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Single nucleotide polymorphisms : methods and protocols / edited by Anton A. Komar. — 2nd ed. — New York : Humana, c2009. – (58.17/M592/v.578) |
Contents
Contents
Preface
Contributors
SECTION I: INTRODUCTION TO SINGLE NUCLEOTIDE POLYMORPHISMS
1. SNPs: Impact on Gene Function and Phenotype
2. Silent (Synonymous) SNPs: Should We Care About Them? 23
SECTION II: BIOINFORMATIC ANALYSIS OF SNPs
3. SNP Databases
4. Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery and Analysis
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
6. Scanning Probe and Nanopore DNA Sequencing: Core Techniques and Possibilities
7. Pyrosequencing for SNP Genotyping
SECTION IV: PKESCREENING (MELTING BASED) METHODS FOR SNP DISCOVERY AND ANALYSIS
8. Single Nucleotide Polymorphism Screening with Denaturing Gradient Gel Electrophoresis 137
9. Temporal Temperature Gradient Electrophoresis for Detection of Single Nucleotide Polymorphisms
SECTION V: PRESCREENING (CONFORMATION BASED) METHODS FOR SNP DISCOVERY AND ANALYSIS
10. Zn(II)-Cyclen Polyacrylamide Gel Electrophoresis for SNP Detection
11. Phosphate-Affinity Polyacrylamide Gel Electrophoresis for SNP Genotyping
12. Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA 193
13. Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection 209
14. The Chemical Cleavage of Mismatch for the Detection of Mutations in Long DNA Fragments
15. Mismatch Oxidation Assay: Detection of DNA Mutations Using a Standard UV/Vis Microplate Reader
SECTION WI: TOWARDS HIGH-THROUGHPUT METHODS OF SNP GENOTYPING
16. High-Throughput Methods for SNP Genotyping
17. High-Throughput SNP Genotyping: Combining Tag SNPs and Molecular Beacons 255
18. SNP Genotyping by the 5'-Nuclease Reaction: Advances in High-Throughput Genotyping with Nonmodel Organisms 277
19. The TaqMan Method for SNP Genotyping 293
20. Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupled with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY) 307
21. SNP Detection Using Trityl Mass Tags 345
22. Putting the Invader: Assay to Work: Laboratory Application and Data Management
23. SNP Genotyping Using Multiplex Single Base Primer Extension Assays 379
24. High-Throughput SNP Detection Based on PCR Amplification on Magnetic Nanoparticles Using Dual-Color Hybridization 393
SECTION VII: OTHER METHODS
25. Restriction Enzyme Analysis of PCR Products
26. Allele-Specific PCR in SNP Genotyping
27. Modified Multiple Primer Extension Method
28. Detection of SNP by the Isothermal Smart Amplification Method
Subject Index
