Array CGH (microarray-based comparative genomic hybridization) is a molecular-cytogenetic examination that analyses copy number variations (CNV) of the entire genome. It allows detection of unbalanced aberrations (sequence losses and gains), whose genomic locations are previously unknown.

The principle of array CGH is a competition of reference and patient DNA, both fluorescently labeled, for binding to complementary sequences present on a microarray chip. The chip is a glass slide coated with oligonucleotides, BAC or SNP sequences that represent an entire human genome. Typically, 24-hour hybridization is followed by washing off unbound DNA. Subsequently, fluorescent signals of both the reference and the patient DNA are detected by a special scanner that can distinguish them. Dedicated software compares fluorochrome intensities and determines their ratio of each spot on the chip, thus analysing copy number of all sequences of the genome. Detected unbalanced aberrations are thus assessed on the gain-loss basis with a precise position in the genome. During data interpretation, the results are compared with gene databases available on the Internet.

Method limitations: point mutations, balanced chromosomal aberrations, low-level mosaics, uniparental disomy, and triploidy/polyploidy cannot be detected by array CGH.

The method is used in postnatal, prenatal, and preimplantation diagnostics.

The array CGH examination is indicated in patients with a suspected congenital developmental defect associated with a genetic aberration that has been undetected using conventional cytogenetic and molecular-genetic methods.

In prenatal cytogenetics, array CGH is the method of first choice, following a normal result of QF PCR. Medical Genetics - genetic examination