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


RESULTS
Buccal cytobrushes stored for approximately 7 years at -80 degrees C prior to extraction yielded sufficient double stranded DNA (dsDNA) to be successfully genotyped on the Affymetrix approximately 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.


CONCLUSIONS
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.
Woo
Jessica G
JG
University of Cincinnati College of Medicine, 321 Albert Sabin Way, Cincinnati, OH 45267, USA. jessica.woo@cchmc.org
Sun
Guangyun
G
Haverbusch
Mary
M
Indugula
Subbarao
S
Martin
Lisa J
LJ
Broderick
Joseph P
JP
Deka
Ranjan
R
Woo
Daniel
D
D000465:Algorithms; D002610:Cheek; D004247:DNA / Q000097:blood / Q000302:isolation & purification*; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D009061:Mouth Mucosa / Q000737:chemistry*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards*; D011786:Quality Control; D015203:Reproducibility of Results; D013048:Specimen Handling / Q000379:methods / Q000592:standards*
D004247:DNA