Currently, structural chromosomal aberrations such as exchanges, deletions, and insertions are routinely assayed by G-band analysis because this technique remains the most efficient and cost-effective method for cytogenetic diagnostic purposes. There is a disparity, however, in how informative this type of analysis is according to the tissue of origin of the metaphase cells being studied. In particular, the complexity of structural aberrations in tumor cells coupled with poor quality in terms of chromosome length, morphology, and mitotic index has contributed to the fact that many recurrent and on-going cytogenetic rearrangements in tumor cells remain poorly defined. One approach taken to improve this is the painting of individual chromosomes using FISH-based methodologies, where the chromosomes selected for ''painting'' are determined based on the initial banding assessment. This strategy is practical and affordable for many cytogenetic services, but has the major disadvantage of only being informative for those chromosomes in the rearrangement that were selected for painting.
Major developments over recent years have changed this. In particular, advances in strategies for combinatorial fluorescent probe labeling and technology for the detection of multiple fluorescent dyes in single experiments have made the high-resolution genome-wide analysis of structural aberrations possible. Below, two hybridization techniques are described which ''paint'' all 22 human autosomes and 2 sex chromosomes as unique identifiable colors: multiplex FISH (m-FISH) and spectral karyotyping (SKY). Both techniques are capable of resolving previously unidentified ''marker'' chromosomes (>10 Mb in size) and also subtle cryptic rearrangements. Importantly, compared with PCR and multiple-color FISH, m-FISH and SKY can be used to screen genome wide and do not require prior knowledge of chromosomal breakpoints.
The detailed analysis of structural chromosomal aberrations is therefore no longer restricted to constitutional anomalies, hematological malignancies, and soft tissue tumors, but is now also feasible for the much larger group of epithelial tumors. Preliminary experiments have revealed a high number of structural chromosomal aberrations in different types of solid tumors, indicating that such changes could play a much more important role in solid tumor carcinogenesis than thus far assumed.
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