Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/86921
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Type: Journal article
Title: Multiplex SNP-SCALE: a cost-effective medium-throughput single nucleotide polymorphism genotyping method
Author: Kenta, T.
Gratten, J.
Watson-Haigh, N.
Hinten, G.
Slate, J.
Butlin, R.
Burke, T.
Citation: Molecular Ecology Resources, 2008; 8(6):1230-1238
Publisher: Blackwell Publishing
Issue Date: 2008
ISSN: 1755-098X
1755-0998
Statement of
Responsibility: 
T. Kenta, J. Gratten, N. S. Haigh, G. N. Hinten, J. Slate, R. K. Butlin, and T. Burke
Abstract: We describe a convenient, cost-effective and flexible medium-throughput single nucleotide polymorphism (SNP) genotyping method, Multiplex SNP-SCALE, which enables the simultaneous amplification by polymerase chain reaction (PCR) of up to 25 (or potentially more) loci followed by electrophoresis in an automated DNA sequencer. We extended the original SNP-SCALE method to include (i) use of a commercial multiplex PCR kit, (ii) a four-dye system, (iii) much-reduced (2-µL) reaction volumes, (iv) drying down of template DNA before PCR, (v) use of pig-tailed primers, (vi) a PCR product weighting system, (vii) a standard optimized touchdown PCR thermocycling programme, and (viii) software (SNP-SCALE Primer Designer) that automatically designs suitable SNP-SCALE primers for a batch of loci. This new protocol was validated for different types of SNPs. The method is cost- and time-effective for medium-scale evolutionary and ecological projects involving 10s to 100s of loci.
Keywords: genotyping; locked nucleic acid (LNA); medium throughput; nonmodel organism; single nucleotide polymorphism (SNP); small reaction scale; universal fluorescent-labelled oligonucleotide (UFO) primer
Rights: © 2008 The Authors
DOI: 10.1111/j.1755-0998.2008.02190.x
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