Assessment of DNA extracted from FTA® cards for use on the Illumina iSelect BeadChip

Matthew C Mcclure,Robert D Schnabel,Jeremy F Taylor,Stephanie D Mckay

doi:10.1186/1756-0500-2-107

Abstract

BackgroundAs FTA® cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact (fragment sizes ≥ 2 kb), and high-quality DNA. Bovine blood and nasal swab samples collected on FTA cards were extracted using the commercially available GenSolve kit with a minor modification. The call rate and concordance of genotypes from each sample were compared to those obtained from whole blood samples extracted by standard PCI extraction.FindingsAn ANOVA analysis indicated no significant difference (P > 0.72) in BovineSNP50 genotype call rate between DNA extracted from FTA cards by the GenSolve kit or extracted from whole blood by PCI. Two sample t-tests demonstrated that the DNA extracted from the FTA cards produced genotype call and concordance rates that were not different to those produced by assaying DNA samples extracted by PCI from whole blood.ConclusionWe conclude that DNA extracted from FTA cards by the GenSolve kit is of sufficiently high quality to produce results comparable to those obtained from DNA extracted from whole blood when assayed by the Illumina iSelect technology. Additionally, we validate the use of nasal swabs as an alternative to venous blood or buccal samples from animal subjects for reliably producing high quality genotypes on this platform.

Highlights

As FTA® cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact, and high-quality DNA
The following samples were collected from two Angus (Bos taurus) bulls: 10 ml of whole blood (WB) collected and stored in vacuum tubes with 15 mg of EDTA (Covidien, Mansfield, MA, USA), WB was collected from ear veins and applied to FTA and FTA Elute cards [15,16], and nasal swab samples were collected using a sterile foam tipped applicator (Whatman) which was rubbed for 10 seconds against the inside of the bull's nose and pressed against an FTA Elute card to transfer cells to the card
We were concerned whether genotypes obtained from DNA harvested from FTA cards would yield reproducible genotypes that were highly concordant with those produced from DNA extracted from WB

Summary

Introduction

As FTA® cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact (fragment sizes ≥ 2 kb), and high-quality DNA. While DNA collected for SNP analysis needs to be of sufficient quality to ensure high genotype call rates, the method of collection used in the field needs to be straightforward. Previous research has shown that multiple genomic sources, including lymphocytes, buccal cells, whole genome amplified samples, and fingernails can be used to generate high-density SNP data provided the DNA sample is of adequate quality and quantity [3,4,5,6]. The ease of collection, transportation, storage, and protection from degradation of samples stored on FTA cards alleviates many of these issues [8]

Methods

Results

Conclusion