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Single Nucleotide Polymorphisms

Methods and Protocols

  • Book
  • © 2003

Overview

Editors:
  1. Pui-Yan Kwok

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

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

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. SNPs: Why Do We Care?

    • Lisa D. Brooks
    Pages 1-14

  3. Denaturing High-Performance Liquid Chromatography

    • Andreas Premstaller, Peter J. Oefner
    Pages 15-35

  4. SNP Detection and Allele Frequency Determination by SSCP

    • Tomoko Tahira, Akari Suzuki, Yoji Kukita, Kenshi Hayashi
    Pages 37-46

  5. Conformation-Sensitive Gel Electrophoresis

    • Arupa Ganguly
    Pages 47-58

  6. Detection of Mutations in DNA by Solid-Phase Chemical Cleavage Method

    • Chinh T. Bui, Jeffrey J. Babon, Andreana Lambrinakos, Richard G. H. Cotton
    Pages 59-70

  7. SNP Discovery by Direct DNA Sequencing

    • Pui-Yan Kwok, Shenghui Duan
    Pages 71-84

  8. Computational SNP Discovery in DNA Sequence Data

    • Gabor T. Marth
    Pages 85-110

  9. Genotyping SNPs With Molecular Beacons

    • Salvatore A. E. Marras, Fred Russell Kramer, Sanjay Tyagi
    Pages 111-128

  10. SNP Genotyping by the ′’-Nuclease Reaction

    • Kenneth J. Livak
    Pages 129-147

  11. Genotyping SNPs by Minisequencing Primer Extension Using Oligonucleotide Microarrays

    • Katarina Lindroos, Ulrika Liljedahl, Ann-Christine Syvänen
    Pages 149-165

  12. Quantitative Analysis of SNPs in Pooled DNA Samples by Solid-Phase Minisequencing

    • Charlotta Olsson, Ulrika Liljedahl, Ann-Christine Syvänen
    Pages 167-176

  13. Homogeneous Primer Extension Assay With Fluorescence Polarization Detection

    • Tony M. Hsu, Pui-Yan Kwok
    Pages 177-187

  14. Pyrosequencing for SNP Genotyping

    • Mostafa Ronaghi
    Pages 189-195

  15. Homogeneous Allele-Specific PCR in SNP Genotyping

    • Søren Germer, Russell Higuchi
    Pages 197-214

  16. Oligonucleotide Ligation Assay

    • Jonas Jarvius, Mats Nilsson, Ulf Landegren
    Pages 215-228

  17. Invader Assay for SNP Genotyping

    • Victor Lyamichev, Bruce Neri
    Pages 229-240

  18. MALDI-TOF Mass Spectrometry-Based SNP Genotyping

    • Niels Storm, Brigitte Darnhofer-Patel
    Pages 241-262

  19. Back Matter

    Pages 263-269
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About this book

Single nucleotide polymorphisms (SNPs) have become the markers of choice in elucidating the relationship between DNA sequence variation and susceptibility to disease and have clearly become the focus of the next phase of the human genome project. In Single Nucleotide Polymorphisms: Methods and Protocols, Pui-Yan Kwok, MD, PhD, has assembled a collection of robust techniques for the difficult process of SNP discovery and genotyping. These cutting-edge protocols for mutation/SNP detection utilize denaturing high-performance liquid chromatography (dHPLC), single-strand conformation polymorphism (SSCP), conformation-sensitive gel electrophoresis (CSGE), chemical cleavage, and direct sequencing. Equally powerful and up-to-date methods are given for genotyping SNPs, including molecular beacons, the Taqman assay, single-base extension approaches, pyrosequencing, ligation, the Invader assay, and primer extension with mass spectrometry detection. Described in step-by-step detail by their inventors, each method provides extensive notes on the technical steps critical for experimental success, time-saving techniques, and tips on avoiding pitfalls.
Comprehensive and authoritative, Single Nucleotide Polymorphisms: Methods and Protocols provides in a readily reproducible format all the major SNP discovery and genotyping techniques in use today, whether for using DNA diagnostics to identify a pathogen, for studying the genetic basis of human disease, or for molecular breeding programs in agriculture.

Editors and Affiliations

  • Cardiovascular Research Institute and Department of Dermatology, University of California, San Francisco, San Francisco, USA

    Pui-Yan Kwok

Bibliographic Information

  • Book Title: Single Nucleotide Polymorphisms

  • Book Subtitle: Methods and Protocols

  • Editors: Pui-Yan Kwok

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1592593275

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2003

  • eBook ISBN: 978-1-59259-327-9Published: 04 February 2008

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 269

  • Number of Illustrations: 24 b/w illustrations, 18 illustrations in colour

  • Topics: Human Genetics

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