Comparative genomic hybridization
Encyclopedia
Comparative genomic hybridization (CGH) or Chromosomal Microarray Analysis (CMA) is a molecular-cytogenetic method for the analysis of copy number changes (gains/losses) in the DNA
content of a given subject's DNA and often in tumor
cells
.
CGH will detect only unbalanced chromosomal changes. Structural chromosome aberrations such as balanced reciprocal translocations
or inversions
cannot be detected, as they do not change the copy number.
During the 1990s Thomas Cremer
realized together with Peter Lichter the concept of comparative genomic hybridization to metaphase chromosomes and to a matrix with DNA spots representing specific genomic sites.
and Kpn family) to suppress repetitive DNA sequences, the mix is hybridized to normal metaphase
chromosomes or, for array- or matrix-CGH
, to a slide containing hundreds or thousands of defined DNA probes. Using epifluorescence microscopy and quantitative image analysis, regional differences in the fluorescence ratio of gains/losses vs. control DNA can be detected and used for identifying abnormal regions in the genome.
Currently, strategically placed Oligos
offer a resolution typically of 20–80 base pairs, as compared to the older BAC
arrays offering resolution of 100kb.
(FITC)) and normal DNA (frequently rhodamine
or Texas Red
) to normal human metaphase preparations.
Preimplantation genetic diagnosis
by CGH may improve the efficiency of IVF in vitro fertilization by increasing embryo implantation rate and reducing multiple pregnancies and spontaneous miscarriages.
The use of array CGH
overcomes many of these limitations, with improvement in resolution and dynamic range, in addition to direct mapping of aberrations to the genome sequence and improved throughput.
Due to the normalization to the most frequent ratio level as "normal", both CGH and array CGH do not provide information as to the ploidy. Since having a balanced DNA content, a tetraploid clone without further rearrangements would appear normal in CGH.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
content of a given subject's DNA and often in tumor
Tumor
A tumor or tumour is commonly used as a synonym for a neoplasm that appears enlarged in size. Tumor is not synonymous with cancer...
cells
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
.
CGH will detect only unbalanced chromosomal changes. Structural chromosome aberrations such as balanced reciprocal translocations
Chromosomal translocation
In genetics, a chromosome translocation is a chromosome abnormality caused by rearrangement of parts between nonhomologous chromosomes. A gene fusion may be created when the translocation joins two otherwise separated genes, the occurrence of which is common in cancer. It is detected on...
or inversions
Chromosomal inversion
An inversion is a chromosome rearrangement in which a segment of a chromosome is reversed end to end. An inversion occurs when a single chromosome undergoes breakage and rearrangement within itself. Inversions are of two types: paracentric and pericentric.Paracentric inversions do not include the...
cannot be detected, as they do not change the copy number.
During the 1990s Thomas Cremer
Thomas Cremer
Thomas Cremer , is a German professor of human genetics and anthropology with a main research focus on molecular cytogenetics and 3D/4D analyses of nuclear structure studied by confocal microscopy and live cell imaging...
realized together with Peter Lichter the concept of comparative genomic hybridization to metaphase chromosomes and to a matrix with DNA spots representing specific genomic sites.
Method
DNA from subject tissue and from normal control tissue (reference) are each labeled with different tags for later analysis by fluorescence. After mixing subject and reference DNA along with unlabeled human cot-1 DNA (placental DNA that is enriched for repetitive DNA sequences such as the AluAlu sequence
An Alu element is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant mobile elements in the human genome. They are derived from the...
and Kpn family) to suppress repetitive DNA sequences, the mix is hybridized to normal metaphase
Metaphase
Metaphase, from the ancient Greek μετά and φάσις , is a stage of mitosis in the eukaryotic cell cycle in which condensed & highly coiled chromosomes, carrying genetic information, align in the middle of the cell before being separated into each of the two daughter cells...
chromosomes or, for array- or matrix-CGH
Array comparative genomic hybridization
Array-comparative genomic hybridization is a technique to detect genomic copy number variations at a higher resolution level than chromosome-based comparative genomic hybridization .-Process:DNA from...
, to a slide containing hundreds or thousands of defined DNA probes. Using epifluorescence microscopy and quantitative image analysis, regional differences in the fluorescence ratio of gains/losses vs. control DNA can be detected and used for identifying abnormal regions in the genome.
Currently, strategically placed Oligos
Oligonucleotide
An oligonucleotide is a short nucleic acid polymer, typically with fifty or fewer bases. Although they can be formed by bond cleavage of longer segments, they are now more commonly synthesized, in a sequence-specific manner, from individual nucleoside phosphoramidites...
offer a resolution typically of 20–80 base pairs, as compared to the older BAC
Bacterial artificial chromosome
A bacterial artificial chromosome is a DNA construct, based on a functional fertility plasmid , used for transforming and cloning in bacteria, usually E. coli. F-plasmids play a crucial role because they contain partition genes that promote the even distribution of plasmids after bacterial cell...
arrays offering resolution of 100kb.
