Abstract
Background: A number of methods of genotyping single nucleotide polymorphisms (SNPs) are currently available, ranging from the traditional restriction fragment length polymorphism (RFLP) and single‐stranded conformational polymorphism (SSCP) to more sophisticated technologies. We determined the utility of three novel methods by genotyping aldehyde dehydrogenase‐2 (ALDH2).Methods: DNA was isolated from blood samples of 241 control subjects and 74 patients with esophageal cancer. The utility of three novel genotyping methods—melting curve analysis using a LightCycler, SNaPshot analysis using an ABI PRISM 310 genetic analyzer, and denaturing high‐performance liquid chromatography using a WAVE DNA fragment analysis system—were compared with that of conventional fluorescent‐based polymerase chain reaction (PCR)‐SSCP using an ALF express DNA sequencer.Results: The frequency of the mutant ALDH2*2 allele was significantly higher in patients with esophageal cancer (27.7%) than in control subjects (16.2%; p < 0.01; habitual alcohol drinkers). The melting curve analysis was accurate, more rapid, and easier to use than the SNaPshot analysis or denaturing high‐performance liquid chromatography analysis. Fluorescent‐based PCR‐SSCP proved useful for analyzing a large number of samples.Conclusion: Melting curve analysis using the LightCycler is suitable for the genotyping of small numbers of samples in a routine clinical setting; fluorescent‐based PCR‐SSCP analysis using the ALF express DNA sequencer can be used for large‐scale genotyping in epidemiologic studies.
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