Single Nucleotide Polymorphisms

Volume 578 of the series Methods in Molecular Biology™ pp 255-276


High-Throughput SNP Genotyping: Combining Tag SNPs and Molecular Beacons

  • Luis B. BarreiroAffiliated withDepartment of Human Genetics, The University of Chicago
  • , Ricardo HenriquesAffiliated withInstitute for Molecular Medicine, Faculty of Medicine of the University of Lisbon, Gene Expression and Biophysics Unit
  • , Musa M. MhlangaAffiliated withGene Expression and Biophysics Unit, Institute for Molecular Medicine, Portugal and Gene Expression and Biophysics Group, CSIR Biosciences

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In the last decade, molecular beacons have emerged to become a widely used tool in the multiplex typing of single nucleotide polymorphisms (SNPs). Improvements in detection technologies in instrumentation and chemistries to label these probes have made it possible to use up to six spectrally distinguishable probes per reaction well. With the remarkable advances made in the characterization of human genome diversity, it has been possible to describe empirical patterns of SNPs and haplotype variation in the genome of diverse human populations. These patterns have revealed that the human genome is structured in blocks of strong linkage disequilibrium (LD). Because SNPs tend to be in LD with each other, common haplotypes share common SNPs and thus the majority of the diversity in a region can be characterized by typing a very small number of SNPs; so-called tag SNPs. Herein lies the advantage of the multiplexing ability of molecular beacons, since it becomes possible to use as few as 30 probes to interrogate several haplotypes in a high-throughput approach. Thus, through the combined use of tag SNPs and molecular beacons it becomes possible to type individuals for clinically relevant haplotypes in a high-throughput manner at a cost that is orders of magnitude less than that for high throughput sequencing methods.

Key words

Linkage disequilibrium single nucleotide polymorphism tagging single nucleotide polymorphisms DC-SIGN Mycobacterium tuberculosis molecular beacons real-time PCR