Medical applications of microarray technologies: A regulatory science perspective

Nature Genetics

Volumn 32, Issue 4S, 2002, Pages 474-479

  Petricoin, Emanuel F ^a   Hackett, Joseph L ^b   Lesko, Lawrence J ^c   Puri, Raj K ^a   Gutman, Steven I ^b   Chumakov, Konstantin ^a   Woodcock, Janet ^c   Feigal, David W ^b   Zoon, Kathryn C ^a   Sistare, Frank D ^c  

^a CENTER FOR BIOLOGICS EVALUATION AND RESEARCH   (United States)

^b CENTER FOR DEVICES AND RADIOLOGICAL HEALTH   (United States)

^c CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; CELL DNA;

CELL CYCLE; CLINICAL RESEARCH; CLINICAL TRIAL; DATA ANALYSIS; DIAGNOSTIC ACCURACY; DNA MICROARRAY; DNA SEQUENCE; DNA SYNTHESIS; DRUG SCREENING; FOOD AND DRUG ADMINISTRATION; GENE TECHNOLOGY; GENOME; GENOMICS; HAPLOTYPE; HUMAN; HYPOTHESIS; INFECTION; MEDICAL PRACTICE; NUCLEOTIDE SEQUENCE; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL; RELIABILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

FORECASTING; GENETICS, MEDICAL; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLICY MAKING; PROTEOMICS; RESEARCH; TECHNOLOGY ASSESSMENT, BIOMEDICAL; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 0036900945     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng1029     Document Type: Article

References (65)

