Five useful approaches for generating more valid gel images of loss of heterozygosity and clonality analysis with an automated 377 DNA sequencer

The recently introduced fluorescence-based gene scan system for assessment of loss of heterozygosity (LOH) and clonality with an automated DNA sequenc er has several advantages over the traditional method. However, the product ion of gel images with this system is subjected to more technical challenge s, including the interference of autofluorescence, weaker and less consiste nt signals that result from the restricted well size and difficulties in sa mple loading. To minimize the impact of these technical difficulties. sever al unique strategies were used, including the following: elimination of fab rics or paper towels in the cleaning of gel plates and containers; use of a modified loading buffer, use of more concentrated gels; use of an innovati ve apparatus to clean gel wells before and after the prerun; and covering t he black printer cartridge with a sheet of scorch tape. With these strategi es, the authors have been able to consistently obtain gel images that can b e presented as either densitometric graphs or as band patterns for direct v isual assessment.