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

TY - JOUR

T1 - The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

AU - Jing, Runchun

AU - Bolshakov, Viacheslav

AU - Flavell, Andrew J.

PY - 2007

Y1 - 2007

N2 - 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.

AB - 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.

KW - SYSTEM

KW - DNA

KW - MUTATION

KW - GENES

KW - MODEL

KW - PCR

U2 - 10.1038/nprot.2006.408

DO - 10.1038/nprot.2006.408

M3 - Article

C2 - 17401351

SN - 1754-2189

VL - 2

SP - 168

EP - 177

JO - Nature Protocols

JF - Nature Protocols

IS - 1

ER -