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. 2018 Jun 14;11(1):382.
doi: 10.1186/s13104-018-3476-5.

Evaluation of buccal swabs for pharmacogenetics

J Sidney Ang  1 , Martin N Aloise  1 , Diana Dawes  1   2 , Maryn G Dempster  1   3 , Robert Fraser  4   5 , Andrea Paterson  1   6 , Paul Stanley  1 , Adriana Suarez-Gonzalez  1 , Martin Dawes  1   7 , Hagit Katzov-Eckert  8
Affiliations

Evaluation of buccal swabs for pharmacogenetics

J Sidney Ang et al. BMC Res Notes. .

Abstract

Objective: A simple, non-invasive sample collection method is key for the integration of pharmacogenetics into clinical practice. The aim of this study was to gain samples for pharmacogenetic testing and evaluate the variation between dry-flocked and sponge-tipped buccal swabs in yield and quality of DNA isolated.

Results: Thirty-one participants collected samples using dry-flocked swabs and sponge-tipped swabs. Samples were assessed for DNA yield, quality and genotyping performance on a qPCR OpenArray platform of 28 pharmacogenetic SNPs and a CYP2D6 TaqMan copy number variant. DNA from sponge-tipped swabs had a significantly greater yield compared to DNA collected with dry-flocked swabs (p = 4.4 × 10-7). Moreover, highest genotyping call rates across all assays and highest CNV confidence scores were observed in DNA samples collected from sponge-tipped swabs (97% vs. 54% dry-flocked swabs; 0.99 vs. 0.88 dry-flocked swabs, respectively). Sample collection using sponge-tipped swabs provides a DNA source of sufficient quantity and quality for pharmacogenetic variant detection using qPCR.

Keywords: Buccal swabs; Copy number variation; OpenArray; Pharmacogenetics; Sample collection.

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Figures

Fig. 1
Fig. 1
Comparisons of concentration on assay performance a OpenArray of 28 SNPs, b CYP2D6 CNV assay
Fig. 2
Fig. 2
Mean genotyping call rate across a 28 SNP pharmacogenetic panel on the OpenArray platform
See this image and copyright information in PMC

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