Tag/anti-tag liquid-phase primer extension array: a flexible and versatile genotyping platform.
This study demonstrates an array-based platform to genotype simultaneously single nucleotide polymorphisms (SNPs) and some short insertions/deletions (indels) by the integration of the universal tag/anti-tag (TAT) system, liquid-phase primer extension (LIPEX), and a novel two-color detection strategy on an array format (TATLIPEXA). The TAT system permits a universal chip to be used for many applications, and the LIPEX simplifies the sample preparation but improves the sensitivity significantly. More importantly, all SNPs and some short indels can be interrogated in a single reaction with only two fluorescent ddNTPs. The concept of TATLIPEXA is demonstrated for nine SNPs (eight point mutations and one single-base insertion), and genotypes obtained show a remarkable concordance rate of 100% with both DNA sequencing and restriction fragment length polymorphism. Moreover, TATLIPEXA is able to provide quantitative information on allele frequency in pooled DNA samples, which could serve as a rapid screening tool for SNPs associated with diseases.
Li
Jing-Guang
JG
Department of Paediatrics, National University of Singapore, 119074, Singapore.
Liljedahl
Ulrika
U
Heng
Chew-Kiat
CK
D003324:Coronary Artery Disease / Q000175:diagnosis / Q000235:genetics*; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics*; D005787:Gene Frequency / Q000235:genetics*; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
D017931:DNA Primers