Quality assessment of buccal versus blood genomic DNA using the Affymetrix 500 K GeneChipReportar como inadecuado




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BMC Genetics

, 8:79

First Online: 08 November 2007Received: 15 May 2007Accepted: 08 November 2007

Abstract

BackgroundWith 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.

ResultsBuccal 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.

ConclusionBuccal 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.

Jessica G Woo, Guangyun Sun contributed equally to this work.

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Autor: Jessica G Woo - Guangyun Sun - Mary Haverbusch - Subbarao Indugula - Lisa J Martin - Joseph P Broderick - Ranjan Deka -

Fuente: https://link.springer.com/article/10.1186/1471-2156-8-79







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