Pharmacogenetics: the Dx perspective

References

• Whelen AC, Persing DH. The role of nucleic acid amplification and detection in the clinical microbiology laboratory. Ann. Rev. Microbiol. 50, 349–373 (1996).
   Google Scholar
• • Useful summary of the impact of molecular testing on the diagnosis of infectious diseases.
   Google Scholar
• Wagener C. Molecular diagnostics. J. Mol. Med. 75(10), 728–744 (1997).
   Google Scholar
• Renegar G, Reiser P, Manasco P. Pharmacogenetics: the Rx perspective. Expert Rev. Mol. Diagn. 1(3), 255–263 (2001).
   Google Scholar
• Collins FS, Patrinos A, Jordan E, Chakravarti A, Gesteland R, Walters L. New goals for the US human genome project: 1998–2003. Science 282(5389), 682–689 (1998).
   Google Scholar
• •• Invaluable reference article describing the short- and medium-term goals of the human genome project.
   Google Scholar
• Uetrecht JP. Is it possible to more accurately predict which drug candidates will cause idiosyncratic drug reactions? Curr. Drug Metabol. 1(2), 133–141 (2000).
   Google Scholar
• Richards B, Skoletsky J, Shuber AP et al. Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs. Hum. Mol. Genet. 2(2), 159–163 (1993).
   Google Scholar
• Abramson RD, Myers TW. Nucleic acid amplification technologies. Curr. Opin. Biotechnol. 4(1), 41–47 (1993).
   Google Scholar
• McGlennen RC. Miniaturization technologies for molecular diagnostics. Clin. Chem. 47(3), 393–402 (2001).
   PubMedGoogle Scholar
• • Interesting article describing microminiaturization technologies and their potential utility in molecular diagnostic testing.
   Google Scholar
• Wisotzkey JD, Bell T, Monk JS. Simultaneous polymerase chain reaction restriction fragment length polymorphism idenfication of the Factor V leiden allele and the prothrombin 20210A mutation. Diagn. Mol. Pathol. 7(3), 180–183 (1998).
   Google Scholar
• Favis R, Barany F. Mutation detection in Kras, BRCA1, BRCA2 and p53 using PCR/ LDR and a universal DNA microarray. Ann. NY Acad. Sci. 906(1), 39–43 (2000).
   Google Scholar
• • Impressive study demonstrating the combined power of PCR-LDR and microarray technology for SNP detection.
   Google Scholar
• Frenkel LM, Wagner LE 2nd, Atwood SM, Cummins TJ, Dewhurst S. Specific, sensitive and rapid assay for human immunodeficiency virus Type 1 pol mutations associated with resistance to zidovudine and didanosine. J. Clin. Microbiol. 33(2), 342–347 (1995).
   Google Scholar
• Nigou M, Parfait B, Clauser E, Olivier JL. Detection and quantification of the A3243G mutation of mitochondrial DNA by ligation detection reaction. Mol. Cell. Probes 12(5), 273–282 (1998).
   Google Scholar
• Iannone MA, Taylor JD, Chen J et al. Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. Cytometry 39(2), 131–140 (2000).
   Google Scholar
• Shi MM. Enabling large-scale pharmacogenetic studies by highthroughput mutation detection and genotyping technologies. Clin. Chem. 47(2), 164–172 (2001).
   Google Scholar
• •• Comprehensive review article comparing methods for detecting genetic variation in large-scale applications.
   Google Scholar
• Livak KJ, Flood SJA, Marmaro J, Giusti W, Deetz K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4(6), 357–362 (1995).
   Google Scholar
• • Key study describing the development of the TaqMan homogeneous PCR amplification and detection system.
   Google Scholar
• Marras SA, Kramer FR, Tyagi S. Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal. 14(5–6), 151–156 (1999).
   Google Scholar
• Livak KJ. Allelic discrimination using fluorogenic probes and the 5– nuclease assay. Genet. Anal. 14(5–6), 143–149 (1999).
   Google Scholar
• Fors L, Lieder KW, Vavra SH, Kwiatkowski RW. Large-scale single nucleotide polymorphisms scoring from unamplified genomic DNA. Pharmacogenomics 1(2), 219–229 (2000).
   Google Scholar
• Hessner MJ, Budish MA, Friedman KD. Genotyping of Factor V G1691A (Leiden) without the use of PCR by invasive cleavage of oligonucleotide probes. Clin. Chem. 46(8), 1051–1056 (2000).
   Google Scholar
• Schweitzer B, Kingsmore S. Combining nucleic acid amplification and detection. Curr. Opin. Biotechnol. 12(1), 21–27 (2001).
   Google Scholar
• • Well-written review of current homogeneous PCR platforms.
   Google Scholar
• Schmalzing D, Koutny L, Salas-Solano O, Adourian A, Matsudaira P, Ehrlich D. Recent developments in DNA sequencing by capillary and microdevice electrophoresis. Electrophoresis 20(15–16), 3066–3077 (1999).
   Google Scholar
• Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11(1), 3–11(2001).
   Google Scholar
• Hacia JG, Collins FS. Mutational analysis using oligonucleotide microarrays. J. Med. Genet. 36(10), 730–736 (1999).
   Google Scholar
• •• Thorough review of microarrays from both technical and clinical viewpoints.
   Google Scholar
• Ramsay G. DNA chips: state-of-the art. Nature Biotechnol. 16(1), 40–44 (1998).
