The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms.
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.
Jing
Runchun
R
Plant Research Unit, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, UK.
Bolshakov
Viacheslav
V
Flavell
Andrew J
AJ
D001710:Biotin; D004251:DNA Transposable Elements / Q000235:genetics*; D005453:Fluorescence; D005819:Genetic Markers / Q000235:genetics*; D046228:Microarray Analysis / Q000379:methods*; D009841:Oligonucleotides; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*
D004251:DNA Transposable Elements; D005819:Genetic Markers; D009841:Oligonucleotides; D001710:Biotin