Springer protocols feed by Pharmacology/Toxicology 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.In Vitro and In Vivo Mouse Models for Pharmacogenetic Studies
The identification of causative genes underlying biomedically relevant phenotypes, particularly complex multigenic traits, is of vital interest to modern medicine. Using genome-wide association analysis, many studies have successfully identified thousands of loci (called quantitative trait loci or QTL), some of these associating with drug response phenotypes. However, the determination and validation of putative genes has been much more challenging. The actions of drugs, both efficacious and deleterious, are complex phenotypes that are controlled or influenced in part by genetic mechanisms. (Source: Springer protocols feed...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
In Vitro Identification of Cytochrome P45 Enzymes Responsible for Drug Metabolism
Metabolism catalyzed by the cytochrome P450 enzymes (CYPs) represents the most important pathway for drug metabolism and elimination in humans. Identification of the CYPs responsible for metabolism of existing and novel drugs is critical for the prediction of adverse reactions caused by drug–drug interactions or individual genetic polymorphism. An integrated approach is described for CYP-mediated metabolic reaction phenotyping using both recombinant enzymes and human liver microsomes in combination of selective inhibitors or inhibitory antibodies. The in vitro method described includes screening of recombinant CYPs f...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Methods to Examine the Impact of Nonsynonymous SNPs on Protein Degradation and Function of Human ABC Transporter
Clinical studies have strongly suggested that genetic polymorphisms and/or mutations of certain ATP-binding cassette (ABC) transporter genes might be regarded as significant factors affecting patients’ responses to medication and/or the risk of diseases. In the case of ABCG2, certain single nucleotide polymorphisms (SNPs) in the encoding gene alter the substrate specificity and/or enhance endoplasmic reticulum-associated degradation (ERAD) of the de novo synthesized ABCG2 protein via the ubiquitin-mediated proteasomal proteolysis pathway. Hitherto accumulated clinical data imply that several nonsynonymous SNPs affect...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
SCAN: A Systems Biology Approach to Pharmacogenomic Discovery
Genome-wide association (GWA) studies have identified thousands of genetic variants that contribute to disease and pharmacologic traits. More recently, high-throughput sequencing studies promise to provide a more complete catalog of genetic variants with roles in human phenotypic variation. Yet, characterizing the influence of functional variants on genes, RNAs, proteins, and ultimately disease or pharmacologic traits is a critical challenge for a vast majority of the implicated susceptibility loci. Here we describe SCAN, a bioinformatics resource we have developed to elucidate the functional consequences of genetic varian...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Allelic Imbalance Assays to Quantify Allele-Specific Gene Expression and Transcription Factor Binding
A growing number of noncoding variants are found to influence the susceptibility to common diseases and interindividual variation in drug response. However, the mechanisms by which noncoding variation affects cellular and clinical phenotypes remain to be elucidated. Allele-specific assays allow testing directly the differential properties of the alleles at a regulatory variant, which are detected as an allelic imbalance. Two widely used allelic imbalance assays target cDNA and DNA from chromatin immunoprecipitation (ChIP) experiments, and therefore revealing allele-specific gene expression and transcription factor binding,...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
The GoldenGate Genotyping Assay: Custom Design, Processing, and Data Analysis
The Illumina GoldenGate Assay is a technique that is widely used in molecular genetics to analyze up to thousands of single nucleotide polymorphism (SNPs) simultaneously, providing data of very high quality in a fast and efficient manner. This technique allows the user to optimize the number of genetic loci to be interrogated in a way that best suits their research goals. Here are described in detail all the steps to be followed in the process of genotyping a custom panel, from panel design through data analysis. (Source: Springer protocols feed by Pharmacology/Toxicology)
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Use of Linkage Analysis, Genome-Wide Association Studies, and Next-Generation Sequencing in the Identification of Disease-Causing Mutations
For the past two decades, linkage analysis and genome-wide analysis have greatly advanced our knowledge of the human genome. But despite these successes the genetic architecture of diseases remains unknown. More recently, the availability of next-generation sequencing has dramatically increased our capability for determining DNA sequences that range from large portions of one individual’s genome to targeted regions of many genomes in a cohort of interest. In this review, we highlight the successes and shortcomings that have been achieved using genome-wide association studies (GWAS) to identify the variants contributi...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Pharmacogenetics Using Luminex® xMAP® Technology: A Method for Developing a Custom Multiplex Single Nucleotide Polymorphism Mutation Assay
