Tumor cytogenetics revisited: comparative genomic hybridization and spectral karyotyping

Abstract

Fluorescence in situ hybridization techniques allow the visualization and localization of DNA target sequences on the chromosomal and cellular level and have evolved as exceedingly valuable tools in basic chromosome research and cytogenetic diagnostics. Recent advances in molecular cytogenetic approaches, namely comparative genomic hybridization and spectral karyotyping, now allow tumor genomes to be surveyed for chromosomal aberrations in a single experiment and permit identification of tumor-specific chromosomal aberrations with unprecedented accuracy. Comparative genomic hybridization utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes. Comparative genomic hybridization is an ideal tool for analyzing chromosomal imbalances in archived tumor material and for examining possible correlations between these findings and tumor phenotypes. Spectral karyotyping is based on the simultaneous hybridization of differentially labeled chromosome painting probes (24 in human), followed by spectral imaging that allows the unique display of all human (and other species) chromosomes in different colors. Spectral karyotyping greatly facilitates the characterization of numerical and structural chromosomal aberrations, therefore improving karyotype analysis considerably. We review these new molecular cytogenetic concepts, describe applications of comparative genomic hybridization and spectral karyotyping for the visualization of chromosomal aberrations as they relate to human malignancies and animal models thereof, and provide evidence that fluorescence in situ hybridization has developed as a robust and reliable technique which justifies its translation to cytogenetic diagnostics.

High-Resolution ROMA CGH and FISH Analysis of Aneuploid and Diploid Breast Tumors

“…It is clear from the profile of WZ1 in Figure 1 that there are at least two major classes of events: large segmental deletions and duplications of one or two copies of chromosome arms and narrow, high-copy-number amplifications, both of which have been observed previously by other CGH microarray methods (Ried et al 1997;Pollack et al 2002;Albertson 2003;Lage et al 2003). The values predicted by ROMA and the observed values measured by FISH are shown above representative loci.…”

“…Kallioniemi et al 1992a,b; O.P. Kallioniemi et al 1992), and this approach has been applied to breast tumors (Kallioniemi et al 1994;Ried et al 1997;Tirkkonen et al 1998). Subsequently, microarray methods employing CGH have increased resolution and reproducibility, and have improved throughput (Ried et al 1995;Pollack et al 2002;Albertson 2003;Lage et al 2003).…”

Clonal chromosomal aberrations in simian virus 40‐transfected human thyroid cells and in derived tumors developed after in vitro irradiation

“…G-banding analysis is not sufficient to resolve complex changes and also to detect hidden abnormalities so, therefore, molecular cytogenetic techniques such as spectral karyotyping (SKY) and comparative genomic hybridization (CGH) must be additionally applied. SKY has been developed to characterize human metaphase spreads after simultaneously hybridizing the chromosomes with 24 chromosome-specific whole chromosome painting probes [8]. This combination of spectroscopic detection methods and in situ hybridization assays using fluorescently tagged probes allows a simultaneous depiction and analysis of the whole human chromosome complement.…”

“…This combination of spectroscopic detection methods and in situ hybridization assays using fluorescently tagged probes allows a simultaneous depiction and analysis of the whole human chromosome complement. Interchromosomal rearrangements can be recognized as differentially stained chromosome segments, thus greatly facilitating the characterization of structural aberrations, especially those with complex patterns [8][9][10] and of hidden chromosome abnormalities [11,12]. If this technique is used in addition to comparative genomic hybridization [13], which depicts copy number changes with high accuracy, a comprehensive picture of chromosomal abnormalities developed during the neoplastic cell transformation can be obtained.…”

Comparative genomic hybridization and chromosomal instability in solid tumours

“…However, the use of metaphase cytogenetic analysis has been limited in solid tumours, mainly due to the difficulties in growing primary cultures in which to generate tumour metaphase chromosomes. However, this changed with the development of comparative genomic hybridization (CGH) and its ability to globally assess the genome of solid tumours for areas of loss and/or gain without the need for tissue culture (Kallioniemi et al, 1992;Forozan et al, 1997;Ried et al, 1997). CGH involves a competitive in situ hybridization of fluorescently labelled tumour DNA and healthy control DNA to normal metaphase chromosomes (Figure 1).…”