Temperature switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs.

Tania Tabone,Diane E Mather,Matthew J Hayden

doi:10.1186/1471-2164-10-580

Abstract

BackgroundMany research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs). Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP), a biphasic four-primer PCR system with a universal primer design that permits amplification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles. TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for individual assay optimization and operator expertise in the deployment of SNP assays.ResultsWe demonstrate the utility of TSP for the rapid construction of robust and convenient endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis by generating a total of 11,232 data points. The TSP assays were performed under standardised reaction conditions, requiring minimal optimization of individual assays. High genotyping accuracy was verified by 100% concordance of TSP genotypes in a blinded study with an independent genotyping method.ConclusionTheoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species.

Highlights

Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs)
We describe the method of temperature-switch PCR (TSP), which was developed to address difficulties that are commonly associated with deploying a variety of singlemarker SNP genotyping methods in the laboratory
The present study demonstrates the utility of TSP for the rapid development of robust endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis in cultivated barley (Hordeum vulgare L.), an agriculturally important crop with a 5,300 Mb diploid genome

Summary

Introduction

Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs). TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for individual assay optimization and operator expertise in the deployment of SNP assays. Regardless of the assay principles, these methods share the common feature that a pair of oligonucleotide probes is designed to cover and flank the SNP. These probes may be used to amplify the target region and manipulate the location of the polymorphism to an optimal position within the PCR fragment that maximises detection sensitivity. Laboratories must typically deploy a suite of genotyping methods

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