Editing Comparative genomic hybridization (section)

{{Short description|Method to evaluate biological samples}}
'''Comparative genomic hybridization''' ('''CGH''') is a molecular [[cytogenetic]] method for analysing [[copy number variations]] (CNVs) relative to [[ploidy]] level in the [[DNA]] of a test sample compared to a reference sample, without the need for culturing cells.  The aim of this technique is to quickly and efficiently compare two genomic DNA samples arising from two sources, which are most often closely related, because it is suspected that they contain differences in terms of either gains or losses of either whole [[chromosomes]] or [[Chromosome regions|subchromosomal regions]] (a portion of a whole chromosome).  This technique was originally developed for the evaluation of the differences between the chromosomal complements of solid tumor and normal tissue,<ref name="Kallioniemi,Kallioniemi,Sudar,Rutovitz,Gray,Waldman,Pinkel">{{cite journal | vauthors = Kallioniemi A, Kallioniemi OP, Sudar DA, Rutovitz D, Gray JW, Waldman F, Pinkel D | year = 1992 | title = Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors | journal = Science | volume = 258 | issue = 5083| pages = 818–821 | doi=10.1126/science.1359641| pmid = 1359641 | bibcode = 1992Sci...258..818K }}</ref> and has an improved resolution of 5–10 [[megabases]] compared to the more traditional cytogenetic analysis techniques of [[giemsa banding]] and [[fluorescence in situ hybridization]] (FISH) which are limited by the resolution of the microscope utilized.<ref name="Strachan">Strachan T, Read AP (2010) Human Molecular Genetics: Garland Science.</ref><ref name="Weiss,Hermsen,Meijer,VanGrieken,Baak,Kuipers,VanDiest">Weiss M, Hermsen M, Meijer G, Van Grieken N, Baak J, Kuipers E, Van Diest P (1999) Comparative genomic hybridization. Molecular Pathology 52:243–251.</ref>

This is achieved through the use of competitive fluorescence in situ hybridization. In short, this involves the isolation of DNA from the two sources to be compared, most commonly a test and reference source, independent labelling of each [[DNA]] sample with [[fluorophores]] (fluorescent molecules) of different colours (usually red and green), [[Denaturation (biochemistry)|denaturation]] of the DNA so that it is single stranded, and the [[Nucleic acid hybridization|hybridization]] of the two resultant samples in a 1:1 ratio to a normal [[metaphase]] spread of chromosomes, to which the labelled DNA samples will bind at their [[locus (genetics)|locus]] of origin.  Using a fluorescence microscope and computer software, the differentially coloured fluorescent signals are then compared along the length of each chromosome for identification of chromosomal differences between the two sources. A higher intensity of the test sample colour in a specific region of a chromosome indicates the gain of material of that region in the corresponding source sample, while a higher intensity of the reference sample colour indicates the loss of material in the test sample in that specific region. A neutral colour (yellow when the fluorophore labels are red and green) indicates no difference between the two samples in that location.<ref name="Strachan" /><ref name="Weiss,Hermsen,Meijer,VanGrieken,Baak,Kuipers,VanDiest" />

CGH is only able to detect unbalanced [[chromosomal abnormality|chromosomal abnormalities]].  This is because balanced chromosomal abnormalities such as [[chromosomal translocation|reciprocal translocations]], [[chromosomal inversion|inversions]] or [[ring chromosomes]] do not affect copy number, which is what is detected by CGH technologies. CGH does, however, allow for the exploration of all 46 human chromosomes in single test and the discovery of deletions and duplications, even on the microscopic scale which may lead to the identification of [[candidate gene]]s to be further explored by other cytological techniques.<ref name="Strachan" />

Through the use of [[DNA microarrays]] in conjunction with CGH techniques, the more specific form of array CGH (aCGH) has been developed, allowing for a locus-by-locus measure of CNV with increased resolution as low as 100 [[kilobase]]s.<ref name="Pinkel,Albertson">Pinkel D, Albertson DG (2005) Comparative genomic hybridization. Annu Rev Genom Hum Genet 6:331–354.</ref><ref name="deRavel,Devriendt,Fryns,Vermeesch">de Ravel TJ, Devriendt K, Fryns J-P, Vermeesch JR (2007) What's new in karyotyping? The move towards array comparative genomic hybridization (CGH). European Journal of Pediatrics 166:637–643.</ref> This improved technique allows for the aetiology of known and unknown conditions to be discovered.