AimThe Factor V Leiden mutation (G1691A) is a clinically important polymorphism that results in an increased risk of thrombosis. The goal of this study was to compare a temperature gradient capillary electrophoresis (TGCE) platform for the detection of Factor V gene mutations to a conventional restriction fragment length polymorphism (RFLP) assay.MethodsThree hundred and four samples were analyzed by both TGCE and a common clinicalMnlI/RFLP assay. Concordance of results between the two assays was observed for 302/304 (99.3%) of the samples.ResultsAll of the Leiden mutants (23/23, 100%) were identified by TGCE. Of the two discrepant results, one was caused by low peak heights in the TGCE output data and was easily rectified by the addition of a minimum peak height threshold. The second discrepancy resulted from the presence of a G→A transition 95bp downstream of the Leiden mutation site. This polymorphism represents a previously unreported alteration of the Factor V gene.ConclusionsThe TGCE assay is less labor-intensive and has a higher throughput capacity than theMnlI/RFLP assay. TGCE is a less specific assay than theMnlI/RFLP assay that allows for the detection of novel polymorphisms, but also creates the need for all positive TGCE results to be confirmed by an alternate method such as sequencing. Our results demonstrate that TGCE is a highly sensitive method for mutation detection and has utility for mutation discovery analysis.