Deborah DiPierro, Susie DelRio, Amy Hayden, Dawn Jarvis and Kevin C. McElfresh
The Bode Technology Group, Sterling, VA

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The Bode Technology Group laboratories have been actively engaged in short tandem repeat (STR) DNA typing for human identification for several years. Originally, the results were detected by silver staining, but since November 1995, all results have been generated using a Hitachi FMBIO^® to detect fluorescently labeled bands. However, since we have ongoing projects, we needed to verify that the data generated using silver stain detection was compatible with the data generated using fluorescence detection. The two analysis methods were compared by examining the average base pair size calls for the same samples, gel to gel variation, and lane to lane variation. We also compared labor and reagent costs for each method.

The results of this study indicate that in fact, the data is quite comparable, and that samples in which silver detection was used could easily be matched to samples that were analyzed using fluorescent detection. Data from 7 alleles over 4 STR loci were compared for samples that were run and detected using both silver and fluorescence detection methods. The range in allele sizes was 168 bp to 315 bp. The average size difference between silver and fluorescent alleles sizes over all alleles and measurements (n=35) was 0.65 bp. For comparison purposes, the average variance in allele sizes within detection methods was 0.128 bp for silver and 0.011 bp for fluorescence. In all cases, the measurement differences are less than a single base pair. It is mostly likely that the increased accuracy between lanes is the result of the improved equipment and software used in the fluorescent detection method. An analysis of variance was done for all sample sets and the results were as expected.

Given that the detection methods are not actually discriminators of a particular technology’s utility with regards to accuracy in the laboratory, the next level of analysis was that of throughput of samples, and the cost to process those samples. There is a clear throughput advantage to the fluorescent system over the silver system. This is achieved via the ability to perform multicolor multiplexing in the fluorescent system versus the single "color" and size limitation of the gel in the silver system. When the cost to remove the hazardous waste associated with silver staining methods (i.e. silver and formaldehyde) is factored into the cost of reagents required to perform the tests, the reagent costs are nearly identical.