Current Applications of Microarrays in Head and Neck Cancer Research

Laryngoscope

Volumn 114, Issue 2, 2004, Pages 241-248

  Warner, Giles C ^a   Reis, Patricia P ^a   Makitie, Antti A ^a   Sukhai, Mahadeo A ^a   Arora, Shilpi ^a   Jurisica, Igor ^a   Wells, Richard A ^a   Gullane, Patrick ^a   Irish, Jonathan ^a   Kamel Reid, Suzanne ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Gene profiling; Head and neck cancer; Microarrays

Indexed keywords

RNA;

CANCER RESEARCH; DATA ANALYSIS; DNA FINGERPRINTING; DNA MICROARRAY; GENE EXPRESSION REGULATION; HEAD AND NECK CANCER; HUMAN; HUMAN CELL; HUMAN TISSUE; METHODOLOGY; PRIORITY JOURNAL; PROGNOSIS; REVIEW; TECHNOLOGY;

DNA MUTATIONAL ANALYSIS; HEAD AND NECK NEOPLASMS; HUMANS; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; PROGNOSIS;

EID: 10744220489     PISSN: 0023852X     EISSN: None     Source Type: Journal    
DOI: 10.1097/00005537-200402000-00013     Document Type: Review

References (35)

1. Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
2. Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet 1999;21:33-37.
3. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767-773.
4. Pease AC, Solas D, Sullivan EJ, Cronin MT, Holmes CP, Fodor SP. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc Natl Acad Sci U S A 1994;91:5022-5026.
5. Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA. Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 1999;24:153-159.
6. Lindblad-Toh K, Tanenbaum DM, Daly MJ, et al. Loss-of-hererozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol 2000;18:1001-1005.
7. McClintick JN, Jerome RE, Nicholson CR, Crabb DW, Edenberg HJ. Reproducibility of oligonucleotide arrays using small samples. BMC Genomics 2003;4:4.
8. Squire JA, Bayani J, Luk C, et al. Molecular cytogenetic analysis of head and neck squamous cell carcinoma: by comparative genomic hybridization, spectral karyotyping, and expression array analysis. Head Neck 2002;24:874-887.
9. Lee S, Baek M, Yang H, et al. Identification of genes differentially expressed between gastric cancers and normal gastric mucosa with cDNA microarrays. Cancer Lett 2002;184:197-206.
10. Alevizos I, Mahadevappa M, Zhang X, et al. Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene 2001;20:6196-6204.
11. Wang E, Miller LD, Ohnmacht GA, et al. High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 2000;18:457-459.
12. Baugh LR, Hill AA, Brown EL, Hunter CP. Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 2001;29:E29.
13. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, Winegarden N. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 2002;20:940-943.
14. Hu L, Wang J, Baggerly K, et al. Obtaining reliable information from minute amounts of RNA using cDNA microarrays. BMC Genomics 2002;3:16.
15. Makrigiorgos GM, Chakrabarti S, Zhang Y, et al. A PCR-based amplification method retaining the quantitative difference between two complex genomes. Nat Biotechnol 2002;20:936-939.
16. Eisen MB, Spellman PT, Brown PO, et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 1998;95:14863-14868.
17. Tamayo P, Slonim D, Mesirov J, et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999;96:2907-2912.
18. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM. Systematic determination of genetic network architecture. Nat Genet 1999;22:281-285.
19. DeRisi J, Penland L, Brown PO, et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 1996;14:457-460.
20. Alon U, Barkai N, Notterman DA, et al. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci U S A 1999;96:6745-6750.
21. Alizadeh AA, Staudt LM. Genomic-scale gene expression profiling of normal and malignant immune cells. Curr Opin Immunol 2000;12:219-225.
22. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-511.
23. Sultan M, Wigle DA, Cumbaa CA, et al. Binary tree-structured vector quantization approach to clustering and visualising microarray data. Bioinformatics 2002;1:1-9.
24. Ross DT, Scherf U, Eisen MB, et al. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 2000;24:227-235.
25. Hacia JG. Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 1999;21:42-47.
26. Debouck C, Goodfellow PN. DNA microarrays in drug discovery and development. Nat Genet 1999;21:48-50.
27. Pollack JR, Perou CM, Alizadeh AA, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999;23:41-46.
28. Beheshti B, Park PC, Braude I, Squire JA. Microarray CGH. Methods Mol Biol 2002;204:191-207.
29. Mantripragada KK, Buckley PG, Benetkiewicz M, et al. High-resolution profiling of an 11Mb segment of human chromosome 22 in sporadic schwannoma using array-CGH. Int J Oncol 2003;22:615-622.
30. Beheshti B, Braude I, Marrano P, Thorner P, Zielenska M, Squire JA. Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. Neoplasia 2003;5:53-62.
31. Kraus J, Pantel K, Pinkel D, Albertson DG, Speicher MR. High-resolution genomic profiling of occult micrometastatic tumor cells. Genes Chrom Cancer 2003;36:159-166.
32. Belbin TJ, Singh B, Barber I, et al. Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. Cancer Res 2002;62:1184-1190.
33. Villaret DB, Wang T, Dillon D, et al. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope 2000;110:374-381.
34. Leethanakul C, Patel V, Gillespie J, et al. Distinct pattern of expression of differentiation and growth-related genes in squamous cell carcinomas of the head and neck revealed by the use of laser capture microdissection and cDNA arrays. Oncogene 2000;19:3220-3224.
35. Squire JA, Bayani J, Luk C, et al. Molecular cytogenetic analysis of head and neck squamous cell carcinoma: by comparative genomic hybridization, spectral karyotyping, and expression array analysis. Head Neck 2002;24:874-887.