The integration of microarray information in the drug development process

Current Opinion in Biotechnology

Volumn 9, Issue 6, 1998, Pages 643-649

  Braxton, Scott ^a   Bedilion, Tod ^a  

^a Synteni Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NEW DRUG;

BIOTECHNOLOGY; DNA HYBRIDIZATION; DNA POLYMORPHISM; DRUG DEVELOPMENT; GENE EXPRESSION REGULATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC POLYMORPHISM; INFORMATION PROCESSING; PHARMACOGENETICS; PRIORITY JOURNAL; REVIEW;

EID: 0032402905     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(98)80144-4     Document Type: Article

References (37)

1. Chee M, Yang R, Hubbell E, Berno A, Huang XC, Stern D, Winkler J, Lockhart DJ, Morris MS, Fodor SP. Accessing genetic information with high-density DNA arrays. Science. 274:1996;610-614.
2. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science. 251:1991;767-773.
3. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
4. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA. 93:1996;10614-10619.
5. Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:1996;639-645.
6. Schena M. Genome analysis with gene expression microarrays. Bioessays. 18:1996;427-443.
7. Fodor SP. DNA sequencing massivly parallel genomics. Science. 277:1997;393-395.
8. Wallraff G, Labadie J, Brock P, DiPietro R, Nguyen T, Huynh T, Hinsberg W, McGall G. DNA sequencing on a chip. Chemtech. 1997;22-32. February.
9. Johnston M. Gene chips: array of hope for understanding gene regulation. Curr Biol. 8:1998;R171-R174.
10. Marshall A, Hodgson J. DNA chips: an array of possibilities. Nat Biotechnol. 16:1998;27-31.
11. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E, Davis RW. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:1998;301-306.
12. Ramsay G. DNA chips: state-of-the art. Nat Biotechnol. 16:1998;40-44.
13. Wodicka L, Dong H, Mittman M, Ho MH, Lockhart DJ. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol. 15:1997;1359-1367.
14. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 14:1996;1675-1680.
15. DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet. 14:1996;457-460.
16. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. of outstanding interest Science. 278:1997;680-686 This is the first example of genome-wide expression monitoring. The authors followed the temporal response of yeast undergoing a shift from fermentation to respiration. About half of the genes that change expression level have no name or currently recognized function. Several key enzymes were altered to force the redirection of metabolites into the TCA cycle. Furthermore, nearly every TCA/glyoxylate cycle and carbohydrate storage gene was induced during this diauxic shift. In addition, the gene expression pattern was measured when TUP1, a transcriptional co-repressor was deleted, or YAP1, a transcriptional activator was overexpressed.
17. Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, McCullough MJ, Mccusker JH, Stevens DA, Wodicka L, Lockhart DJ, Davis RW. Direct allelic variation scanning of the yeast genome. of special interest Science. 281:1998;1194-1197 Nearly four thousand biallelic markers were identified by competitive hybridization of two different strains of yeast to a high-density oligonucleotide array. This was accomplished without prior knowledge of sequence or the specific nature of the variations between the two strains and did not require the design and synthesis of specific PCR primers, nor the creation of new strains or constructs. These markers were used to map several loci, with high resolution.
18. Kozal MJ, Shah N, Shen N, Yang R, Fucini R, Merigan TC, Richman DD, Morris D, Hubbell E, Chee M, Gingeras TR. Extensive polymorphisms observed in HIV-1 clade B protease gene using high-density oligonucleotide arrays. Nat Med. 2:1996;753-759.
19. Cronin MT, Fucini RV, Kim SM, Masino RS, Wespi RM, Miyada CG. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum Mutat. 7:1996;244-255.
20. Yershov G, Barsky V, Belgovsky A, Kirillov E, Kreindlin E, Ivanov I, Parinov S, Guschin D, Drobishev A, Dubiley S, Mirzabekov A. DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci USA. 93:1996;4913-4918.
21. Hacia JG, Edgemon K, Sun B, Stern D, Fodor SPA, Collins FS. Two color hybridization analysis using high density oligonucleotide arrays and energy transfer dyes. Nucleic Acids Res. 26:1998;3865-3866.
22. Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. of special interest Science. 280:1998;1077-1082 2.3 megabases of DNA were sequenced by gel-based systems, and resequenced from seven individuals using about 150 independent oligonucleotide array designs. 2748 candidate SNPs were identified, slightly more than one per kilobase. The average spacing between markers was about 2cM, with an average heterozygosity of 34%. This is a first step toward a human genome-wide SNP map, but covers less than 0.1% of the genome.
23. Nelson SF, McCusker JH, Sander MA, Kee Y, Modrich P, Brown PO. Genomic mismatch scanning: a new approach to genetic linkage mapping. Nat Genet. 4:1993;11-18.
24. Nelson SF. Genomic mismatch scanning: current progress and potential applications. Electrophoresis. 16:1995;279-285.
25. Cheung VG, Nelson SF. Genomic mismatch scanning identifies human genomic DNA shared identical by descent. Genomics. 47:1998;1-6.
26. Mirzayans F, Mears AJ, Guo SW, Pearce WG, Walter MA. Identification of the human chromosomal region containing the iridogoniodysgenesis anomaly locus by genomic-mismatch scanning. Am J Hum Genet. 61:1997;111-119.
27. Feingold E, Brown PO, Siegmund D. Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent. Am J Hum Genet. 53:1993;234-251.
28. Dupuis J, Brown PO, Siegmund D. Statistical methods for linkage analysis of complex traits from high-resolution maps of identity by descent. Genetics. 140:1995;843-856.
29. Cheung VG, Gregg JP, Gogolin-Ewens KJ, Bandong J, Stanley CA, Baker L, Higgins MJ, Nowak NJ, Shows TB, Ewens WJ, et al. Linkage-disequilibrium mapping without genotyping. Nat Genet. 18:1998;225-230.
30. Xiong M, Guo SW. Fine-scale genetic mapping based on linkage disequilibrium: theory and applications. Am J Hum Genet. 60:1997;1513-1531.
31. Guo SW. Linkage disequilibrium measures for fine-scale mapping: a comparison. Hum Hered. 47:1997;301-314.
32. Kruglyak L. The use of a genetic map of biallelic markers in linkage studies. Nat Genet. 17:1997;21-24.
33. Zhao LP, Aragaki C, Hsu L, Quiaoit F. Mapping of complex traits by single-nucleotide polymorphisms. Am J Hum Genet. 63:1998;225-240.
34. Devlin B, Risch N. A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics. 29:1995;311-322.
35. Heller RA, Schena M, Chai A, Shalon D, Bedilion T, Gilmore J, Woolley DE, Davis RW. Discovery and analysis of inflammatory disease-related genes using cDNA microarrays. Proc Natl Acad Sci USA. 94:1997;2150-2155.
36. Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, et al. An information-intensive approach to the molecular pharmacology of cancer. of outstanding interest Science. 275:1997;343-349 The NCI has screened more than 60,000 compounds against 60 well-characterized tumor cell lines. This paper tries to make sense of the vast amount of data, and various interesting patterns emerge. Tumor cells with similar molecular lesions respond to similar drugs. Clustering information is useful for determination of the mechanism of action of a new compound. Multidimensional structure-activity relationship (SAR) information from this set of data will be applied to large chemical libraries, and better anti-cancer drugs are more likely to be found.
37. Gray NS, Wodicka L, Thunnissen AM, Norman TC, Kwon S, Espinoza FH, Morgan DO, Barnes G, Leclerc S, Meijer L, et al. Exploiting chemical libraries, structure, and genomics in the search for kinase inhibitors. of special interest Science. 281:1998;533-538 The authors measured the gene expression changes in yeast induced by several inhibitors of the kinase Cdc28p. Although several genes changed in common for these treatments, more than half of the mRNA changes were distinct. Gene expression monitoring suggests that these compounds inhibit the target to different degrees, or that other targets are also affected. Comparison of the gene expression pattern of drug treatment to yeast with a temperature-sensitive mutation in Cdc28p should have yielded similar patterns, but did not on the whole. These results were confounded by incomplete gene inactivation and the bevy of changes associated with heat shock and cell cycle arrest. The approach outlined here should be more practical when a drug interacts with only one target, and the target can be specifically ablated.