Pharmacogenomics: Methods and Protocols / Edition 1

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Overview

Expert researchers and physician/clinicians describe in detail the newest and most commonly used technologies today in this rapidly advancing field. The authors provide readily reproducible methods for assessing the functional consequences of a certain polymorphism, evaluate the variety of genotyping platforms currently available, and discuss the management of pharmacogenomic information. Highlights include techniques for making a snapshot of the allele-specific variation in human gene expression, genome wide analysis of allele-specific expression using oligo microarrays, in vivo assays with HaploChIP, SNP genotyping in DNA pools, and PharmGKB, the pharmacogenetics and pharmacogenomics knowledge base. The methodologies for genotyping include denaturing high-performance liquid chromarography, pyrosequencing, kinetic-fluorescence detection, mass spectrometry, and TaqMan assay for insertion/deletions.

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Product Details

  • ISBN-13: 9781588294401
  • Publisher: Springer-Verlag New York, LLC
  • Publication date: 8/28/2005
  • Series: Methods in Molecular Biology Series , #311
  • Edition description: 2005
  • Edition number: 1
  • Pages: 224
  • Product dimensions: 9.20 (w) x 6.20 (h) x 0.80 (d)

Table of Contents

Part I. History and Overview

Pharmacogenomics: Historical Perspective and Current Status
Werner Kalow

Part II. Functional Analysis of Gene Variation

Transfection Assays With Allele-Specific Constructs: Functional Analysis of UDP-Glucuronosyltransferase Variants
Hideto Jinno, Nobumitsu Hanioka, Toshiko Tanaka-Kagawa, Yoshiro Saito, Shogo Ozawa, and Jun-ichi Sawada

Snapshot of the Allele-Specific Variation in Human Gene Expression
Hai Yan

Genome-Wide Analysis of Allele-Specific Gene Expression Using Oligo Microarrays
Maxwell P. Lee

HaploChIP: An In Vivo Assay
Julian Charles Knight

Part III. Genotyping Techniques

Aspects Influencing Genotyping Method Selection
Peter Imle

Denaturing High-Performance Liquid Chromatography for Mutation Detection and Genotyping
Donna Lee Fackenthal, Pei Xian Chen, and Soma Das

Pyrosequencing of Clinically Relevant Polymorphisms
Sharon Marsh, Cristi R. King, Adam A. Garsa, and Howard L. McLeod

Kinetic Fluorescence-Quenching Detection Assay for Allele Frequency Estimation
Ming Xiao and Pui-Yan Kwok

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Matthias Wjst and Dirk van den Boom

Fluorescence-Based Fragment Size Analysis
Peter Imle

Single-Nucleotide Polymorphism Genotyping in DNA Pools
Ian Craig, Emma Meaburn, Lee Butcher, Linzy Hill, and Robert Plomin

TaqMan Genotyping of Insertion/Deletion Polymorphisms
Renato Robledo, William R. Beggs, and Patrick K. Bender

Part IV. Management of Pharmacogenomic Information

PharmGKB: The Pharmacogenetics and Pharmacogenomics Knowledge Base
Caroline F. Thorn, Teri E. Klein, and Russ B. Altman

Systems for the Management of Pharmacogenomic Information
Alexander Sturn, Michael Maurer, Robert Molidor, and ZlatkoTrajanoski

Index

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