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

Fowler, Katie E., Reitter, Chris P, Walling, Grant A, Griffin, Darren K. (2012) Novel approach for deriving genome wide SNP analysis data from archived blood spots. BMC Research Notes, 5 (1). p. 503. ISSN 1756-0500. (doi:10.1186/1756-0500-5-503) (KAR id:34145)

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http://dx.doi.org/10.1186/1756-0500-5-503

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.

Item Type: Article
DOI/Identification number: 10.1186/1756-0500-5-503
Subjects: Q Science
Divisions: Divisions > Division of Natural Sciences > Biosciences
Depositing User: Darren Griffin
Date Deposited: 06 Jun 2013 08:39 UTC
Last Modified: 16 Nov 2021 10:11 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/34145 (The current URI for this page, for reference purposes)
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
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