CGH stands for comparative genomic hybridization, a genetic testing technique that detects missing or extra chunks of DNA across an entire genome in a single test. It works by comparing a patient’s DNA against a healthy reference sample, then flagging any regions where the patient has too much or too little genetic material. Originally developed for cancer research, CGH is now used to diagnose developmental disorders in children, screen embryos during IVF, and investigate the genetic makeup of tumors.
How CGH Works
The core idea behind CGH is a competitive binding test. Two DNA samples, one from the patient and one from a healthy reference, are each tagged with a different fluorescent color. The patient’s DNA is typically labeled green, and the reference DNA is labeled red. These two samples are mixed in equal amounts and allowed to bind to a target, which is either a set of normal chromosomes on a glass slide (in conventional CGH) or thousands of tiny DNA fragments arranged on a microarray chip (in array CGH).
Because both samples compete to attach to the same locations, the color at each spot reveals what’s happening in the patient’s genome. If a region glows more green than red, the patient has extra copies of that DNA segment, called a gain. If a region is more red than green, the patient is missing genetic material there, called a loss. A scanner reads the color ratio across the entire genome and produces a map showing exactly where these gains and losses occur.
Conventional CGH vs. Array CGH
The original form of CGH, developed in the early 1990s, used normal human chromosomes spread on a microscope slide as the target. This version could detect gains and losses of genetic material, but only if the affected region was fairly large, roughly 3 to 10 million base pairs (Mb) or more. That’s useful for spotting big chromosomal changes, but too coarse to catch many clinically important small deletions or duplications.
Array CGH (often written aCGH) replaced the chromosome slide with a microarray chip containing thousands of precisely mapped DNA fragments. Because each fragment on the chip covers a small, known region of the genome, the resolution jumps dramatically. Modern clinical arrays can detect changes as small as 100 to 400 kilobases, roughly 100 times more precise than a standard karyotype, which has a resolution of about 5 to 10 Mb. This means aCGH catches submicroscopic imbalances that would be completely invisible on a traditional chromosome analysis.
What CGH Can and Cannot Detect
CGH excels at finding copy number variations, regions where DNA has been gained or lost. This includes whole extra or missing chromosomes (like trisomy 21 in Down syndrome), large chromosomal deletions and duplications, and tiny submicroscopic imbalances linked to conditions like developmental delay, intellectual disability, or congenital anomalies.
What CGH cannot do is detect balanced rearrangements. If a chunk of chromosome has broken off and reattached to a different chromosome without any DNA being gained or lost, the green-to-red ratio stays normal, and CGH will miss it. For the same reason, CGH does not detect inversions (where a segment of a chromosome flips orientation) or point mutations (single-letter changes in the DNA code). It also struggles with low-level mosaicism, where only a small percentage of cells carry an abnormality while the rest are normal.
Uses in Cancer
CGH was originally built for cancer research, and tumor profiling remains one of its most important applications. Many cancers involve multiple gains and losses of chromosomal segments, and mapping these changes helps researchers identify the genes driving tumor growth. Because solid tumors are notoriously difficult to grow in the lab for traditional chromosome analysis, CGH’s ability to work directly on extracted DNA, without needing to culture cells, was a major advantage from the start.
In clinical oncology, array CGH helps characterize the genetic fingerprint of a tumor, which can guide treatment decisions and provide prognostic information. It has been applied across a wide range of cancers with reproducible results, and it also supports gene discovery by pinpointing regions of the genome that are consistently altered in specific cancer types.
Uses in Prenatal and Reproductive Medicine
Array CGH has become a standard tool in prenatal diagnosis. When an amniocentesis or chorionic villus sampling reveals a potential problem, or when an ultrasound flags a structural abnormality, aCGH can scan the fetal genome for submicroscopic deletions and duplications that a karyotype would miss. Most European guidelines recommend using array platforms with a minimum resolution of about 400 kilobases for prenatal testing, balancing the ability to find meaningful abnormalities against the risk of detecting variants of uncertain significance.
In IVF, CGH played a key role in the evolution of preimplantation genetic testing for aneuploidy (PGT-A). By screening embryos for extra or missing chromosomes before transfer, clinicians can select embryos with a normal chromosome count, improving the chance of a successful pregnancy. While newer methods like next-generation sequencing have largely taken over this role, aCGH was the technology that first made comprehensive, reliable embryo screening practical.
Uses in Diagnosing Developmental Disorders
For children with unexplained developmental delay, intellectual disability, or multiple birth defects, aCGH is considered a first-line diagnostic test. Traditional chromosome analysis catches only large-scale abnormalities, and many children with these conditions have a normal-looking karyotype. Array CGH closes that gap by detecting the small deletions and duplications responsible for conditions that would otherwise go undiagnosed.
CGH has been used to identify chromosomal causes of congenital anomalies, autism spectrum features, and rare genetic syndromes. In studies of children with intellectual disability and a normal karyotype, aCGH consistently identifies clinically significant copy number changes in a meaningful proportion of cases, giving families answers that older testing methods could not provide.
What Happens in the Lab
The laboratory process for array CGH follows a series of well-defined steps. First, DNA is extracted from the patient sample and from a reference sample. Each is labeled with a different fluorescent dye, typically Cyanine 3 (green) and Cyanine 5 (red), by incorporating dye-tagged building blocks into the DNA through an enzymatic reaction. After labeling, the two samples are combined, purified to remove unused dye molecules, and dissolved in a hybridization solution.
This mixture is then applied to the microarray chip and incubated at 37°C. During incubation, a large amount of repetitive “filler” DNA is added to block common repeat sequences from creating background noise. After hybridization is complete, the chip is washed to remove loosely bound DNA, then scanned. Software measures the fluorescence ratio at each spot on the array and flags regions where the ratio deviates from normal. A ratio skewed toward the patient’s dye color indicates a gain; a ratio skewed toward the reference color indicates a loss.
Clinical laboratories typically set a minimum size threshold for reporting, often around 200 kilobases, requiring at least five consecutive data points to confirm a finding. This reduces false positives and limits the detection of variants whose clinical meaning is unclear.