Current Applications of Microarrays in Head and Neck Cancer Research
Giles C. Warner MSc, FRCS Eng
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorPatricia P. Reis PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorAntti A. Makitie MD, PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorMahadeo A. Sukhai MSc
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorShilpi Arora PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorIgor Jurisica PhD
Department of Computer Science, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorRichard A. Wells MD, PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorPatrick Gullane MD
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorJonathan Irish MD
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorCorresponding Author
Suzanne Kamel-Reid PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Suzanne Kamel-Reid, PhD, 610 University Avenue, Room 9-622, Princess Margaret Hospital, Ontario Cancer Institute, University of Toronto, Toronto, Ontario, CanadaSearch for more papers by this authorGiles C. Warner MSc, FRCS Eng
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorPatricia P. Reis PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorAntti A. Makitie MD, PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorMahadeo A. Sukhai MSc
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorShilpi Arora PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorIgor Jurisica PhD
Department of Computer Science, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorRichard A. Wells MD, PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorPatrick Gullane MD
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorJonathan Irish MD
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Search for more papers by this authorCorresponding Author
Suzanne Kamel-Reid PhD
Department of Cellular and Molecular Biology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Otolaryngology and Surgical Oncology, Ontario Cancer Institute and Princess Margaret Hospital, University Health Network and University of Toronto, Toronto, Ontario, Canada
Suzanne Kamel-Reid, PhD, 610 University Avenue, Room 9-622, Princess Margaret Hospital, Ontario Cancer Institute, University of Toronto, Toronto, Ontario, CanadaSearch for more papers by this authorAbstract
Objectives/Hypothesis: The objective was to introduce microarray technology and its applications in cancer research to the head and neck clinician.
Study Design: Literature review combined with methodology and examples from the authors' experiences with microarray analysis of tumors of the head and neck.
Methods: Search of literature and the authors' experience was made for technical details, alternative methods of data analysis, available bioinformatics tools, and applications of microarrays in cancer research.
Results: Microarrays allow the simultaneous analysis of the expression of thousands of genes. The use of a well-developed microarray study design leads to informative results. There are various bioinformatics resources widely available to aid in the analysis of microarray data. However, there is not yet a gold standard for analysis because this methodology is still evolving.
Conclusion: Microarray studies may allow researchers to identify genetic changes relevant to diagnosis and prognosis in patients with head and neck cancer. Although still relatively new, this powerful methodology has immense potential to aid in understanding of the genetic changes that are important in head and neck cancer.
Bibliography
- 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 ohgonucleotide arrays for rapid DNA sequence analysis Proc Nati Acad Sci USA 1994, 91, 5022–5026
- 5
Nuwaysir EF,
Bittner M,
Trent J,
Barrett JC,
Afshan CA.
Microarrays and toxicology the advent of toxicogenomics
Mol Carunog
1999,
24, 153–159
10.1002/(SICI)1098-2744(199903)24:3<153::AID-MC1>3.0.CO;2-P CAS PubMed Web of Science® Google Scholar
- 6 Lmdblad Toh K, Tanenbaum DM, Daly MJ, et al. Loss-of heterozygosity analysis of small cell lung carcinomas using single-nucleotide polymorphism arrays Nat Bwtechnol 2000, 18, 1001–1005
- 7 McChntick JN, Jerome RE, Nicholson CR, Crabb DW, Eden-berg HJ. Reproducibihty of ohgonucleotide arrays using small samples BMC Genomici, 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 differ entially 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 fies 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 Genomic 2002, 3, 16
- 15 Makngiorgos 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 Nati Acad Sci US 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 Pi oc Nati Acad Sci US 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 ohgonucleotide arrays Proc Nati Acad Sci U S A 1999, 96, 6745–6750
- 21 Ahzadeh AA, Staudt LM. Genomic-scale gene expression profiling of normal and malignant immune cells Curi Opin Immunol 2000 12 219–225
- 22 Ahzadeh 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 oh gonucleotide 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, Ahzadeh 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 Mantnpragada 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 genomit hybridization Neoplasia 2003, 5, 53–62
- 31 Kraus J, Pantel K, Pinkel D, Albertson DG, Speicher MR. High-resolution genomic profiling of occult micrometa-static 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 mi-croarrays. 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.
Citing Literature
