Open Access Research article

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

Jessica G Woo12*, Guangyun Sun1, Mary Haverbusch1, Subbarao Indugula1, Lisa J Martin12, Joseph P Broderick1, Ranjan Deka1 and Daniel Woo1

Author Affiliations

1 University of Cincinnati College of Medicine, 321 Albert Sabin Way, Cincinnati, OH 45267, USA

2 Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA

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BMC Genetics 2007, 8:79  doi:10.1186/1471-2156-8-79

Published: 8 November 2007



With the advent of genome-wide genotyping, the utility of stored buccal brushes for DNA extraction and genotyping has been questioned. We sought to describe the genomic DNA yield and concordance between stored buccal brushes and blood samples from the same individuals in the context of Affymetrix 500 K Human GeneChip genotyping.


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.