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Microsatellites are important genetic markers and have been broadly employed in many genetic studies. Currently, polymorphisms in microsatellites are often detected by an automated system of capillary electrophoresis with fluorescent dyes. In this situation, different dye combinations may cause pull-up/bleed-through problems, which introduce noise signals from one dye channel into another, causing genotyping errors. Here, we report the detection of such a problem at two microsatellite loci that used the HEX dye. Using three datasets, we tested for noise effects in four allele-scoring programmes: Genemapper, Genemarker, Gelquest and Fragman. We found that, because some allele sizes were identical or close to the size of one of the internal size standards, all four programmes gave allele size calling errors due to wrongly identifying pull-up signals as the internal size standard. In addition, because allele miscalling in this study was caused by the fluorescent dye that the microsatellites used introducing noise of the same colour as the internal size standard used, the pull-up correction function in Genemapper, Genemarker and Fragman failed to deal with this. Considering that pull-up peak scoring errors can occur with any dye colour, the phenomenon is not limited to the current HEX dye. Using different software and visual scoring of each result will allow accurate sizing of microsatellite alleles.

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Allele Size Miscalling due to the Pull-Up Effect Influencing Size Standard Calibration in Capillary Electrophoresis: A Case Study Using HEX Fluorescent Dye in Microsatellites