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The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

Nature Protocols volume 2, pages 168–177 (2007)Cite this article

Abstract

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion–deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

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Figure 1: The tagged microarray marker (TAM) approach.
Figure 2: Post-hybridization washing setup for microarray slides.
Figure 3: Examples of tagged microarray marker (TAM) results.

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Acknowledgements

This method could not have been developed without intellectual input from Pete Isaac and Noel Ellis. We are grateful to Mike Ferguson, without whom we would not have had easy access to microarray facilities.

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  1. Viacheslav Bolshakov

    Present address: Present address: University of Reading, Biocentre, Whiteknights, Box 221, Reading, Berkshire RG6 6AS, UK.,

Authors and Affiliations

  1. Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee, DD2 5DA, UK

    Runchun Jing & Andrew J Flavell

  2. Post-Genomics and Molecular Interactions Centre, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK

    Viacheslav Bolshakov

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  1. Runchun Jing
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Correspondence to Andrew J Flavell.

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Jing, R., Bolshakov, V. & Flavell, A. The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms. Nat Protoc 2, 168–177 (2007). https://doi.org/10.1038/nprot.2006.408

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