Molecular cytogenetics

detection of target DNA sequences directly on chromosome preparation (in situ) using specific fluorescently labeled DNA probe, the probe is hybridized with complementary segments of the chromosomal DNA
different modifications according sequences of interest:
- centromeric probes – rapid counting of particular chromosome number (e.g. sex chromosomes, anuploidies)
- locus-specific probes – microdeletion syndromes, subtelomeric regions...
- whole-chromosome (painting) probes – translocations, insertions...
- M- FISH (multicolor) - all chromosomes labeled by different combination of five fluorochromes to differ each other, detection of complex rearrangement (e.g. in leukemia cells)
- M-banding – multicolor combinations of fluorochromes along the chromosome enable to detect breakpoints in specific chromosome rearrangements; method is used especially in haematooncologic patients to help with assessment of prognosis and individual therapy indication according to their tumor subtype

detection of quantitative - unbalanced genomic changes (gain or loss), not able to detect balanced rearrangements
comparison of testing and control DNA (labeled with different fluorochromes, used as probes on normal chromosomal preparation) used in ratio 1:1
primarily developed for analysis of solid tumors

molecular cytogenetic method with much more higher resolution level (10-100 kb) then routine cytogenetics (karyotyping, 5-10 Mb)
whole-genome analysis
main disadvantage – method is targeted only on unbalanced changes, not able to detect balanced rearrangements
great for detection of submicroscopic microdeletions or microduplications in patients with unexplained mental retardation and/or developmental delay
reaction is performed on special slides („chips“) with small target region of thousands pits with short specific chromosomal fragment in each; after reaction the slide is scanned and result from every pit is demonstrated on the chromosome map with the precise location
data are compared with international databases and genotype-phenotype correlation with prognosis assessment should be commented in clinical report
two basic modifications: array-CGH x SNP-array
- Array-CGH: based on CGH method (above) but with higher resolution
- SNP-array: based on detection of single nucleotide polymorphisms (SNPs) in the genome