Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies

Background: Pharmacogenetics is a scientific discipline that examines the g enetic basis for individual variations in response to therapeutics. Pharmac ogenetics promises to develop individualized medicines tailored to patients ' genotypes. However, identifying and genotyping a vast number of genetic p olymorphisms in large populations also pose a great challenge. Approach: This article reviews the recent technology development in mutatio n detection and genotyping with a focus on genotyping of single nucleotide polymorphisms (SNPs). Content: Novel mutations/polymorphisms are commonly identified by conformat ion-based mutation screening and direct high-throughput heterozygote sequen cing. With a large amount of public sequence information available, in sili co SNP mapping has also emerged as a cost-efficient way for new polymorphis m identification. Gel electrophoresis-based genotyping methods for known po lymorphisms include PCR coupled with restriction fragment length polymorphi sm analysis, multiplex PCR, oligonucleotide ligation assay, and minisequenc ing. Fluorescent dye-based genotyping technologies are emerging as high-thr oughput genotyping platforms, including oligonucleotide ligation assay, pyr osequencing, single-base extension with fluorescence detection, homogeneous solution hybridization such as TaqMan(R), and molecular beacon genotyping. Rolling circle amplification and Invader(TM) assays are able to genotype d irectly from genomic DNA without PCR amplification. DNA chip-based microarr ay and mass spectrometry genotyping technologies are the latest development in the genotyping arena. Summary: Large-scale genotyping is crucial to the identification of the gen etic make-ups that underlie the onset of diseases and individual variations in drug responses. Enabling technologies to identify genetic polymorphisms rapidly, accurately, and cost effectively will dramatically impact future drug and development processes. (C) 2001 American Association for Clinical Chemistry.