A COMPARISON OF METHODS FOR DNA EXTRACTION FROM PARAFFIN-EMBEDDED TISSUE FOR MICROSATELLITE INSTABILITY ANALYSIS BY POLYMERASE-CHAIN-REACTION

In a prospective study, nuclear DNA was extracted from colorectal tumo urs and normal mucosa which had been fixed in buffered formalin and em bedded into paraffin. DNA-extraction was performed using three differe nt methods: a commercial kit which was not especially created for this use; a known fast procedure without DNA-cleaning steps; and a more co nventional DNA-preparation protocol with DNA-cleaning. Using the polym erase chain reaction (PCR), DNA was amplified by being targeted onto t wo beta-globin fragments with different lengths (536 bp and 989 bp) an d (CA)n repeats localized on chromosome 5q (D5S346) and chromosome 17p (TP53CA) with a length of about 100bp for detection of microsatellite instability. The success rate of microsatellite amplification was 100 % with all methods. The 536 bp beta-globin fragment could be amplified with a success rate ranging from 40% to 100%. The amplification of th e 989 bp beta-globin fragment was unsuccessful. Significant difference s were observed between the three methods in the final DNA concentrati on and DNA yield. In microsatellite instability studies of paraffin-em bedded tissues, the investigator can expect a high success rate of nea rly 100% using any of the described methods.