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Oragene is compatible with TaqMan SNP genotyping

J. Chartier and H.C. Birnboim
DNA Genotek Inc., Ottawa, ON, Canada

DNA collected with Oragene works well with TaqMan SNP Genotyping Assays. SNPs in the thymidylate synthetase and apolipoprotein E genes were reliably detected.


Introduction
Single-nucleotide polymorphisms (SNPs) are highly abundant, and are estimated to occur at 1 out of every 1,000 bases in the human genome (ref. 1). In addition to diagnostic applications, SNPs are useful as markers in population genetics and evolutionary studies (ref. 2). The TaqMan 5 nuclease assay is a widely-used SNP genotyping technology from Applied Biosystems. The purpose of this study was to evaluate the compatibility of Oragene DNA Self-Collection Kits with TaqMan SNP Genotyping Assays.


Materials and Methods
DNA collection
Saliva was collected from 25 donors using Oragene kits. DNA was purified from 200 L aliquots of Oragene/saliva samples using the ethanol precipitation protocol supplied with the kits. Purified DNA was redissolved in 200 L of TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0). DNA was quantified using a fluorimeter and SYBR Green I dye (Molecular Probes) according to the F/D Protocol (ref. 3).

SNP genotyping
Validated TaqMan SNP Genotyping Assays were obtained from Applied Biosystems. The assays are described in Table 1. The probes were labeled with FAM or VIC dye at the 5 end and a minor-groove binder and non-fluorescent quencher at the 3 end. The reaction components for the allelic discrimination reactions were set up according to Table 2. Although it is recommended to use 1 to 20 ng of DNA per reaction
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