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The TaqMan Method for SNP Genotyping

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Single Nucleotide Polymorphisms

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 578))

Abstract

Single nucleotide polymorphisms (SNPs) are common DNA sequence variations that occur at single bases within the genome. SNPs have been instrumental in elucidating the genetic basis of common, complex diseases using genome-wide association studies, candidate gene case-control association studies, and genome-wide linkage analyses. A key to these studies is genotyping of SNPs. Various methods for SNP genotyping have been developed. For a particular genotyping project, the choice of method is dependent on the number of SNPs (n) and the number of DNA samples (m) to be genotyped. For a genome-wide or large-scale project with very high n and small m, the Affymetrix SNP GeneChip and Illumina GoldenGate BeadChips assays are the ideal methods. For a project involving a small number of SNPs (small n) and a large population (high m), the TaqMan assay is the preferred technology as it has high throughput and is highly accurate, precise, time-efficient, and cost-effective. Here, we describe the detailed procedures for TaqMan SNP genotyping assay, including preparation of high-quality DNA samples, the operating protocol, clarification of technical issues, and discussion of several cautionary notes.

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Acknowledgments

This work was supported by NIH grants R01 HL66251, P50 HL77107, and P50 HL81011, and an American Heart Association Established Investigator award (to Q.K.W.). K.G.A. was supported by a seed grant award from the American Medical Association Foundation and funding from the Cleveland Clinic Lerner College of Medicine.

Author information

Authors and Affiliations

  1. Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

    Gong-Qing Shen & Kalil G. Abdullah

  2. Center for Cardiovascular Genetics, Department of Cardiovascular Medicine, Cleveland Clinic, Cleveland, OH, USA

    Qing Kenneth Wang

  3. Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA

    Qing Kenneth Wang

Authors
  1. Gong-Qing Shen
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  2. Kalil G. Abdullah
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  3. Qing Kenneth Wang
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Editor information

Editors and Affiliations

  1. Center for Gene Regulation in, Cleveland State University, Euclid Ave. 2121, Cleveland, 44115, U.S.A.

    Anton A. Komar

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC 2003

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Shen, GQ., Abdullah, K.G., Wang, Q.K. (2009). The TaqMan Method for SNP Genotyping. In: Komar, A. (eds) Single Nucleotide Polymorphisms. Methods in Molecular Biology™, vol 578. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60327-411-1_19

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  • DOI: https://doi.org/10.1007/978-1-60327-411-1_19

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60327-410-4

  • Online ISBN: 978-1-60327-411-1

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