Multiplex SNP-SCALE: A cost-effective medium-throughput SNP genotyping method

Kenta, T., Gratten, J., Haigh, N. S., Hinten, G. N., Slate, J., Butlin, R. K. and Burke, T. (2008) Multiplex SNP-SCALE: A cost-effective medium-throughput SNP genotyping method. Molecular Ecology Resources, 8 6: 1230-1238. doi:10.1111/j.1755-0998.2008.02190.x


Author Kenta, T.
Gratten, J.
Haigh, N. S.
Hinten, G. N.
Slate, J.
Butlin, R. K.
Burke, T.
Title Multiplex SNP-SCALE: A cost-effective medium-throughput SNP genotyping method
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-098X
1755-0998
Publication date 2008-11-01
Year available 2008
Sub-type Article (original research)
DOI 10.1111/j.1755-0998.2008.02190.x
Open Access Status
Volume 8
Issue 6
Start page 1230
End page 1238
Total pages 9
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
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.
Keyword Genotyping
Locked nucleic acid (LNA)
Medium throughput
Nonmodel organism
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Queensland Brain Institute Publications
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Created: Sat, 22 Oct 2011, 00:55:40 EST by Jake Gratten on behalf of Queensland Brain Institute