Use of pyrosequencing to detect clinically relevant polymorphisms in dihydropyrimidine dehydrogenase.

Evaluation of a new PCR assay with competitive internal control sequence for blood donor screening. TaqMan 5Ј-nuclease human immunodefi-ciency virus type 1 PCR assay with phage-packaged competitive internal control for high-throughput blood donor screening. detection and quantification of RNA of Ebola and Marburg viruses, Lassa virus, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus, Dengue virus, and yellow fever virus by real-time reverse transcription-PCR. Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis. MT. Simultaneous identification of Mycobacterium genus and Mycobacte-rium tuberculosis complex in clinical samples by 5Ј-exonuclease fluorogenic PCR. specific detection of the Mycobacterium tuberculosis complex using fluoro-genic probes and real-time PCR. fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. Detection of specific polymerase chain reaction product by utilizing the 5Ј-3Ј exonuclease activity of Thermus aquaticus DNA polymerase. Simplified acetylcysteine-alkali digestion-decontamination procedure for isolation of mycobacteria from clinical specimens. Common human diseases, such as cancer, have been associated with multiple types of variation in the genome, including sequence repeats and deletions and single-nucleotide polymorphisms (SNPs) (1). Of these, SNPs are the most abundant in the human genome (2, 3). As a result of the efforts of many groups (4), an estimated 5 million SNPs are now deposited in public databases (5), providing a resource for determining how genomic variation affects human biology. Building on this work, many groups have shown that drug response is also influenced by genomic variation (6). Multiple SNPs have been identified that have a major impact on response to chemother-apy (7–11); it is therefore necessary to have rapid and efficient SNP evaluation techniques to analyze genes that influence chemotherapy response. Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the three-step degradation of uracil to ␤-alanine (12). This is the only endogenous pathway for production of the neurotransmitter ␤-alanine (13). DPD also degrades Ͼ80% of the anticancer agent 5-fluorouracil (5-FU), a pyrimidine analog used to treat colorectal cancer, and limits the oral absorption of the drug (13). DPD activity is found to be highest in liver and mononuclear cells, but it is also present in most other human tissues (14). Variation in DPD activity can lead to nonbeneficial physiologic conditions. A complete absence of DPD has been associated with the hereditary metabolic disorder thymine-uraciluria (9). This is characterized by mental retardation …