Pub. Date:
Springer-Verlag New York, LLC
Single Nucleotide Polymorphisms: Methods and Protocols / Edition 2

Single Nucleotide Polymorphisms: Methods and Protocols / Edition 2

by Anton A. Komar


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Product Details

ISBN-13: 9781603274104
Publisher: Springer-Verlag New York, LLC
Publication date: 10/27/2009
Series: Methods in Molecular Biology , #578
Edition description: 2nd ed. 2009
Pages: 464
Product dimensions: 7.60(w) x 10.40(h) x 1.30(d)

Table of Contents

Preface v

Contributors xi

Section I Introduction to Single Nucleotide Polymorphisms

1 SNPs: Impact on Gene Function and Phenotype Barkur S. Shastry 3

2 Silent (Synonymous) SNPs: Should We Care About Them? Ryan Hunt Zuben E. Sauna Suresh V. Ambudkar Michael M. Gottesman Chava Kimchi-Sarfaty 23

Section II Bioinformatic Analysis of SNPs

3 SNP Databases Christopher Phillips 43

4 Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery and Analysis Jan van Oeveren Antoine Janssen 73

Section III SNP Identification and Detection Strategies: Whole Genome Sequencing and Re-Sequencing

5 Next-Generation Sequencing Methods: Impact of Sequencing Accuracy on SNP Discovery Eugene Y. Chan 95

6 Scanning Probe and Nanopore DNA Sequencing: Core Techniques and Possibilities John Lund Babak A. Parviz 113

7 Pyrosequencing for SNP Genotyping Jose Luis Royo Jose Jorge Galán 123

Section IV Prescreening (Melting Based) Methods for SNP Discovery and Analysis

8 Single Nucleotide Polymorphism Screening with Denaturing Gradient Gel Electrophoresis Leslie A. Knapp 137

9 Temporal Temperature Gradient Electrophoresis for Detection of Single Nucleotide Polymorphisms Bethan M. Jones Leslie A. Knapp 153

Section V Prescreening (Conformation Based) Methods for SNP Discovery and Analysis

10 Zn(II)-Cyclen Polyacrylamide Gel Electrophoresis for SNP Detection Emiko Kinoshita-Kikuta Eiji Kinoshita Tohru Koike 169

11 Phosphate-Affinity Polyacrylamide Gel Electrophoresis for SNP Genotyping Eiji Kinoshita Emiko Kinoshita-Kikuta Tohru Koike 183

12 Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA Tomoko Tahira Yoji Kukita Koichiro Higasa Yuko Okazaki Aki Yoshinaga Kenshi Hayashi 193

13 Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection Igor A. Prokhorenko Irina V. Astakhova Kuvat T. Momynaliev Timofei S. Zatsepin Vladimir A. Korshun 209

14 The Chemical Cleavage of Mismatch for the Detection of Mutations in Long DNA Fragments Tania Tabone Georgina Sallmann Richard G. H. Cotton 223

15 Mismatch Oxidation Assay: Detection of DNA Mutations Using a Standard UV/Vis Microplate Reader Tania Tabone Georgina Sallmann Richard G. H. Cotton 235

Section VI Towards High-Throughput Methods of SNP Genotyping

16 High-Throughput Methods for SNP Genotyping Chunming Ding Shengnan Jin 245

17 High-Throughput SNP Genotyping: Combining Tag SNPs and Molecular Beacons Luis B. Barreiro Ricardo Henriques Musa M. Mhlanga 255

18 SNP Genotyping by the 5′ -Nuclease Reaction: Advances in High-Throughput Genotyping with Nonmodel Organisms James E. Seeb Carita E. Pascal Ramesh Ramakrishnan Lisa W. Seeb 277

19 The TaqMan Method for SNP Genotyping Gong-Qing Shen Kalil G. Abdullah Qing Kenneth Wang 293

20 Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY®) Paul Oeth Guy del Mistro George Marnellos Tao Shi Dirk van den Boom 307

21 SNP Detection Using Trityl Mass Tags Klara R. Birikh Pablo L. Bernad Vadim V. Shmanai Andrei D. Malakhov Mikhail S. Shchepinov Vladimir A. Korshun 345

22 Putting the Invader® Assay to Work: Laboratory Application and Data Management Yi Zhang Edward Smith Michael Olivier 363

23 SNP Genotyping Using Multiplex Single Base Primer Extension Assays Daniele Podini Peter M. Vallone 379

24 High-Throughput SNP Detection Based on PCR Amplification on Magnetic Nanoparticles Using Dual-Color Hybridization Nongyue He Song Li Hongna Liu 393

Section VII Other Methods

25 Restriction Enzyme Analysis of PCR Products Masao Ota Hideki Asamura Takahito Oki Masaharu Sada 405

26 Allele-Specific PCR in SNP Genotyping Muriel Gaudet Anna-Giulia Fara Isacco Beritognolo Maurizio Sabatti 415

27 Modified Multiple Primer Extension Method Toshihide Yanagawa Hisashi Koga 425

28 Detection of SNP by the Isothermal Smart Amplification Method Alexander Lezhava Yoshihide Hayashizaki 437

Subject Index 453

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