Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors

O. P. Kallioniemi, A. Kallioniemi, J. Piper, J. Isola, F. M. Waldman, Joe Gray, D. Pinkel

Research output: Contribution to journalArticle

931 Citations (Scopus)

Abstract

Comparative genomic hybridization (CGH) is a powerful new method for molecular cytogenetic analysis of cancer. In a single hybridization, CGH provides an overview of DNA sequence copy number changes (losses, deletions, gains, amplifications) in a tumor specimen and maps these changes on normal chromosomes. CGH is based on the in situ hybridization of differentially labeled total genomic tumor DNA and normal reference DNA to normal human metaphase chromosomes. After hybridization and fluorescent staining of the bound DNAs, copy number variations among the different sequences in the tumor DNA are detected by measuring the tumor/normal fluorescence intensity ratio for each locus in the target metaphase chromosomes. CGH is in particular useful for analysis of DNA sequence copy number changes in common solid tumors where high-quality metaphase preparations are often difficult to make, and where complex karyotypes with numerous markers, double minutes, and homogeneously stained chromosomal regions are common. CGH only detects changes that are present in a substantial proportion of tumor cells (i.e., clonal aberrations). It does not reveal translocations, inversions, and other aberrations that do not change copy number. At present, CGH is a research tool that complements previous methods for genetic analysis. CGH will advance our understanding of the genetic progression of cancer and highlight important genomic regions for further study. Direct clinical applications of CGH are possible, but will require further development and validation of the technique. We describe here our recent optimized procedures for CGH, including DNA labeling, hybridization, fluorescence microscopy, digital image analysis, data interpretation, and quality control, emphasizing those steps that are most critical. We will also assess sensitivity and resolution limits of CGH as well as discuss possible future technical improvements.

Original languageEnglish (US)
Pages (from-to)231-243
Number of pages13
JournalGenes Chromosomes and Cancer
Volume10
Issue number4
DOIs
StatePublished - 1994
Externally publishedYes

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DNA Copy Number Variations
Comparative Genomic Hybridization
Neoplasms
Metaphase
DNA
Chromosomes
Cytogenetic Analysis
Human Chromosomes
Karyotype
Fluorescence Microscopy
Quality Control
In Situ Hybridization
Fluorescence

ASJC Scopus subject areas

  • Cancer Research
  • Genetics

Cite this

Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. / Kallioniemi, O. P.; Kallioniemi, A.; Piper, J.; Isola, J.; Waldman, F. M.; Gray, Joe; Pinkel, D.

In: Genes Chromosomes and Cancer, Vol. 10, No. 4, 1994, p. 231-243.

Research output: Contribution to journalArticle

Kallioniemi, O. P. ; Kallioniemi, A. ; Piper, J. ; Isola, J. ; Waldman, F. M. ; Gray, Joe ; Pinkel, D. / Optimizing comparative genomic hybridization for analysis of DNA sequence copy number changes in solid tumors. In: Genes Chromosomes and Cancer. 1994 ; Vol. 10, No. 4. pp. 231-243.
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