title: Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChip.
abstract: 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.
authors.affiliation: University of Cincinnati College of Medicine, 321 Albert Sabin Way, Cincinnati, OH 45267, USA. jessica.woo@cchmc.org
authors.forename: Jessica G
authors.initials: JG
authors.lastname: Woo
authors.forename: Guangyun
authors.initials: G
authors.lastname: Sun
authors.forename: Mary
authors.initials: M
authors.lastname: Haverbusch
authors.forename: Subbarao
authors.initials: S
authors.lastname: Indugula
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Martin
authors.forename: Joseph P
authors.initials: JP
authors.lastname: Broderick
authors.forename: Ranjan
authors.initials: R
authors.lastname: Deka
authors.forename: Daniel
authors.initials: D
authors.lastname: Woo
mesh_terms: 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*
chemical_list: D004247:DNA