Cancer
The method is based on the hybridization of fluorescently labeled tumor DNA (frequently fluoresceinFluorescein
Fluorescein is a synthetic organic compound available as a dark orange/red powder soluble in water and alcohol. It is widely used as a fluorescent tracer for many applications....
(FITC)) and normal DNA (frequently rhodamine
Rhodamine
Rhodamine is a family of related chemical compounds, fluorone dyes. Examples are Rhodamine 6G and Rhodamine B. They are used as a dye and as a dye laser gain medium. They are often used as a tracer dye within water to determine the rate and direction of flow and transport...
or Texas Red
Texas Red
Texas Red or sulforhodamine 101 acid chloride is a red fluorescent dye, used in histology for staining cell specimens, for sorting cells with fluorescent-activated cell sorting machines, in fluorescence microscopy applications, and in immunohistochemistry.Texas Red fluoresces at about 615 nm,...
) to normal human metaphase preparations.
Other
Aside from analyzing cancer cells, the test is valuable at looking for previously unknown mutations that can lead to children with dysmorphic features, developmental delays, mental retardation, and autism.Preimplantation genetic diagnosis
Preimplantation genetic diagnosis
In medicine and genetics pre-implantation genetic diagnosis refers to procedures that are performed on embryos prior to implantation, sometimes even on oocytes prior to fertilization. PGD is considered another way to prenatal diagnosis...
by CGH may improve the efficiency of IVF in vitro fertilization by increasing embryo implantation rate and reducing multiple pregnancies and spontaneous miscarriages.
Limitations
Chromosomal CGH is capable of detecting loss, gain and amplification of the copy number at the levels of chromosomes. However, it is considered that to detect a single copy loss the region must be at least 5–10 Mb in length. Detection of amplifications (e.g. tens or hundreds of copies of one or few neighboring genes) is known to be sensitive down to less than 1 Mb. Therefore, one must take into consideration that while CGH is sensitive to specific types of copy number gains, the resolution of regional deletions is more limited.The use of array CGH
Array comparative genomic hybridization
Array-comparative genomic hybridization is a technique to detect genomic copy number variations at a higher resolution level than chromosome-based comparative genomic hybridization .-Process:DNA from...
overcomes many of these limitations, with improvement in resolution and dynamic range, in addition to direct mapping of aberrations to the genome sequence and improved throughput.
Due to the normalization to the most frequent ratio level as "normal", both CGH and array CGH do not provide information as to the ploidy. Since having a balanced DNA content, a tetraploid clone without further rearrangements would appear normal in CGH.
See also
- Array based Comparative Genomic HybridizationArray comparative genomic hybridizationArray-comparative genomic hybridization is a technique to detect genomic copy number variations at a higher resolution level than chromosome-based comparative genomic hybridization .-Process:DNA from...
- OncogeneOncogeneAn oncogene is a gene that has the potential to cause cancer. In tumor cells, they are often mutated or expressed at high levels.An oncogene is a gene found in the chromosomes of tumor cells whose activation is associated with the initial and continuing conversion of normal cells into cancer...
- Tumor suppressor geneTumor suppressor geneA tumor suppressor gene, or anti-oncogene, is a gene that protects a cell from one step on the path to cancer. When this gene is mutated to cause a loss or reduction in its function, the cell can progress to cancer, usually in combination with other genetic changes.-Two-hit hypothesis:Unlike...
- CarcinomaCarcinomaCarcinoma is the medical term for the most common type of cancer occurring in humans. Put simply, a carcinoma is a cancer that begins in a tissue that lines the inner or outer surfaces of the body, and that generally arises from cells originating in the endodermal or ectodermal germ layer during...
- SarcomaSarcomaA sarcoma is a cancer that arises from transformed cells in one of a number of tissues that develop from embryonic mesoderm. Thus, sarcomas include tumors of bone, cartilage, fat, muscle, vascular, and hematopoietic tissues...
- LymphomaLymphomaLymphoma is a cancer in the lymphatic cells of the immune system. Typically, lymphomas present as a solid tumor of lymphoid cells. Treatment might involve chemotherapy and in some cases radiotherapy and/or bone marrow transplantation, and can be curable depending on the histology, type, and stage...
- LeukemiaLeukemiaLeukemia or leukaemia is a type of cancer of the blood or bone marrow characterized by an abnormal increase of immature white blood cells called "blasts". Leukemia is a broad term covering a spectrum of diseases...
- Virtual KaryotypeVirtual KaryotypeVirtual karyotype detects genomic copy number variations at a higher resolution level than conventional karyotyping or chromosome-based comparative genomic hybridization .-Background:...
External links
- Virtual Grand Rounds: "Differentiating Microarray Technologies and Related Clinical Implications" by Arthur Beaudet, MD
- Progenetix database: A large collection of CGH and aCGH data from publications (ca. 20000 cases, November 2008).
- CGH article tracker: An attempt to list all (a)CGH publications containing original case data. This is part of the Progenetix project.
- NCBI's Cancer Chromosomes: Cancer Chromosome is an integral part of NCBI's Entrez system, which combines several databases with (molecular-) cytogenetic data.
- A bibliography on copy number variation