Array CGH genome-wide search for loss and gain in genetic material

Molecular karyotyping for the detection of chromosomal imbalances

Array CGH analysis compares the entire genome of a patient with that of clinically inconspicuous individuals for losses and gains in genetic material. Identical DNA quantities of the test person and the reference DNA are labelled with different fluorescent dyes and then co-hybridised on the array. The microarray itself is a glass slide containing immobilized genomic DNA fragments (so-called oligonucleotides) in a raster pattern. If there is a genomic loss or gain in the patient sample compared to the reference DNA, there is a shift in the hybridization ratio. This manifests itself in a color change of the fluorescence signal, which is detected by a laser scanner. The data is then extracted and evaluated with special software.

Array CGH analysis is a high-resolution diagnostic examination and is indicated for patients with the following criteria:
 

• Developmental delay and mental retardation
• Dysmorphic features
• Congenital anomalies (e.g. heart defects, hand abnormalities)
• Malformations and dysfunctions of the brain
• Pre- and postnatal growth retardation
• Certain growth abnormalities (e.g. microcephaly)
• Behavioral problems (e.g. autism spectrum disorders)
• Combined occurrence of the aforementioned anomalies
•  Precision of chromosome analysis:  Detailed breakpoint definition, characterization of the material in cytogenetically recognizable gains and losses

• Clarification of apparently balanced chromosomal structural changes with unspecific dysmorphic features

• Clarification of genomic rearrangements (e.g. marker chromosomes).

Clinical benefit

Array CGH analysis can detect much smaller deviations (microdeletions and duplications) in the patient's genome than conventional chromosome analysis. Using conventional chromosome analysis, structural genomic changes can be detected in only 3 to 4 percent of patients with developmental delays. Molecular cytogenetic techniques such as subtelomer FISH (fluorescence in situ hybridization) showed a further slight improvement in the detection rate. While FISH diagnostics is used to analyse specific regions for microdeletion/ duplication syndromes, array CGH can be used to detect changes at (almost) any location in the genome. In up to 20% of patients, array CGH analysis can be used to detect causal changes.

In addition to the resolution of unclear cases of mental retardation and rare syndromic disease patterns, array CGH can also be used to specify the gains and losses already detected by chromosome analysis by exact breakpoint determination, thus enabling a more precise genotype-phenotype correlation.

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