ABSTRACT:

DNA fragment analysis examines the comparative mobility of DNA fragments as they move through a gel matrix under electrophoresis. Fragment analysis may be performed to measure size, as in polymorphic markers for linkage analysis, or to reveal sequence changes, as in single strand conformation polymorphisms. Accuracy and reproducibility are essential when gel results from different sources are merged, whether within one laboratory or within a collaboration. Several factors affect fragment mobility including instrumentation, gel formulations, size standards and gel running conditions. This study compares these and other variables to determine their effect on the allele-size calling of three polymorphic PCR amplicons of known sequence.