Abstract
Comparative genomic hybridization (CGH) to metaphase chromosome targets (1,2) has significantly contributed to our understanding of the cancer cytogenetics of more complex malignancies such as solid tumors (3,4). This molecular cytogenetics-based technique (hereafter referred to as “chromosome CGH”) is capable of defining genome-wide DNA copy number imbalances in sample cells relative to a normal reference in a single experiment. Chromosome CGH has greatly increased our understanding of tumor biology and progression since the minimal recurrent regions of chromosomal gain and loss are likely to contain novel oncogene(s) and tumor suppressor gene(s) respectively.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Kallioniemi A., Kallioniemi O. P., Sudar D., et al. (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258, 818–821.
Kallioniemi O. P., Kallioniemi A., Sudar D., et al. (1993) Comparative genomic hybridization: a rapid new method for detecting and mapping DNA amplification in tumors. Semin. Canc. Biol. 4, 41–46.
Forozan F., Karhu R., Kononen J., Kallioniemi A., and Kallioniemi O. P. (1997)Genome screening by comparative genomic hybridization. Trends Genet. 13, 405–409.
James L. A. (1999) Comparative genomic hybridization as a tool in tumour cytogenetics. J. Pathol. 187, 385–395.
Parente F., Gaudray P., Carle G. F., and Turc-Carel C. (1997) Experimental assessment of the detection limit of genomic amplification by comparative genomic hybridization CGH. Cytogenet. Cell Genet. 78, 65–68.
Lennon G., Auffray C., Polymeropoulos M., and Soares M. B. (1996) The I. M. A. G. E. Consortium: an integrated molecular analysis of genomes and their expression. Genomics 33, 151–152.
Schena M., Shalon D., Davis R. W., and Brown P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.
DeRisi J., Penland L., Brown P. O., et al. (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14, 457–460.
Pollack J. R., Perou C. M., Alizadeh A. A., et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet. 23, 41–46.
Beheshti B., Braude I., Marrano P., Thorner P., Zielenska M., and Squire J. A. (2002) Survey of DNA amplifications in neuroblastoma tumors using cDNA microarrays. Submitted to Neoplasia.
Solinas-Toldo S., Lampel S., Stilgenbauer S., et al. (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chr. Canc. 20, 399–407.
Pinkel D., Segraves R., Sudar D., et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20, 207–211.
Heiskanen M. A., Bittner M. L., Chen Y., et al. (2000) Detection of gene amplification by genomic hybridization to cDNA microarrays. Canc. Res. 60, 799–802.
Raap A. K., van de Corput M. P., Vervenne R. A., van Gijlswijk R. P., Tanke H. J., and Wiegant J. (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotinor fluorochrome tyramides. Hum. Mol. Genet. 4, 529–534.
Jones T. A., Flomen R. H., Senger G., Nizetic D., and Sheer D. (2000) The homeobox gene MEIS1 is amplified in IMR-32 and highly expressed in other neuroblastoma cell lines. Eur. J. Canc. 36, 2368–2374.
Spieker N., van Sluis P., Beitsma M., et al. (2001) The MEIS1 oncogene is highly expressed in neuroblastoma and amplified in cell line IMR32. Genomics 71, 214–221.
Pei J., Beheshti B., Squire J. A., and Zielenska M. (2002) cDNA array CGH analysis of pediatric osteosarcomas identifies regions of amplification on chromosome 17. In preparation.
Halgren R. G., Fielden M. R., Fong C. J., and Zacharewski T. R. (2001) Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones. Nucl. Acids Res. 29, 582–588.
Albertson D. G., Ylstra B., Segraves R., et al. (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat. Genet. 25, 144–146.
Bruder C. E., Hirvela C., Tapia-Paez I., et al. (2001) High resolution deletion analysis of constitutional DNA from neurofibromatosis type 2 (NF2) patients using microarray-CGH. Hum. Mol. Genet. 10, 271–282.
Daigo Y., Chin S. F., Gorringe K. L., et al. (2001) Degenerate oligonucleotide primedpolymerase chain reaction-based array comparative genomic hybridization for extensive amplicon profiling of breast cancers: a new approach for the molecular analysis of paraffin-embedded cancer tissue. Am. J. Pathol. 158, 1623–1631.
Weber T., Weber R. G., Kaulich K., et al. (2000) Characteristic chromosomal imbalances in primary central nervous system lymphomas of the diffuse large B-cell type. Brain Pathol. 10, 73–84.
Geschwind D. H., Gregg J., Boone K., et al. (1998) Klinefelter’s syndrome as a model of anomalous cerebral laterality: testing gene dosage in the X chromosome pseudoautosomal region using a DNA microarray. Dev. Genet. 23, 215–229.
Hui A. B., Lo K. W., Yin X. L., Poon W. S., and Ng H. K. (2001) Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization. Lab. Invest. 81, 717–723.
Cheung V. G., Nowak N., Jang W., et al. (2001) Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 409, 953–958.
Telenius H., Carter N. P., Bebb C. E., Nordenskjold M., Ponder B. A., and Tunnacliffe A. (1992) Degenerate oligonucleotide-primed PCR: general amplification of target DNA by a single degenerate primer. Genomics 13, 718–725.
Cheng S., Fockler C., Barnes W. M., and Higuchi R. (1994) Effective amplification of long targets from cloned inserts and human genomic DNA. Proc. Natl. Acad. Sci. USA 91, 5695–5699.
Lichter P., Joos S., Bentz M., and Lampel S. (2000) Comparative genomic hybridization: uses and limitations. Semin. Hematol. 37, 348–357.
Wilgenbus K. K. and Lichter P. (1999) DNA chip technology ante portas. J. Mol. Med. 77, 761–768.
King W., Proffitt J., Morrison L., Piper J., Lane D., and Seelig S. (2000) The role of fluorescence in situ hybridization technologies in molecular diagnostics and disease management. Mol. Diagn. 5, 309–319.
Cheung V. G., Morley M., Aguilar F., Massimi A., Kucherlapati R., and Childs G. (1999) Making and reading microarrays. Nat. Genet. 21, 15–19.
Eisen M. B., Spellman P. T., Brown P. O., and Botstein D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14,863–14,868.
Brazma A. and Vilo J. (2000) Gene expression data analysis. FEBS Lett. 480, 17–24.
Kerr M. K., Martin M., and Churchill G. A. (2000) Analysis of variance for gene expression microarray data. J. Comput. Biol. 7, 819–837.
Sherlock G., Hernandez-Boussard T., Kasarskis A., et al. (2001) The Stanford Microarray Database. Nucl. Acids Res. 29, 152–155.
Phimister B. (1999) Going Global (Editorial). Nat. Genet. 21, 1.
Alon U., Barkai N., Notterman D. A., et al. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96, 6745–6750.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Humana Press Inc.
About this protocol
Cite this protocol
Beheshti, B., Park, P.C., Braude, I., Squire, J.A. (2002). Microarray CGH. In: Fan, YS. (eds) Molecular Cytogenetics. Methods in Molecular Biology™, vol 204. Humana Press. https://doi.org/10.1385/1-59259-300-3:191
Download citation
DOI: https://doi.org/10.1385/1-59259-300-3:191
Publisher Name: Humana Press
Print ISBN: 978-1-58829-006-9
Online ISBN: 978-1-59259-300-2
eBook Packages: Springer Protocols