Abstract
A method of high resolution, array-based comparative genomic hybridization is described for the mapping of copy-number changes associated with chromosomal amplifications, deletions, and translocations. The method involves the design of whole-genome or targeted, fine-tiling arrays for synthesis on a high-density digital microarray-synthesis platform. The arrays can span entire eukaryotic genomes or be targeted to specific chromosomal regions for high-resolution identification of copy-number changes and the corresponding breakpoint locations. The methods described include the bioinformatics required for array design, and the protocols for DNA fragmentation, dual-color labeling, microarray hybridization, and array scanning. The processes for data extraction, normalization, and segmentation analysis are also described.
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References
Nuwaysir, E. F., Huang, W., Albert, T. J., et al. (2002) Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749–1755.
Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20–24.
Barrett, M. T., Scheffer, A., Ben-Dor, A., et al. (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc. Natl. Acad. Sci. USA 101, 17,765–17,770.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
http://www.sanger.ac.uk/Software/analysis/SSAHA/.
http://www.nimblegen.com/products/software/arrayscribe/.
Workman, C., Jensen, L. J., Jarmer, H., et al. (2002) A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol. research0048.1-research0048.16.
http://genomebiology.com/2002/3/9/research/0048.
Petri, A., Fleckner, J., and Matthiessen, M. W. (2004) Array-A-Lizer: a serial DNA microarray quality analyzer. BMC Bioinformatics 5, 12.
http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtmL.
Olshen, A. B., Venkatraman, E. S., Lucito, R., and Wigler, M. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572.
http://www.bioconductor.org.
http://genome.ucsc.edu/.
Fare, T. L., Coffey, E. M., Dai, H., et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal. Chem. 75, 4672–4675.
http://genomics.princeton.edu/dunham/ozone.html.
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© 2007 Humana Press Inc., Totowa, NJ
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McCormick, M.R., Selzer, R.R., Richmond, T.A. (2007). Methods in High-Resolution, Array-Based Comparative Genomic Hybridization. In: Rampal, J.B. (eds) Microarrays. Methods in Molecular Biology™, vol 381. Humana Press. https://doi.org/10.1007/978-1-59745-303-5_9
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DOI: https://doi.org/10.1007/978-1-59745-303-5_9
Publisher Name: Humana Press
Print ISBN: 978-1-58829-589-7
Online ISBN: 978-1-59745-303-5
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