Computer image analysis of comparative genomic hybridization

Jim Piper, Denis Rutovitz, Damir Sudar, Anne Kallioniemi, Olli‐P ‐P Kallioniemi, Frederic M. Waldman, Joe W. Gray, Dan Pinkel

Research output: Contribution to journalArticlepeer-review

240 Scopus citations


We describe and evaluate the image‐processing and analysis techniques we have developed for the quantitative analysis of comparative genomic hybridization (CGH; Science 258:818, 1992). In a typical CGH application, two genomic DNA samples are simultaneously hybridized to metaphase chromosomes and detected with different fluorochromes. The primary data in CGH are contained in the intensity ratios of the fluorochromes as a function of position on the chromosomes, which reflect variation in DNA copy number ratio between the two DNA samples. Analysis involves chromosome segmentation, intensity normalization, background corrections, and calculation of the fluorescence intensity profiles and the ratio profile along the chromosome's length. Profiles from several copies of the same chromosome in different metaphases are averaged to reduce the noise. Confidence intervals are calculated and displayed for the mean profiles. The techniques were evaluated by examining the variability found in comparisons of two normal genomic DNAs, where the ratio was expected to be constant, and by measuring the ratios obtained for cell lines with cytogenetically documented copy number changes involving several chromosomal segments. The limits of sensitivity of CGH analysis were investigated by simulation. Guidelines for the interpretation of CGH data and indications of areas for future development of the analytical techniques are also presented. © 1995 Wiley‐Liss, Inc.

Original languageEnglish (US)
Pages (from-to)10-26
Number of pages17
Issue number1
StatePublished - Jan 1 1995
Externally publishedYes


  • Amplification
  • background correction
  • deletion
  • fluorescence in situ hybridization
  • genomic DNA
  • image analysis
  • intensity profile
  • molecular cytogenetics
  • ratio profile
  • simulation
  • tumor cytogenetics

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Biophysics
  • Hematology
  • Endocrinology
  • Cell Biology


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