Comparative Genome Hybridization (CGH) with Isis

The software module for comparative genome hybridization (CGH) analysis is available as an upgrade for Isis. CGH allows to detect copy number changes (gains and losses) of a given genomic DNA. The sample DNA and normal reference DNA are labeled with different fluorochromes. Both samples are mixed (ratio 1:1) and co-hybridized onto normal metaphase chromosomes. Test and reference DNAs will compete for binding sites, with binding probabilities depending on the abundance of the respective DNA. When hybridizing the two differently labeled DNAs to a normal metaphase spread, imbalances show up as color changes of the chromosomes. The color ratio profiles along each chromosome form the basis for the quantitative analysis which yields the DNA copy number differences between sample and reference DNA. The method uses isolated DNA, so that proliferating cells are not necessary. Therefore, CGH can even be performed with paraffin-embedded material.

Isis CGH Options and Links
Isis CGH is a software module for the Isis FISH imaging system.	more...

While performing CGH analysis, the resulting ratio profiles usually exhibit deviations from the expected copy numbers (e.g. in the case of sex mismatch of test and reference DNAs). MetaSystems' unique 4-color CGH approach (patent pending) uses a second, differently labelled reference DNA with known numeric aberrations of one or several genomic loci (publication). The additional information is used for internal calibration of the intensity ratios providing automatic correction for more precise results.

Isis CGH offers many helpful tools to analyse the color profiles of a CGH preparation. The metaphases can be easily karyotyped with the help of the Isis color karyotyping module, and each karyotype can be immediately checked with control profiles. The analysis is done by averaging all chromosomes of a given class over all karyotypes of the case, or even over different cases. Limits for the profiles can be set as fixed limits, as multiples of the standard deviation or as probability limits. The simultaneous gain/loss display of different cases allows the direct comparison of patients, tissues or preparations in order to detect common gain or loss regions.

* Requires the optional color karyotyping and CGH software.