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

BMC Research Notes

Darren K Griffin²  Grant A Walling¹  Chris P Reitter³  Katie E Fowler² 

[1] JSR Genetics, Southburn, Driffield, East Yorkshire, YO25 9ED, UK;School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NZ, UK;Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK

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

Others  :  1165709
DOI  :  10.1186/1756-0500-5-503

 received in 2012-05-23, accepted in 2012-09-03,  发布年份 2012

【 摘 要 】

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.

【 授权许可】

   
2012 Fowler et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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