Pharmacogenomics: Methods and Protocols

Part I: Introduction to Pharmacogenomics

1. Pharmacogenomics: Historical Perspective and Current Status

Rosane Charlab and Lei Zhang

Part II: Techniques for Interrogating Variation in Human Genes and Genomes

2. Denaturing High-Performance Liquid Chromatography for Mutation Detection and Genotyping

Donna Lee Fackenthal, Pei Xian Chen, Ted Howe, and Soma Das

3. Clinical SNP Detection by the SmartAmp Method

Toshihisa Ishikawa and Yoshihide Hayashizaki

4. MALDI-TOF Mass Spectrometry

Dirk van den Boom, Matthias Wjst, and Robin Everts

5. TaqMan® Drug Metabolism Genotyping Assays for the Detection of Human Polymorphisms Involved in Drug Metabolism

Toinette Hartshorne

6. Pyrosequencing of Clinically Relevant Polymorphisms

Cristi R. King and Sharon Marsh

7. Pharmacogenetics Using Luminex^® xMAP^® Technology: Method for Developing a Custom Multiplex Single Nucleotide Polymorphism Mutation Assay

Gonnie Spierings and Sherry A. Dunbar

8. Use of Linkage Analysis, Genome-Wide Association Studies, and Next-Generation Sequencing in the Identification of Disease-Causing Mutations

Eric Londin, Priyanka Yadav, Saul Surrey, Larry J. Kricka, and Paolo Fortina

9. The GoldenGate Genotyping Assay: Custom Design, Processing, and Data Analysis

Anna González-Neira

10. Genome-Wide Gene Expression Profiling, Genotyping, and Copy Number Analyses of Acute Myeloid Leukemia Using Affymetrix GeneChips

Mathijs A. Sanders and Peter J.M. Valk

11. Epigenetic Techniques in Pharmacogenetics

Sandra G. Heil

12. Plasmid Derived External Quality Controls for Genetic Testing

Tahar van der Straaten and Henk-Jan Guchelaar

Part III: Functional Assessment of Genetic Variation: In Vitro and In Vivo Methods

13. Allelic Imbalance Assays to Quantify Allele-Specific Gene Expression and Transcription Factor Binding

Francesca Luca and Anna Di Rienzo

14. SCAN: A Systems Biology Approach to Pharmacogenomic Discovery

Eric R. Gamazon, R. Stephanie Huang, and Nancy J. Cox

15. Methods to Examine the Impact of Nonsynonymous SNPs on Protein Degradation and Function of Human ABC Transporter

Toshihisa Ishikawa, Kanako Wakabayashi-Nakao, and Hiroshi Nakagawa

16. In Vitro Identification of Cytochrome P450 Enzymes Responsible for Drug Metabolism

Zhengyin Yan and Gary W. Caldwell

17. In Vitro and In Vivo Mouse Models for Pharmacogenetic Studies

Amber Frick, Oscar Suzuki, Natasha Butz, Emmanuel Chan, and Tim Wiltshire

18. The Hydrodynamic Tail Vein Assay as a Tool for the Study of Liver Promoters and Enhancers

Mee J. Kim and Nadav Ahituv

Part IV: Tools for Translation and Implementation of Pharmacogenetic Markers

19. A Guide to the Current Web-Based Resources in Pharmacogenomics

Dylan M. Glubb, Steven W. Paugh, Ron H.N. van Schaik, and Federico Innocenti

20. PharmGKB: The Pharmacogenomics Knowledge Base

Caroline F. Thorn, Teri E. Klein, and Russ B. Altman

21. Genetic Databases in Pharmacogenomics: The Frequency of Inherited Disorders Database (FINDbase)

Marianthi Georgitsi and George P. Patrinos

22. Development of Predictive Models for Estimating Warfarin Maintenance Dose Based on Genetic and Clinical Factors

Lu Yang and Mark W. Linder

23. Evidence Based Drug Dosing and Pharmacotherapeutic Recommendations Per Genotype

Understanding an individual's genetic makeup is the key to creating personalized drugs with greater efficacy and safety, and pharmacogenomics aims to study the complex genetic basis of inter-patient variability in response to drug therapy. Based upon the success of its first edition, the second edition of Pharmacogenomics: Methods And Protocols aims to continue providing readers with high-quality content on the most innovative and commonly adopted technologies in the field of pharmacogenomics as presented by experts in the field. Broken into several sections, this detailed volume examines techniques for interrogating variation in human genes and genomes, functional assessment of genetic variation, both in vitro and in vivo, as well as tools for translation and implementation of pharmacogenetic markers. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to the respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Comprehensive and thoroughly updated, Pharmacogenomics: Methods And Protocols, Second Edition serves as an essential reference and an invaluable source on the latest information in this field.