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Pyrosequencing of Clinically Relevant Polymorphisms

  • Sharon Marsh
  • Cristi R. King
  • Adam A. Garsa
  • Howard L. McLeod
Part of the Methods in Molecular Biology™ book series (MIMB, volume 311)

Abstract

The data generated from the Human Genome Project has led to an explosion of technology for low-, medium-, and high-throughput genotyping methods. Pyrosequencing is a genotyping assay based on sequencing by synthesis. Short runs of sequence around each polymorphism are generated, allowing for internal controls for each sample. Pyrosequencing can also be used to identify tri-allelic, indel, and short-repeat polymorphisms, as well as determining allele percentages for methylation or pooled sample assessment. Assays details for Pyrosequencing of clinically relevant polymorphisms are described in this chapter.

Key Words

Pyrosequencing genotype polymorphism 

References

  1. 1.
    Sachidanandam, R., Weissman, D., Schmidt, S. C., et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933.PubMedCrossRefGoogle Scholar
  2. 2.
    Kwok, P. Y. (2001) Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2, 235–258.PubMedCrossRefGoogle Scholar
  3. 3.
    Freimuth, R. R., Ameyaw, M.M., Pritchard, S. C., Kwok, P. Y., and McLeod, H. L. (2004) High-throughput genotyping methods for pharmacogenomic studies. Curr. Pharmacogenom. 2, 21–33.CrossRefGoogle Scholar
  4. 4.
    Ahluwalia, R., Freimuth, R., McLeod, H. L., and Marsh, S. (2003) Use of pyrosequencing to detect clinically relevant polymorphisms in dihydropyrimidine dehydrogenase. Clin. Chem. 49, 1661–1664.PubMedCrossRefGoogle Scholar
  5. 5.
    Mathijssen, R. H., Marsh, S., Karlsson, M. O., et al. (2003) Irinotecan pathway genotype analysis to predict pharmacokinetics. Clin. Cancer Res. 9, 3246–3253.PubMedGoogle Scholar
  6. 6.
    Saeki, M., Saito, Y., Jinno, H., et al. (2003) Comprehensive UGT1A1 genotyping in a Japanese population by pyrosequencing. Clin. Chem. 49, 1182–1185.PubMedCrossRefGoogle Scholar
  7. 7.
    Garsa, A., S. Marsh, S., and McLeod, H. L. CYP3A4 and CYP3A5 genotyping by pyrosequencing. BMC Medical Genetics. In press.Google Scholar
  8. 8.
    Rose, C. M., Marsh, S., Ameyaw, M. M., and McLeod, H. L. (2003) Pharmacogenetic analysis of clinically relevant genetic polymorphisms. Methods Mol. Med. 85, 225–237.PubMedGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2005

Authors and Affiliations

  • Sharon Marsh
    • 1
  • Cristi R. King
    • 1
  • Adam A. Garsa
    • 1
  • Howard L. McLeod
    • 1
  1. 1.Division of Molecular OncologyWashington University School of MedicineSt. Louis

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