The key difference between FISH and CGH is that FISH is a molecular technique that detects specific DNA sequence on a chromosome using fluorescently labeled probes, while CGH is another molecular cytogenetic technique that detects alterations in the genomic DNA.
Cytogenetic analysis plays an important role in medicine when detecting chromosomal abnormalities such as aneuploidies, deletions, duplications, and rearrangements, etc. Chromosomal abnormalities eventually lead to genetic diseases such as cancer, infertility, Down syndrome, Klinefelter syndrome, Turner syndrome, leukemia, etc. There are various molecular cytogenetic methods to detect above-mentioned defects and diseases. Among them, FISH (fluorescent in situ hybridization) and CGH (comparative genomic hybridization) are two powerful hybridization techniques. However, both methods have pros and cons.
What is FISH?
FISH is a nucleic acid hybridization technique performed on a portion or section of tissue, in the entire tissue or cells. It is a probe-based method. The technique depends on the theory of Watson Crick complementary base pairing, resulting in either DNA – DNA hybrids or DNA – RNA hybrids, which can thus detect mutated genes or can identify the gene of interest. Further, this technique uses single-stranded DNA sequences, double-stranded DNA sequences, single-stranded RNA sequences or synthetic oligonucleotide prepared using nick translation as probes that are complementary to gene sequences of interest. Besides, the most important feature of this technique is the labeling of probes with fluorescence dyes. Thus, the probes bind with the complementary parts of the chromosome and make it easy for detection.
Moreover, FISH is a highly sensitive and specific method. Hence, it is a common technique in both research and diagnosis of hematological malignancies and solid tumors. But, FISH shows low resolution. It also requires prior knowledge of the target abnormality to design probe sequences.
There are many applications of FISH, mainly in the molecular diagnostics of infectious diseases to identify the presence of pathogens and to confirm the pathogen via molecular diagnostics. Moreover, FISH is a commonly used technique in the fields of developmental biology, karyotyping and phylogenetic analysis and physical mapping of chromosomes.
What is CGH?
Comparative genomic hybridization (CGH) is another DNA based molecular cytogenetic technique that can detect the alterations of genomic DNA sequences. The method is an advanced method which can analyze chromosome and gene modifications to detect the changes or alterations in the genomic DNA sequences. Further, CGH requires the isolation and fragmentation of DNA from the experimental sample and reference sample. Then, the samples should be labeled using two different fluorescent dyes (usually red and green). Later, both samples are mixed and allowed for competitive hybridization. The final step is the analysis of the samples for alterations in DNA such as gene duplication, gene loss, etc. Especially, it measures the DNA copy number differences between the test sample and the control sample.
Another version of CGH is available now; it is a more advanced method than the normal CGH. It is a technique called array-based CGH or aCGH. aCGH allows the precise identification of gene or sequence deletions in many thousand sequences in one single experiment.
What are the Similarities Between FISH and CGH?
- FISH and CGH are two molecular techniques.
- Both FISH and CGH rely upon nucleic acid hybridization.
- Also, both techniques need designed probes to detect specific DNA targets.
- We use them for pre‐natal and post‐natal diagnosis of genetic diseases.
- Furthermore, both FISH and CGH are very powerful tools to study genomic alterations.
- They use fluorescent dyes to label probes.
What is the Difference Between FISH and CGH?
FISH is an in situ hybridization procedure that uses fluorescent probes to detect specific DNA sequences, while CGH is a molecular hybridization technique that detects the alterations of genomic DNA sequences. So, this is the key difference between FISH and CGH.
Moreover, FISH requires prior knowledge of the target abnormality to design probe sequences, while CGH does not require prior knowledge. Also, a further difference between FISH and CGH is that FISH shows limited resolution while aCGH shows high resolution.
The below infographic summarizes the difference between FISH and CGH.
Summary – FISH vs CGH
FISH and CGH are two molecular cytogenetic techniques that facilitate the detection of gene sequences of interest. FISH facilitates the detection of specific DNA sequence on a chromosome using fluorescently labeled probes while CGH facilitates the detection of alterations in the genomic DNA. So, this is the key difference between FISH and CGH.
1. “Fluorescence In Situ Hybridization (FISH)” Nature News, Nature Publishing Group, Available here.
2. Hester, Susan D, et al. “Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms.” Journal of Biomolecular Techniques: JBT, The Association of Biomolecular Resource Facilities, Apr. 2009, Available here.
1. “Multiplex ViewRNA FISH Assay in Jurkat and HeLa cells” By Ryan Jeffs – Own work (CC BY-SA 3.0) via Commons Wikimedia
2. “CGH schema” By Mbaudis (talk) (Uploads) – Own work (CC BY 2.5) via Commons Wikimedia