SNP-SCALE: SNP scoring by colour and length exclusion

Hinten, G. N., Hale, M. C., Gratten, J., Mossman, J. A., Lowder, B. V., Mann, M. K. and Slate, J. (2007) SNP-SCALE: SNP scoring by colour and length exclusion. Molecular Ecology Notes, 7 3: 377-388. doi:10.1111/j.1471-8286.2006.01648.x

Author Hinten, G. N.
Hale, M. C.
Gratten, J.
Mossman, J. A.
Lowder, B. V.
Mann, M. K.
Slate, J.
Title SNP-SCALE: SNP scoring by colour and length exclusion
Journal name Molecular Ecology Notes   Check publisher's open access policy
ISSN 1755-098X
Publication date 2007-05-01
Year available 2007
Sub-type Article (original research)
DOI 10.1111/j.1471-8286.2006.01648.x
Open Access Status
Volume 7
Issue 3
Start page 377
End page 388
Total pages 12
Place of publication Oxford, United Kingdom
Publisher Wiley-Blackwell Publishing
Language eng
Abstract Here we present SNP-SCALE, a new single nucleotide polymorphism genotyping protocol based on allele-specific polymerase chain reaction (AS-PCR), but with two critical modifications designed to maximize accuracy, efficiency and throughput and minimize costs. The first is the addition of a locked nucleic acid (LNA) at the 3′-SNP position of each of the two allele-specific forward primers. The second is the addition of size-differentiating M13 tails at the 5′ end of each primer, which facilitates the use of universal fluorescent primers. The use of LNAs makes SNP-SCALE significantly more sensitive and specific than standard AS-PCR. Moreover, SNP-SCALE is ideally suited to a touchdown-like PCR protocol, such that PCRs can be standardized, PCR optimization is straightforward, and medium-high throughput can be readily achieved. We anticipate that the SNP-SCALE protocol will be useful to molecular ecologists for a broad range of studies.
Keyword Association mapping
Gene mapping
Locked nucleic acid
Population genomics
Single nucleotide polymorphism
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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Citation counts: TR Web of Science Citation Count  Cited 12 times in Thomson Reuters Web of Science Article | Citations
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Created: Sat, 22 Oct 2011, 01:09:11 EST by Jake Gratten on behalf of Queensland Brain Institute