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The analysis of gene differential expression is complicated by the potentially subtle differences associated with alterations in a single allele as well as by variations between individuals that arise from environmental or physiological factors. To circumvent these analytic p ...

Human variation is largely caused by deoxyribonucleic acid polymorphism and difference in gene expression. Common disease/common variant hypotheses suggest that quantitative differences among different alleles may be the basis for complex diseases. Quantitative diffe ...

The characterization of protein-deoxyribonucleic acid (DNA) interactions occurring at an allele-specific level is important to resolving the functional consequences of genetic variation in non-coding DNA for gene expression and regulation. The approach of haplotype-spe ...

Major strengths of mass spectrometry analysis include the accuracy of the detection principle and the automatic data storage, making it a premier choice for high-throughput single-nucleotide polymorphism genotyping. We explain the assay principle in detail and give step-by-step ...

To undertake partial, or complete, genome screens by association-based methodology for quantitative trait loci, multiple individuals have to be screened for large numbers of genetic markers. Consequently, much recent interest has focused on methods enabling accurate allele qua ...

The successful application of capillary electrophoresis technology to the genotyping of various types of polymorphisms has been well documented. The flexibility and automation of the Applied Biosystems 3100 Genetic Analyzer make it an excellent capillary electrophoresis p ...

The 5′ fluorogenic (TaqMan) assay has been successfully used in screening for singlenucleotide polymorphisms; the very few steps required and the ability to automate each step allow for high-throughput screening. Insertion/deletion polymorphisms are an important class of marke ...

The variety of genotyping methods currently available and the evolution of their capabilities have facilitated an expansion of the field of pharmacogenomics. Traditionally, limited genotyping capabilities have restricted the generation and application of genotyping data ...

The data generated from the Human Genome Project has led to an explosion of technology for low-, medium-, and high-throughput genotyping methods. Pyrosequencing is a genotyping assay based on sequencing by synthesis. Short runs of sequence around each polymorphism are generated, allowi ...

Denaturing high-performance liquid chromatography (DHPLC) is an accurate and efficient screening technique used for detecting deoxyribonucleic acid sequence changes by heteroduplex analysis. It can also be used for genotyping of single-nucleotide polymorphisms. The hi ...

The analysis of human genetic variations, such as single-nucleotide polymorphisms (SNPs), has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenc ...

The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB) is an interactive tool for researchers investigating how genetic variation effects drug response. The PharmGKB web site, http://www.pharmgkb.org, displays genotype, molecular, and clinical primary da ...

Recent breakthroughs in biological research have been made possible by remarkable advances in high-performance computing and the establishment of a highly sophisticated information technology infrastructure. This chapter gives an overview of the main and most important tec ...

Bifunctional DNA damaging agents continue to be the mainstay in various chemotherapeutic regimens used in the clinic. DNA interstrand crosslinks are considered to be the critical cytotoxic lesions for the biological activity of such agents. Gel-based electrophoretic assays can e ...

The Single Cell Gel Electrophoresis (Comet) assay, originally developed to allow visualisation of DNA strand break damage in individual cells, has been adapted to measure DNA interstrand cross-links. DNA interstrand cross-links are formed in cells by a number of commonly used cancer che ...

Anomalous scattering is commonly used to solve X-ray structures. As discussed here, anomalous scattering is also useful for characterizing complex systems with mixed and partial occupancies, where true electron density is represented by unresolvable ensemble averages. The sol ...

We describe a molecular modelling method for calculating the binding affinity of ligands for DNA. Though theoretically applicable to any form of noncovalent interaction, we concentrate on the case of predicting the sequence selectivity of a minor-groove binding ligand. The method is ba ...

The mouse lymphoma assay (MLA) using the thymidine kinase (Tk1) gene is widely used to detect the potential genotoxicity of a wide variety of chemical agents. The assay is recommended as a part of the core battery of genetic toxicology tests. Although the assay was developed more than 30 yr ago, there have ...

The use of the human S9 fraction in mutagenicity testing systems may be valuable for evaluating the mutagenicity of chemicals in humans. When using a crude human liver S9 fraction, which is obtained following the centrifugation of the tissue homogenate for 20 min at 9000g, in the Ames test, we may somet ...

The human homologue of the ether-a-go-go-related-gene (HERG) has been implicated in the “iatrogenic” long QT syndrome, with several products withdrawn from the market because of their interaction with this K + channel. The resultant impact on the pharmaceutical industry has been profou ...