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BMC Genetics  2007 

Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip

DOI: 10.1186/1471-2156-8-79

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Abstract:

Buccal cytobrushes stored for ~7 years at -80°C prior to extraction yielded sufficient double stranded DNA (dsDNA) to be successfully genotyped on the Affymetrix ~262 K NspI chip, with yields between 536 and 1047 ng dsDNA. Using the BRLMM algorithm, genotyping call rates for blood samples averaged 98.4%, and for buccal samples averaged 97.8%. Matched blood samples exhibited 99.2% concordance, while matched blood and buccal samples exhibited 98.8% concordance.Buccal cytobrushes stored long-term result in sufficient dsDNA concentrations to achieve high genotyping call rates and concordance with stored blood samples in the context of Affymetrix 500 K SNP genotyping. Thus, given high-quality collection and storage protocols, it is possible to use stored buccal cytobrush samples for genome-wide association studies.While blood is considered the optimal source for DNA, inclusion of a blood draw may deter study participation [1]. Buccal cytobrush collection is a simple, painless procedure that allows for effective DNA sampling from a large population, and has been used in several large epidemiologic studies [2,3]. However, concerns regarding the use of buccal brushes have included the lower quantity of genomic DNA isolated [4], lower quality of DNA [4,5], and the fidelity of results from buccal brushes compared with blood samples [5-7]. In addition, there is a concern that older buccal brush samples may not yield as high-quality results as fresh samples [8].The advent of large scale genotyping platforms has also resulted in a reduction in the amount of DNA required. The Affymetrix 500 K GeneChip requires only 250 ng of total genomic DNA per chip, 500 ng total, and this DNA quantity has not changed with the recent release of the Affymetrix 5.0 and 6.0 chips, which enable genotyping up to 1.8 million genetic markers [9-11]. Thus, the DNA requirements of the Affymetrix chips are well below the expected yield of total DNA for buccal samples. As the Affymetrix system uses restri

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