Kinetic Fluorescence-Quenching Detection Assay for Allele Frequency Estimation View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2005-08-15

AUTHORS

Federico Innocenti , Ming Xiao , Pui-Yan Kwok

ABSTRACT

The analysis of human genetic variations, such as single-nucleotide polymorphisms (SNPs), has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching detection. The template-directed dye-terminator incorporation with fluorescence quenching detection (FQ-TDI) assay is based on the observation that the intensity of fluorescent dye R110- and R6G-labeled acycloterminators is universally quenched once they are incorporated onto a deoxyribonucleic acid (DNA) oligonucleotide primer. By comparing the rate of fluorescence quenching of the two allelic dyes in real time, we have extended this method for allele frequency estimation of SNPs in pooled DNA samples. The kinetic FQ-TDI assay is highly accurate and reproducible both in genotyping and in allele frequency estimation. Allele frequencies estimated by the kinetic FQ-TDI assay correlated well with known allele frequencies, with an r2 value of 0.993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations. More... »

PAGES

115-124

References to SciGraph publications

  • 2002-11. DNA Pooling: a tool for large-scale association studies in NATURE REVIEWS GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1385/1-59259-957-5:115

    DOI

    http://dx.doi.org/10.1385/1-59259-957-5:115

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1051955002

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/16100403


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