Email updates

Keep up to date with the latest news and content from BMC Research Notes and BioMed Central.

Open Access Technical Note

Novel approach for deriving genome wide SNP analysis data from archived blood spots

Katie E Fowler1*, Chris P Reitter2, Grant A Walling3 and Darren K Griffin1

Author Affiliations

1 School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NZ, UK

2 Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK

3 JSR Genetics, Southburn, Driffield, East Yorkshire, YO25 9ED, UK

For all author emails, please log on.

BMC Research Notes 2012, 5:503  doi:10.1186/1756-0500-5-503

Published: 13 September 2012

Abstract

Background

The ability to transport and store DNA at room temperature in low volumes has the advantage of optimising cost, time and storage space. Blood spots on adapted filter papers are popular for this, with FTA (Flinders Technology Associates) Whatman™TM technology being one of the most recent. Plant material, plasmids, viral particles, bacteria and animal blood have been stored and transported successfully using this technology, however the method of porcine DNA extraction from FTA Whatman™TM cards is a relatively new approach, allowing nucleic acids to be ready for downstream applications such as PCR, whole genome amplification, sequencing and subsequent application to single nucleotide polymorphism microarrays has hitherto been under-explored.

Findings

DNA was extracted from FTA Whatman™TM cards (following adaptations of the manufacturer’s instructions), whole genome amplified and subsequently analysed to validate the integrity of the DNA for downstream SNP analysis. DNA was successfully extracted from 288/288 samples and amplified by WGA. Allele dropout post WGA, was observed in less than 2% of samples and there was no clear evidence of amplification bias nor contamination. Acceptable call rates on porcine SNP chips were also achieved using DNA extracted and amplified in this way.

Conclusions

DNA extracted from FTA Whatman cards is of a high enough quality and quantity following whole genomic amplification to perform meaningful SNP chip studies.

Keywords:
FTA Whatman™TM cards; Single nucleotide polymorphism; SNP; DNA extraction; Whole genome amplification; WGA; STR-PCR