Fully updated from the first edition to offer cutting-edge methods for SNP detection and analysis
Offers a unique overview of next generation sequencing and genotyping approaches
Contains review chapters comparing methods capabilities, error rates, and costs
Provides advanced techniques as well as deillegalscriptions of simple approaches which do not require sophisticated equipment
Low and high-throughput, single and multiplex applications are presented
Fully updated from the first edition to offer cutting-edge methods for SNP detection and analysis
Offers a unique overview of next generation sequencing and genotyping approaches
Contains review chapters comparing methods capabilities, error rates, and costs
Provides advanced techniques as well as deillegalscriptions of simple approaches which do not require sophisticated equipment
Low and high-throughput, single and multiplex applications are presented
Includes supplementary material: sn.pub/extras
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.
Single Nucleotide Polymorphisms: Methods and ProtocolsAnton A. Komar, Ed. Table of ContentsPrefaceContributors 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 STRATEGIESWhole Genome Sequencing and Re-SequencingNext-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 AnalysisSingle 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 AnalysisZn(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 GenotypingHigh-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
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)
In this updated second edition, researchers explore the latest advances in this area, highlighting the progress made in SNP genotyping, recent developments in high-throughput genotyping, and our new understanding of the impact of SNPs on gene function.
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(TM) 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.
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)
Inhaltsverzeichnis
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
Klappentext
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.nnCurrent 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.
Fully updated from the first edition to offer cutting-edge methods for SNP detection and analysis
n
Offers a unique overview of next generation sequencing and genotyping approaches
n
Contains review chapters comparing methods capabilities, error rates, and costs
n
Provides advanced techniques as well as deillegalscriptions of simple approaches which do not require sophisticated equipment
n
Low and high-throughput, single and multiplex applications are presented
n
Includes supplementary material: sn.pub/extras
n
