A polymerase chain reaction-based microsatellite typing assay used for tumor cell line identification

In this report we describe the application of a polymerase chain reaction (PCR)-based DNA typing assay to the analysis of tumor cell line identity. We have applied the technique to analyze four tumor cell lines purchased from the American Type Culture Collection (SK-OV-3, SK-BR-3, OVCAR, HeLa) and four lines isolated from the ascites fluids of ovarian cancer patients (YAOVBIX1, YAOVBIX3, OC194, and OC346). In this assay, three polymorphic tetranucleotide microsatellite loci (GABARB1, TH01, and HPRTB) were amplified from tumor cell line DNAs in radioactive PCR-reactions. The products were resolved in polyacrylamide gels and exposed to film to produce individual-specific patterns for five of the cell lines (HeLa, SK-BR-3, OVCAR, YAOVBIX3, and OC194). However, three of the cell lines, SK-OV-3, YAOVBIX1, and OC436 had identical "fingerprints" at all three loci. The probability that the observed profile match could occur between three randomly selected heterologous cell lines was calculated to be 1.32 x 10(-13). On the basis of this analysis, we have identified two independent cross-contamination events involving the SK-OV-3 ovarian adenocarcinoma cell line. The PCR-based analysis of tetranucleotide microsatellite loci is technically straightforward and produces discrete allelic bands associated with known population frequencies, allowing for the unequivocal interpretation of typing patterns.