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Single Nucleotide Polymorphisms pp 129–147Cite as

SNP Genotyping by the ′’-Nuclease Reaction

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Part of the Methods in Molecular Biology™ book series (MIMB,volume 212)

Abstract

The chief attribute of the fluorogenic 5′ nuclease assay is that it is completely homogeneous. After mixing the sample and reaction components, the assay is run in a closed tube format with no postpolymerase chain reaction (PCR) processing steps. Results are obtained by simply measuring the fluorescence of the completed reactions. By eliminating post-PCR processing, allelic discrimination with fluorogenic probes reduces the time of analysis, eliminates the labor and supply costs of post-PCR steps, reduces the risk of crossover contamination, and minimizes sources of error. The assay has the sensitivity of PCR so that a minimum amount of genomic DNA is required. The use of endpoint fluorescence measurements maximizes throughput. Using a single ABI Prism® 7900HT Sequence Detection System and 24-h operation, it is possible to generate up to 250,000 SNP results per day. TaqMan® MGB probes and the entire operating system outlined below make it possible to quickly apply the 5′ nuclease assay to any allelic discrimination application where high throughput is of paramount concern.

Keywords

  • Allelic Discrimination
  • 7900HT Sequence Detection System
  • Minor Groove Binder
  • Fluorogenic Probe
  • Nuclease Assay

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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  • DOI: 10.1385/1-59259-327-5:129
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Author information

Authors and Affiliations

  1. Applied Biosystems, Foster City, CA

    Kenneth J. Livak

Authors
  1. Kenneth J. Livak
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Editor information

Editors and Affiliations

  1. Cardiovascular Research Institute and Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA

    Pui-Yan Kwok MD, PhD

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© 2003 Humana Press Inc.

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Livak, K.J. (2003). SNP Genotyping by the ′’-Nuclease Reaction. In: Kwok, PY. (eds) Single Nucleotide Polymorphisms. Methods in Molecular Biology™, vol 212. Springer, Totowa, NJ. https://doi.org/10.1385/1-59259-327-5:129

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  • DOI: https://doi.org/10.1385/1-59259-327-5:129

  • Publisher Name: Springer, Totowa, NJ

  • Print ISBN: 978-0-89603-968-1

  • Online ISBN: 978-1-59259-327-9

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