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Pharmacogenomics encompasses several major areas: the study of polymorphic variations in drug response and disease susceptibility, identification of the effects of drugs/xenobiotics at the genomic level, and genotype/phenotype associations. The most common type of human genetic variations is single-nucleotide polymorphisms (SNPs). Several novel approaches to detection of SNPs are currently available. The range of new methods includes modifications of several conventional techniques, such as PCR, mass spectrometry (ms), and sequencing, as well as more innovative technologies such as fluorescence resonance energy transfer (FRET) and microarrays. The application of each of these techniques is largely dependent on the number of SNPs to be screened and sample size. The current chapter presents an overview of the general concepts of a variety of genotyping technologies, with an emphasis on the recently developed methodologies, including a comparison of the advantages, applicability, cost efficiency, and limitations of these methods.

The analysis of gene expression is an integral part of any gene function research. A wide variety of techniques have been developed for this purpose, each with its own advantages and limitations. The following chapter seeks to provide an overview of some of the most recent as well as conventional methods to study gene expression. These approaches include Northern blot analysis, ribonuclease protection assay, reverse transcription polymerase chain reaction, expressed tag sequencing, differential display, cDNA arrays, serial analysis of gene expression, and transcriptome sequencing. The current applications of the information derived from gene expression studies require most of the assays to be adaptable for the quantitative analysis of a large number of samples and endpoints within a short period of time coupled with cost-effectiveness. A comparison of some of these features of each analytical approach as well as their advantages and disadvantages has also been provided.