a change in the number of repeating units in hundreds of thousands of microsatellite sequences in the tumor cell genome, underlies the carcinogenesis of a variety of tumors including sporadic and hereditary nonpolyposis colon cancers. This enhanced microsatellite instability was discovered using arbitrarily primed polymerase chain reaction (AP-PCR) fingerprinting of DNA from colon cancers. In this study, we found an arbitrary primer that can amplify multiple DNA fragments containing repeated sequences, including the poly A tracts found in the Alu repeats of the human genome. The combined use of primer labeling with fluorescence and an automated DNA sequencing analysis of AP-PCR products (FAP-PCR) detected alterations in fingerprint bands in all DNA samples previously determined to belong to the MMP. Fluorescent AP-PCR fingerprinting using this single arbitrary primer provides a convenient and efficient method for detecting tumor specific fingerprint alterations that are usually undetectable by conventional fingerprinting.