Abstract
Recent advances in DNA microarray technology have enabled researchers to comprehensively characterize the complex genomes of higher eukaryotic organisms at an unprecedented level of detail. Array-based comparative genomic hybridization (Array-CGH) has been widely used for detecting DNA copy number alterations on a genomic scale, where the mapping resolution is limited only by the number of probes on the DNA microarray. In this chapter, we present a validated protocol utilizing print-tip spotted HEEBO (Human Exonic Evidence Based Oligonucleotide) microarrays for conducting array-CGH using as little as 25 ng of genomic DNA from a wide variety of sources, including cultured cell lines and clinical specimens, with high spatial resolution and array-to-array reproducibility.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ylstra, B., van den Ijssel, P., Carvalho, B., Brakenhoff, R. H., and Meijer, G. A. (2006) BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34, 445–450.
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.
Wodicka, L., Dong, H., Mittmann, M., Ho, M. H., and Lockhart, D. J. (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol. 15, 1359–1367.
Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., et al. (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286, 531–537.
Hill, A. A., Hunter, C. P., Tsung, B. T., Tucker-Kellogg, G., and Brown, E. L. (2000) Genomic analysis of gene expression in C. elegans. Science 290, 809–812.
Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19, 342–347.
Ramaswamy, S., Ross, K. N., Lander, E. S., and Golub, T. R. (2003) A molecular signature of metastasis in primary solid tumors. Nat. Genet. 33, 49–54.
Lucito, R., Healy, J., Alexander, J., Reiner, A., Esposito, D., Chi, M., et al. (2003) Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 13, 2291–2305.
Barrett, M. T., Scheffer, A., Ben-Dor, A., Sampas, N., Lipson, D., Kincaid, R., et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. U S A 101, 17765–17770.
Carvalho, B., Ouwerkerk, E., Meijer, G. A., and Ylstra, B. (2004) High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J. Clin. Pathol. 57, 644–646.
Zhao, X., Li, C., Paez, J. G., Chin, K., Janne, P. A., Chen, T. H., et al. (2004) An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 64, 3060–3071.
Kwei, K. A., Kim, Y. H., Girard, L., Kao, J., Pacyna-Gengelbach, M., Salari, K., et al. (2008) Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. Oncogene 27, 3635–3640.
Friedman, J. M., Baross, A., Delaney, A. D., Ally, A., Arbour, L., Armstrong, L., et al. (2006) Oligonucleotide microarray analysis of genomic imbalance in children with mental retardation. Am. J. Hum. Genet. 79, 500–513.
Ming, J. E., Geiger, E., James, A. C., Ciprero, K. L., Nimmakayalu, M., Zhang, Y., et al. (2006) Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum. Mutat. 27, 467–473.
Balciuniene, J., Feng, N., Iyadurai, K., Hirsch, B., Charnas, L., Bill, B. R., et al. (2007) Recurrent 10q22–q23 deletions: a genomic disorder on 10q associated with cognitive and behavioral abnormalities. Am. J. Hum. Genet. 80, 938–947.
Pinkel, D., and Albertson, D. G. (2005) Array comparative genomic hybridization and its applications in cancer. Nat. Genet. 37 Suppl, S11–S17.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kim, Y.H., Pollack, J.R. (2009). Comparative Genomic Hybridization on Spotted Oligonucleotide Microarrays. In: Pollack, J. (eds) Microarray Analysis of the Physical Genome. Methods in Molecular Biology™, vol 556. Humana Press. https://doi.org/10.1007/978-1-60327-192-9_3
Download citation
DOI: https://doi.org/10.1007/978-1-60327-192-9_3
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60327-191-2
Online ISBN: 978-1-60327-192-9
eBook Packages: Springer Protocols