Single Nucleotide Polymorphisms Methods and Protocols

In recent years, single nucleotide polymorphisms have received increased and special attention in a rapidly developing field of personalized medicine and drug treatment. Comprising more than eighty percent of all known polymorphisms, single nucleotide polymorphisms (SNPs) are primarily responsible for phenotypic differences between individuals, and have been suggested to affect the development of diseases in humans and the response to drug treatment and environmental stress. In Single Nucleotide Polymorphisms: Methods and Protocols, Second Edition, expert researchers explore the latest advances in this area, highlighting the substantial progress that has been made in SNP genotyping, examining recent developments in high-throughput genotyping approaches, and exploring our new understanding of the impact of SNPs on gene function. Chapters address the impact of SNPs on phenotype, examine SNP databases, look at methods that have been applied for SNP bioinformatics discovery and analysis, and discuss advanced experimental approaches used for SNP detection. Composed in the highly successful Methods in Molecular Biology™ series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls.

Current and innovative, Single Nucleotide Polymorphisms: Methods and Protocols, Second Edition is an essential guidebook for individual researchers as well as institutions and companies working in the field.

to Single Nucleotide Polymorphisms.- SNPs: Impact on Gene Function and Phenotype.- Silent (Synonymous) SNPs: Should We Care About Them?.- Bioinformatic Analysis of SNPs.- SNP Databases.- Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery and Analysis.- SNP Identification and Detection Strategies: Whole Genome Sequencing and Re-Sequencing.- Next-Generation Sequencing Methods: Impact of Sequencing Accuracy on SNP Discovery.- Scanning Probe and Nanopore DNA Sequencing: Core Techniques and Possibilities.- Pyrosequencing for SNP Genotyping.- Prescreening (Melting Based) Methods for SNP Discovery and Analysis.- Single Nucleotide Polymorphism Screening with Denaturing Gradient Gel Electrophoresis.- Temporal Temperature Gradient Electrophoresis for Detection of Single Nucleotide Polymorphisms.- Prescreening (Conformation Based) Methods for SNP Discovery and Analysis.- Zn(II)–Cyclen Polyacrylamide Gel Electrophoresis for SNP Detection.- Phosphate-Affinity Polyacrylamide Gel Electrophoresis for SNP Genotyping.- Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA.- Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection.- The Chemical Cleavage of Mismatch for the Detection of Mutations in Long DNA Fragments.- Mismatch Oxidation Assay: Detection of DNA Mutations Using a Standard UV/Vis Microplate Reader.- Towards High-Throughput Methods of SNP Genotyping.- High-Throughput Methods for SNP Genotyping.- High-Throughput SNP Genotyping: Combining Tag SNPs and Molecular Beacons.- SNP Genotyping by the 5?-Nuclease Reaction: Advances in High-Throughput Genotyping with Nonmodel Organisms.- The TaqMan Method for SNP Genotyping.- Qualitative and Quantitative Genotyping Using Single Base Primer Extension Coupledwith Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MassARRAY®).- SNP Detection Using Trityl Mass Tags.- Putting the Invader® Assay to Work: Laboratory Application and Data Management.- SNP Genotyping Using Multiplex Single Base Primer Extension Assays.- High-Throughput SNP Detection Based on PCR Amplification on Magnetic Nanoparticles Using Dual-Color Hybridization.- Other Methods.- Restriction Enzyme Analysis of PCR Products.- Allele-Specific PCR in SNP Genotyping.- Modified Multiple Primer Extension Method.- Detection of SNP by the Isothermal Smart Amplification Method.