Advertisement

Microarrays pp 189-211 | Cite as

Methods in High-Resolution, Array-Based Comparative Genomic Hybridization

  • Mark R. McCormick
  • Rebecca R. Selzer
  • Todd A. Richmond
Part of the Methods in Molecular Biology™ book series (MIMB, volume 381)

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.

Key Words

Amplification breakpoint cancer CGH, comparative genomic hybridization copy number deletion DNA microarray segmentation translocation 

References

  1. 1.
    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.CrossRefGoogle Scholar
  2. 2.
    Lipshutz, R. J., Fodor, S. P., Gingeras, T. R., and Lockhart, D. J. (1999) High density synthetic oligonucleotide arrays. Nat. Genet. 21, 20–24.CrossRefGoogle Scholar
  3. 3.
    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.CrossRefGoogle Scholar
  4. 4.
    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.Google Scholar
  5. 5.
    http://www.sanger.ac.uk/Software/analysis/SSAHA/.Google Scholar
  6. 6.
    http://www.nimblegen.com/products/software/arrayscribe/.Google Scholar
  7. 7.
    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.Google Scholar
  8. 8.
    http://genomebiology.com/2002/3/9/research/0048.Google Scholar
  9. 9.
    Petri, A., Fleckner, J., and Matthiessen, M. W. (2004) Array-A-Lizer: a serial DNA microarray quality analyzer. BMC Bioinformatics 5, 12.CrossRefGoogle Scholar
  10. 10.
    http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtmL.Google Scholar
  11. 11.
    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.CrossRefGoogle Scholar
  12. 12.
    http://www.bioconductor.org.Google Scholar
  13. 13.
    http://genome.ucsc.edu/.Google Scholar
  14. 14.
    Fare, T. L., Coffey, E. M., Dai, H., et al. (2003) Effects of atmospheric ozone on microarray data quality. Anal. Chem. 75, 4672–4675.CrossRefGoogle Scholar
  15. 15.
    http://genomics.princeton.edu/dunham/ozone.html.Google Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2007

Authors and Affiliations

  • Mark R. McCormick
    • 1
  • Rebecca R. Selzer
    • 1
  • Todd A. Richmond
    • 1
  1. 1.NimbleGen Systems Inc.Madison

Personalised recommendations