the comparison of the effectiveness of a modified conformation sensitive gel electrophoresis with denaturing high performance liquid chromatography

background: several methods have been developed for detection of sequence variation in genes and each has its advantages and disadvantages. a disadvantage of them is that the simpler, cost-effective methods are commonly perceived as being less sensitive in their detection of sequence variation, whereas those with proven sensitivity have a requirement for complex or expensive laboratory equipment. in this context, we undertook improvements to the conformation sensitive gel electrophoresis (csge) method which provides a cost-effective approach to mutation detection and compared the results with scanning carried out using denaturing high performance liquid chromatography (dhplc) which utilises a dedicated analyser. methods: we designed pcr primers to amplify the seven protein-coding exons of the human spp2 gene which encodes secreted phosphoprotein 24 (spp24) such that the amplified products included the immediately-adjacent intronic regions. five improvements were made to the csge method that was used to the scan the pcr-amplified dna. the scanning was then repeated using dhplc and the results were compared. results: using csge, a single nucleotide polymorphism was discovered in exon 2 and another in intron 2 of the gene. re-scanning of the same regions by dhplc detected no additional sequence polymorphisms. conclusion: with modification of the original protocol, csge is capable of providing a simple and cost-effective approach to the detection of dna sequence polymorphisms that appears to be comparable in sensitivity to dhplc.