Comparative analysis of short tandem repeat data obtained by automated and gel electrophoresis techniques

Short tandem repeats (STRs) are commonly used as genetic markers. The detection and analysis of STRs can be used to gather information on polymorphisms of interest to forensic geneticists. Denaturing polyacrylamide gel electrophoresis (PAGE) is an affordable method for the detection of minor sequence changes in DNA, while capillary electrophoresis (CE) is the gold standard for genotyping analysis. This appears to be the first study to directly compare data obtained using the two electrophoretic techniques. We analyzed genomic DNA from 209 individuals to compare genotyping results from seven Combined DNA Index System (CODIS) STR markers obtained by both techniques. The automated electrophoresis was carried out using a MegaBACE^TM 1000 DNA analysis system. Full concordance was found in 1297 of 1308 STR allele calls. Kappa and McNemar-Bowker tests indicated that there were no statistically significant differences between the results from the two methods. There was no statistically significant difference in precision between denaturing PAGE followed by silver nitrate staining, despite a longer protocol, compared with CE when applied to population studies. STR allele frequency data from non-automated genotyping techniques seem to be just as reliable as from automated genotyping methods.