Library Science

Pui-Yan Kwok, MD, PhD, has assembled a comprehensive collection of readily reproducible techniques for the difficult process of single nucleotide polymorphisms (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.

Authors: P-Y. Kwok

single-nucleotide-polymorphisms.pdf

Table of Contents

• SNPs: Why Do We Care? (pp. 001-014)
  Brooks, Lisa D.
• Denaturing High-Performance Liquid Chromatography (pp. 015-035)
  Premstaller, Andreas; Oefner, Peter J.
• SNP Detection and Allele Frequency Determination by SSCP (pp. 037-046)
  Tahira, Tomoko; Suzuki, Akari; Kukita, Yoji; Hayashi, Kenshi
• Conformation-Sensitive Gel Electrophoresis (pp. 047-058)
  Ganguly, Arupa
• Detection of Mutations in DNA by Solid-Phase Chemical Cleavage Method: A Simplified Assay (pp. 059-070)
  Bui, Chinh T.; Babon, Jeffrey J.; Lambrinakos, Andreana; Cotton, Richard G. H.
• SNP Discovery by Direct DNA Sequencing (pp. 071-084)
  Kwok, Pui-Yan; Duan, Shenghui
• Computational SNP Discovery in DNA Sequence Data (pp. 085-110)
  Marth, Gabor T.
• Genotyping SNPs With Molecular Beacons (pp. 111-128)
  Marras, Salvatore A. E.; Kramer, Fred Russell; Tyagi, Sanjay
• SNP Genotyping by the 5-Nuclease Reaction (pp. 129-147)
  Livak, Kenneth J.
• Genotyping SNPs by Minisequencing Primer Extension Using Oligonucleotide Microarrays (pp. 149-165)
  Lindroos, Katarina; Liljedahl, Ulrika; Syvanen, Ann-Christine
• Quantitative Analysis of SNPs in Pooled DNA Samples by Solid-Phase Minisequencing (pp. 167-176)
  Olsson, Charlotta; Liljedahl, Ulrika; Syvanen, Ann-Christine
• Homogeneous Primer Extension Assay With Fluorescence Polarization Detection (pp. 177-187)
  Hsu, Tony M.; Kwok, Pui-Yan
• Pyrosequencing for SNP Genotyping (pp. 189-195)
  Ronaghi, Mostafa
• Homogeneous Allele-Specific PCR in SNP Genotyping (pp. 197-214)
  Germer, Soren; Higuchi, Russell
• Oligonucleotide Ligation Assay (pp. 215-228)
  Jarvius, Jonas; Nilsson, Mats; Landegren, Ulf
• Invader Assay for SNP Genotyping (pp. 229-240)
  Lyamichev, Victor; Neri, Bruce
• MALDI-TOF Mass Spectrometry-Based SNP Genotyping (pp. 241-262)
  Storm, Niels; Darnhofer-Patel, Brigitte; van den Boom, Dirk; Rodi, Charles P.

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