1. Warrington, J.A., Dee, S. and Trulson, M. Large-scale genomic analysis using Affymetrix GeneChipR probe arrays. in Microarray Biochip Technology (ed. Schena, M.) 119-148 (BioTechniques Books, Natick, MA, 2000).
2. Tefferi, A., Bolander, M.E., Ansell, S.M., Wieben, E.D. and Spelsberg, T.C. Primer on medical genomics part III: Microarray experiments and data analysis. Mayo Clin. Proc. 77, 927-940 (2002).
3. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610-614 (1996).
4. Cronin, M.T., Fucini, R.V., Kim, S.M., Masino, R.S., Wespi, R.M. and Miyada, C.G. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mutat. 7, 244-255 (1996).
5. Hacia, J.G., Brody, L.C., Chee, M.S., Fodor, S.P.A. and Collins, F.S. Detection of heterzygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nature Genet. 14, 444-447 (1996).
6. Hacia, J.G. et al. Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. Genome Res. 8, 1245-1258 (1998).
7. Favis, R. and Barany, F. Mutation detection in K-ras, BRCA1, BRCA2, and p53 using PCR/LDR and a universal DNA microarray. Ann. NY Acad. Sci. 906, 39-43 (2000).
8. Mei, R. et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res.10, 1126-1137 (2000).
9. Cutler, D.J. et al. High-throughput variation detection and genotyping using microarrays. Genome Res. 11, 1913-1925 (2001).
10. Raitio, M. et al. Y-chromosomal SNPs in Finn-Ugric-speaking populations analyzed by minisequencing on microarrays. Genome Res. 11, 471-482 (2001).
11. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
12. Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotech. 14, 1675-1680 (1996).
13. Shalon, D., Smith, S.J. and Brown, P.O. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639-345 (1996).
14. Brown, P.O. and Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21 (1 Suppl), 33-37 (1999).
15. DeRisi, J. et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet. 14, 457-460 (1996).
16. Golub, T.R. et al. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
17. Bubendorf, L. et al. Hormone therapy failure in human prostate cancer: Analysis by complementary DNA and tissue microarrays. J. Natl. Cancer Inst. 91, 1758-1764 (1999).
18. Alizadeh, A.A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503-511 (2000).
19. Stamey, T.A. et al. Molecular genetic profiling of Gleason grade 4/5 prostate cancers compared to benign prostatic hyperplasia. J. Urology 166, 2171-2177 (2001).
20. Luo, J. et al. Human prostate cancer and benign prostatic hyperplasia: Molecular dissection by gene expression profiling. Cancer Research 61, 4683-4688 (2001).
21. West, M. et al. Predicting the clinical status of human breast cancer by using gene expression profiles. Proc. Natl. Acad. Sci. USA 98, 11462-11467 (2001).
22. Hedenfalk, I. et al. Gene expression profiles in hereditary breast cancer. N. Engl. J. Med. 244, 539-548 (2001).
23. Shirota, Y., Kaneko, S., Honda, M., Hawai, H.F. and Kobayashi, K. Identification of differentially expressed genes in hepatocellular carcinoma with cDNA microarrays. Heptatology 33, 832-840 (2001).
24. Okabe, H. et al. Genome-wide analysis of gene expression in human hepatocellular carcinomas using cDNA microarray: Identification of genes involved in viral carcinogenesis and tumor progression. Cancer Res. 61, 2129-2137 (2001).
25. van’t Veer, L.J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530-536 (2002).
26. Rosenwald, A. et al. The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med. 346, 1937-1947 (2002).
27. Shipp, M. et al. Diffuse large B-cell lymphoma outcome prediction by gene expression profiling and supervised machine learning. Nature Med. 8, 68-74 (2002).
28. Bittner, M. et al. Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406, 536-540 (2000).
29. Pomeroy, S.L. et al. Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415, 436-442 (2002).
30. Armstrong, S.A. et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nature Genet. 30, 41-47 (2002).
31. Alevizos, I. et al. Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene 20, 6196-6204 (2001).
32. Welsch, P.L. et al. BRCA1 transcriptionally regulates genes involved in breast tumorigenesis. Proc. Natl Acad. Sci. USA 99, 7560-7565 (2002).
33. Sreekumar, A. et al. Profiling of cancer cells using protein microarrays: Discovery of novel radiation-regulated proteins. Cancer Res. 61, 7585-7593 (2001).
34. MacBeath, G. Proteomics comes to the surface. Nature Biotech. 19, 828-829 (2001).
35. Walter, G., Bussow, K., Lueking, A. and Glokler, J. High-throughput protein arrays: Prospects for molecular diagnostics. Trends Mol. Med. 8, 250-253 (2002).
36. Kuruvilla, F.G., Shamji, A.F., Sternson, S.M., Hergenrother, P.J. and Schreiber, S.L. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653-657 (2002).
37. Paweletz, C.P. et al. Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front. Oncogene 20, 1981-1989 (2001).
38. Torhorst, J. et al. Tissue microarrays for rapid linking of molecular changes to clinical endpoints. Am. J. Pathol. 159, 2249-2256 (2001).
39. Figeys, D. and Pinto, D. Proteomics on a chip: promising developments. Electrophoresis 22, 208-216 (2001).
40. Petricoin, E.F., Zoon, K.C., Kohn, E.C., Barrett, J.C. and Liotta, L.A. Clinical proteomics: Translating benchside practice into bedside reality. Nature Rev. Drug Disc. 1, 663-686 (2002).
41. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863-14868 (1998).
42. Khan, J. et al. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Med. 7, 673-679 (2001).
43. Petricoin, E.F. et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572-577 (2002).
44. Roses, A.D. Genome-based pharmacogenetics and the pharmaceutical industry. Nature Rev. Drug Disc. 1, 541-548 (2002).
45. Seungchan, K. et al. Multivariate measurement of gene expression relationships. Genomics 67, 201-209 (2000).
46. Altman, R.B. and Klein, T.E. Challenges for biomedical informatics and pharmacogenomics. Ann. Rev. Pharm. Toxicol. 42, 113-133 (2002).
47. Lee, M.-L.T., Kuo, F.C., Whitmore, G.A. and Sklar, J. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl Acad. Sci. USA 97, 9834-9839 (2000).
48. Tseng, G.C., Oh, M.-K., Rohlin, L., Liao, J.C. and Wong, W.H. Issues in cDNA microarray analysis: Quality filtering, channel normailization, models of variations and assessment of gene effects. Nucleic Acids Res. 29, 2549-2557 (2001).
49. Mills, J.C. and Gordon, J.I. A new approach for filtering noise from high-density oligonucleotide microarray datasets. Nucleic Acids Res. 29, e72 (2001).
50. Bakay, M., Chen, Y.-W., Borup, R., Zhao, P., Nagaraju, K. and Hoffman, E.P. Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformatics 3, 4 (2002).
51. King, H.C. and Sinha, A.A. Gene expression profile analysis by DNA microarrays: Promise and pitfalls. JAMA 286, 2280-2288 (2001).
52. Nuwaysir, E.F., Bittner, M., Trent, J., Barrett, J.C. and Afshari, C.A. Microarrays and toxicology: The advent of toxicogenomics. Mol. Carcinogenesis 24, 153-159 (1999).
53. Waring, J.F. et al. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Nature Genet. 29, 365-371 (2001).
54. Hamadeh, H.K. et al. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 67, 219-231 (2002).
55. Thomas, R.S. et al. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol. Pharmacol. 60, 1189-1194 (2001).
56. Huang, Q. et al. Assessment of cisplatin-induced nephrotoxicity by microarray technology. Toxicol. Sci 63, 196-207 (2001).
57. Brown, P.O. and Hartwell, L. Genomics and human disease-variations on variation. Nature Genet. 18, 91-93 (1998).
58. He, B., Munson, A.E. and Meade, B.J. Analysis of gene expression induced by irritant and sensitizing chemicals using oligonucleotide arrays. Internat. Immunopharm. 1, 867-879 (2001).
59. Ramakrishnan, R. et al. An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications. Nucleic Acids Res. 30, e30 (2002).
60. Modrek, B. and Lee, C. A genomic view of alternative splicing. Nature Genet. 30, 13-19 (2002).
61. Brem, R.B., Yuert, G., Clinton, R. and Kruglyak, L. Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752-755 (2002).
62. Cantor, C.R. Pharmacogenetics becomes pharmacogenomics: Wake up and get ready. Mol. Diagnostics 4, 287-288 (1999).
63. Hamadeh, H.K., Bushel, P., Tucker, C.J., Martin, K., Paules, R. and Afshari, C.A. Detection of diluted gene expression alterations using cDNA arrays. Biotechniques 32, 322-329 (2002).
64. Stoeckert, C.J., Causton, H.C. and Ball, C.A. Microarray databases standards and ontologies. Nature Genet. 32, 469-473 (2002).
65. Brazma, A. et al. Minimal information about a microarray experiment (MIAME)- toward standards for microarray data. Nature Genet.29, 365-371 (2001).