Variability of mixed DNA profiles separated on a 3130 and 3500 capillary electrophoresis instrument

In this paper, the variability of peak heights for mixed DNA profiles separated on two different models of a capillary electrophoresis instrument is examined. The Applied Biosystems 3500xl instrument produces larger peaks than the 3130xl instrument. If the relative difference in peak heights between the two instruments was a constant factor then all relative heights should be preserved. However, if that factor differed, say, for small versus large peaks then relative heights would change. The effect of peak height and dye on the relative difference in peak height between injections of the same amplicon on a 3500xl and 3130xl instrument for a series of mixed DNA profiles using the Promega PowerPlex 21 multiplex is described. The ratio of peak heights between instrument models resulted in values up to four times higher on the 3500 compared with the 3130. The magnitude of this difference was shown to be dependent on the dye but not on the peak heights themselves. Relative parameters stutter, heterozygote balance, and mixture proportion were very similar between the two instrument models, indicating that the interpretation guidelines developed on one machine are likely to be transportable to different capillary electrophoresis instrument models and different machines of the same model.