Single Nucleotide Polymorphisms: Methods and Protocols

ISBN-13: 9781603274104 / Angielski / Twarda / 2009 / 464 str.

Anton A. Komar

Opis

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

Recenzje

From the reviews of the second edition:

"This second edition brings 11 new chapters ... . Its target audience continues to be researchers and laboratory personnel. One helpful feature the book includes is a set of 'notes' at the end of each chapter ... to be very useful for readers choosing to utilize a technique for the first time. ... Overall, this book is a good addition to any laboratory setting actively working on complex human traits or interested in personalized medicine and drug treatments." (Alexandre R. Vieira, Birth Defects Research (Part A): Clinical and Molecular Teratology, Vol. 88 (12), 2010)

Spis treści

Single Nucleotide Polymorphisms: Methods and Protocols Anton A. Komar, Ed. Table of Contents Preface Contributors INTRODUCTION TO SINGLE NUCLEOTIDE POLYMORPHISMS: SNPs: Impact on Gene Function and Phenotype. Barkur S. Shastry. Silent (Synonymous) SNPs: Should We Care About Them? Ryan Hunt, Zuben E. Sauna, Suresh V. Ambudkar, Michael M. Gottesman and Chava Kimchi-Sarfaty BIOINFORMATIC ANALYSIS OF SNPs: SNPs Databases. Christopher Phillips. Mining SNPs from DNA Sequence Data; Computational Approaches to SNP Discovery and Analysis. Jan van Oeveren and Antoine Janssen. SNP INDENTIFICATION AND DETECTION STRATEGIES Whole Genome Sequencing and Re-Sequencing Next-Generation Sequencing Methods: Impact of Sequencing Accuracy on SNP Discovery. Eugene Y. Chan. Scanning Probe and Nanopore DNA Sequencing: Core Techniques and Possibilities. John Lund and Babak A. Parviz. Pyrosequencing for SNP Genotyping. Jose Luis Royo and Jose Jorge Galán. Prescreening (Melting Based) Methods for SNP Discovery and Analysis Single Nucleotide Polymorphism Screening with Denaturing Gradient Gel Electrophoresis (DGGE). Leslie Knapp. Temporal Temperature Gradient Electrophoresis (TTGE) for Detection of Single Nucleotide Polymorphisms. Bethan M. Jones and Leslie A. Knapp. Prescreening (Conformation Based) Methods for SNP Discovery and Analysis Zn(II)–Cyclen Polyacrylamide Gel Electrophoresis for SNPDetection. Emiko Kinoshita-Kikuta, Eiji Kinoshita and Tohru Koike. Phosphate-Affinity Polyacrylamide Gel Electrophoresis for SNP Genotyping. Eiji Kinoshita, Emiko Kinoshita-Kikuta, and Tohru Koike. Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA. Tomoko Tahira, Yoji Kukita, Koichiro Higasa, Yuko Okazaki, Aki Yoshinaga and Kenshi Hayashi. Phenylethynylpyrene Excimer Forming Hybridization Probes for Fluorescence SNP Detection. Igor A. Prokhorenko, Irina V. Astakhova, Kuvat T. Momynaliev, Timofei S. Zatsepin and Vladimir A. Korshun. The Chemical Cleavage of Mismatch for the Detection of Mutations in Long DNA Fragments. Tania Tabone, Georgina Sallmann and Richard G. H. Cotton. Mismatch Oxidation Assay: Detection of DNA Mutations using a Standard UV/Vis Microplate Reader. Tania Tabone, Georgina Sallmann, and Richard G. H. Cotton. Towards High-Throughput Methods of SNP Genotyping High-throughput Methods for SNP Genotyping. Chunming Ding and Shengnan Jin. High-throughput SNP Genotyping: Combining TagSNPs and Molecular Beacons. Luis B. Barreiro, Ricardo Henriques and Musa M. Mhlanga. SNP Genotyping by the 5'-nuclease Reaction: Advances in High Throughput Genotyping with Non-Model Organisms. James E. Seeb, Carita E. Pascal, Ramesh Ramakrishnan and Lisa W. Seeb. TaqMan Method for SNP Genotyping. Gong-Qing Shen, Kalil G. Abdullah and Qing Kenneth Wang. 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 and Dirk van den Boom. SNP