Collection of genomic DNA by buccal swabs for polymerase chain reaction-based biomarker assays

Studies in molecular and genetic epidemiology require a high-throughput, lo w cost, and reliable means of genomic DNA collection. Buccal (cheek) swabs have been proposed as a means of achieving these goals, but there is little information about the practical application of this approach. From January 1995 to December 1997, we processed 995 buccal swabs for use in polymerase chain reaction (PCR)-based genotype assays in the context of ongoing molec ular epidemiologic studies. Six hundred forty-seven of these swabs were pro cessed immediately after collection and 348 were received by mail. We were able to obtain at least one genotype from 99.7% (645 of 647) of fresh-proce ssed and 97.4% (330 of 339) of mailed biosamples. A PCR success rate of 90. 3% (2,546 genotypes from 2,819 assays) was achieved. Genotypes were obtaine d from 96.1% (1,865 genotypes from 1,941 assays) of fresh-processed biosamp les and 77.6% (681 genotypes from 878 assays) of mailed biosamples. PCR suc cess rates at any single locus ranged from 92.6 to 98.8% (fresh-processed) and 75.5 to 79.6% (mailed). The PCR success rate among fresh-processed bios amples was significantly higher than among mailed biosamples (Fisher's exac t test p < 0.0001), and more attempts were required to obtain a successful PCR result for mailed biosamples as compared to fresh-processed biosamples. For one locus (CYP3A4), a subset of mailed biosamples was purified if two or more PCR failures occurred. Additional genotypes were obtained in 58.3% of these previously failed biosamples. Time from biosample receipt to DNA e xtraction had no effect on PCR success. After storage of processed biosampl es for as long as 3 years, there was no appreciable decrease in the rate of PCR success. These results suggest that adequate DNA for PCR-based applica tions can be obtained from buccal swabs,but sampling or processing consider ations may be important in obtaining optimal results.