   Google Scholar
• Wang DG, Fan JB, Siao CJ et al. Largescale identification, mapping and genotyping of single-nucleotide polymorphisms in the human genome. Science 280(5366), 1077–1082 (1998).
   Google Scholar
• •• Powerful demonstration of the potential of microarrays for large-scale genotyping.
   Google Scholar
• Kozal MJ, Shah N, Shen N et al. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nature Med. 2(7), 753–759.
   Google Scholar
• Nguyen LT, Ramanathan M, Weinstock- Guttman B et al. Detection of cytochrome P450 and other drug-metabolizing enzyme mRNAs in peripheral blood mononuclear cells using DNA arrays. Drug Metab. Dispos. 28(8), 987–993 (2000).
   Google Scholar
• Hacia JG, Brody LC, Chee MS et al. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-color fluorescence analysis. Nature Genet. 14(4), 441–447 (1996).
   Google Scholar
• Laken SJ, Jackson PE, Kunzler KW et al. Genotyping by mass spectrometric analysis of short DNA fragments. Nature Biotechnol. 16(13), 1352–1356 (1998).
   Google Scholar
• Braun A, Little D, Kostler H. Detecting CFTR gene mutations using primer oligo base extension and mass spectrometry. Clin. Chem. 43(7), 1151–1158 (1997).
   Google Scholar
• • Good demonstration of the potential utility of mass spectrometry as a mutation detection technology.
   Google Scholar
• Coffin JM. HIV viral dynamics. AIDS 10\(Suppl. 3), S75–84 (1996).
   Google Scholar
• •• Excellent review of the biology of the HIV virus and the implications of viral biology for interventional strategies aimed at preventing AIDS.
   Google Scholar
• Hirsch MS, Brun-Vezinet F, DAquila RT et al. Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel. JAMA 283(18), 2417–2426 (2000).
   Google Scholar
• Wilson JW, Bean P, Robins T, Graziano F, Persing DH. Comparative evaluation of three human immunodeficiency virus genotyping systems: the HIV-GenotypR method, the HIV PRT GeneChip assay and the HIV-1 RT line probe assay. J. Clin. Microbiol. 38(8), 3022–3028 (2000).
   Google Scholar
• Erali M, Page S, Reimer LG, Hillyard DR. Human immunodeficiency virus Type 1 drug resistance testing: a comparison of three sequence-based methods. J. Clin. Microbiol. 39(6), 2157–2165 (2001).
   Google Scholar
• Baxter JD, Mayers DL, Wentworth DN et al. A randomized study of antiretroviral management based on plasma genotypic antiretroviral resistance testing in patients failing therapy. CPCRA 046 Study Team for the Terry Beirn Community Programs for Clinical Research on AIDS. AIDS 14(9), F83–93 (2000).
   Google Scholar
• Durant J, Clevenbergh P, Halfon P et al. Drug resistance genotyping in HIV-1 therapy: the VIRADAPT randomised controlled trial. Lancet 353(9171), 2195– 2199 (1999).
   Google Scholar
• • First placebo-controlled clinical trial demonstrating the value of performing drug-resistance genotype prior to selecting antiretroviral regimens for therapy of HIV infection.
   Google Scholar
• Wegner SA, Brodine SK, Mascola JR et al. Prevalence of genotypic and phenotypic resistance to antiretroviral drugs in a cohort of therapy-nave HIV-1 infected US military personnel. AIDS 14(8), 1009–1015 (2000).
   Google Scholar
• Cook J, Dasbach E, Coplan P et al. Modeling the long-term outcomes and costs of HIV antiretroviral therapy using HIV RNA levels: applications to a clinical trial. AIDS Res. Hum. Retroviruses 15(6), 499–508 (1999).
   Google Scholar
• Ravdin P. The use of HER2 testing in the management of breast cancer. Semin. Oncol. 27(5), 33–42 (1999).
   Google Scholar
• •• Excellent review of the controversial area of HER2 testing in breast cancer management.
   Google Scholar
• Winstanley J, Cooke T, Murray GD et al. The long-term prognostic significance of cerbB- 2 in primary breast cancer. Br. J. Cancer 63(3), 337–340 (1991).
   Google Scholar
• Vargas-Roig LM, Gago FE, Tello O et al. cerbB- 2 (HER-2/neu) protein and drug resistance in breast cancer patients treated with induction chemotherapy. Int. J. Cancer 84(2), 129–134 (1999).
   Google Scholar
• Treish I, Schwartz R, Lindley C. Pharmacology and therapeutic use of trastuzumab in breast cancer. Am. J. Health Syst. Pharm. 57(22), 2063–2079 (2000).
   Google Scholar
• Umek RM, Lin SW, Vielmetter J et al. Electronic detection of nucleic acids: a versatile platform for molecular diagnostics. J. Molec. Diagn. 3(2), 74–84 (2001).
   Google Scholar
• • Interesting article describing a novel method for detecting nucleic acids in a microminiaturized, handheld device.
   Google Scholar
• Hess P, Cooper D. Impact of pharmacogenomics on the clinical laboratory. Mol. Diagn. 4(4), 289–298 (1999).
   Google Scholar
• •• Well-written critical review of the issues surrounding the implementation of pharmacogenetic testing in the clinical laboratory.
   Google Scholar
• Rusnak JM, Kisabeth RM, Herbert DP et al. Pharmacogenomics: a clinicians primer on emerging technologies for improved patient care. Mayo Clin. Proc. 76(3), 299–309.
   Google Scholar