Sequence variations in the human genome can affect the development of diseases and provide markers for the identification of genetic diseases and drug susceptibility. Single Nucleotide Polymorphisms (SNPs), the most abundant sequence variations in the genome, are used in pharmacogenetics as indicators of drug therapy efficacy in individuals and are important road maps in the route to personalized medicine. This chapter describes the development of PCR based custom multiplex SNP mutation analysis assays using Luminex® Multi-Analyte Profiling (xMAP®) Technology. Up to 500 different mutations can be detected in a sing...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Pyrosequencing of Clinically Relevant Polymorphisms
Despite the influx of high throughput sequencing techniques, there is still a niche for low-medium throughput genotyping technologies for small-scale screening and validation purposes. Pyrosequencing is a genotyping assay based on sequencing-by-synthesis. Short runs of sequence around each polymorphism are generated, allowing for internal controls for each sample. Pyrosequencing can also be utilized to identify tri-allelic, indel, and short repeat polymorphisms, as well as determining allele percentages for methylation or pooled sample assessment. This range of applications makes it well-suited to the research laboratory a...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
TaqMan® Drug Metabolism Genotyping Assays for the Detection of Human Polymorphisms Involved in Drug Metabolism
Polymorphisms associated with genes that code for various drug-metabolizing enzymes (DMEs) and associated transport proteins can influence the rate of drug metabolism within individuals, thus potentially affecting drug efficacy and the occurrence of side effects. There are 2,700 unique TaqMan® Drug Metabolism Genotyping Assays (Life Technologies) for detecting single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and multinucleotide polymorphisms (MNPs) in both coding and regulatory regions. These research assays are useful tools for better understanding genetic variation in drug metabolism. Here w...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
MALDI-TOF Mass Spectrometry
Major strengths of mass spectrometry analysis include the accuracy of the detection principle, automatic data storage as well as simplicity and flexibility of assay design making it a premier choice for targeted genotyping of sequence variations. We explain the assay principle in detail and give step-by-step laboratory instructions. Finally, references point toward further use of mass spectrometry analysis for molecular haplotyping, re-sequencing, and quantitative analysis for copy number variations and gene expression studies are given. (Source: Springer protocols feed by Pharmacology/Toxicology)
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Clinical SNP Detection by the SmartAmp Method
For advancing personalized medicine, it is important to incorporate pharmacogenomics data into routine clinical practice. The SmartAmp method enables us to detect genetic polymorphisms or mutations in target genes within 30–40 min without DNA isolation and PCR amplification. The SmartAmp method has been developed based on the concept that DNA amplification per se is the signal for the presence of a specific target sequence. Differing from the widely used PCR, the SmartAmp reaction is an isothermal DNA amplification, where the initial step of copying a target sequence from the template DNA is critically important. For...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Denaturing High-Performance Liquid Chromatography for Mutation Detection and Genotyping
Denaturing high-performance liquid chromatography (DHPLC) is an accurate and efficient screening technique used for detecting DNA sequence changes by heteroduplex analysis. It can also be used for genotyping of single nucleotide polymorphisms (SNPs). The high sensitivity of DHPLC has made this technique one of the most reliable approaches to mutation analysis and, therefore, used in various areas of genetics, both in the research and clinical arena. This chapter describes the methods used for mutation detection analysis and the genotyping of SNPs by DHPLC on the WAVE™ system from Transgenomic Inc. (“WAVE”...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Plasmid Derived External Quality Controls for Genetic Testing
Since the human genome has been fully sequenced, and presence of single nucleotide polymorphisms (SNPs) appeared abundant, many studies are associating SNPs with clinical response or even with disease. For some diseases or drug treatments these associations are clear, so that genetic screening for such SNPs or mutations is a standard procedure. For that reason, many different techniques have been developed for fast and easy screening for such specific SNPs/mutations. For reliable screening, the use of controls with known genotypes is indispensable. Plasmids are an ideal tool for making controls which can serve as an inexha...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
Epigenetic Techniques in Pharmacogenetics
Pharmacoepigenetics is an emerging field, which can be studied by several approaches. Addressing DNA methylation status of drug-metabolizing enzymes and transporters (DMET) is challenging and might provide answers in relation to interindividual differences in pharmacokinetics and pharmacodynamics. Studying genetic variation in DMET genes in relation to drug response has been the main focus of pharmacogenetics laboratories; it is, however, expected that epigenetic modifications will play a role in drug responses as well. Some of the variations in drug-responses cannot be explained by genetic variation in DMET genes. For tho...
Source: Springer protocols feed by Pharmacology/Toxicology - July 8, 2013 Category: Drugs & Pharmacology Source Type: news
