Editing Comparative genomic hybridization (section)

===Technological approaches to array CGH===

[[File:ACGH profile of the IMR32 neuroblastoma cell line.svg|right|thumb|ACGH profile of the IMR32 neuroblastoma cell line]]
Array CGH has been implemented using a wide variety of techniques. Therefore, some of the advantages and limitations of array CGH are dependent on the technique chosen.
The initial approaches used arrays produced from large insert genomic DNA clones, such as [[bacterial artificial chromosome|BACs]]. The use of BACs provides sufficient intense signals to detect single-copy changes and to locate aberration boundaries accurately. However, initial DNA yields of isolated BAC clones are low and DNA amplification techniques are necessary. These techniques include [[Covalent bond|ligation]]-mediated polymerase chain reaction (PCR), degenerate primer PCR using one or several sets of primers, and [[rolling circle amplification]].<ref>{{cite journal | vauthors = Fiegler H, Carr P, Douglas EJ, Burford DC, Hunt S, Scott CE, Smith J, Vetrie D, Gorman P, Tomlinson IP, Carter NP | year = 2003 | title = DNA microarrays for comparative genomic hybridization based on DOP-PCR amplification of BAC and PAC clones | journal = Genes Chromosomes Cancer | volume = 36 | issue = 4| pages = 361–374 | doi=10.1002/gcc.10155| pmid = 12619160 | s2cid = 6929961 }}</ref> Arrays can also be constructed using cDNA. These arrays currently yield a high spatial resolution, but the number of cDNAs is limited by the genes that are encoded on the chromosomes, and their sensitivity is low due to cross-hybridization.<ref name="Oostlander,Meijer,Ylstra" /> This results in the inability to detect single copy changes on a genome wide scale.<ref>{{cite journal | vauthors = Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO | year = 1999 | title = Genome-wide analysis of DNA copy number changes using cDNA microarrays | doi = 10.1038/12640 | pmid = 10471496 | journal = Nat Genet | volume = 23 | issue = 1| pages = 41–46 | s2cid = 997032 }}</ref> The latest approach is spotting the arrays with short oligonucleotides. The amount of oligos is almost infinite, and the processing is rapid, cost-effective, and easy. Although oligonucleotides do not have the sensitivity to detect single copy changes, averaging of ratios from oligos that map next to each other on the chromosome can compensate for the reduced sensitivity.<ref>{{cite journal | vauthors = Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B | year = 2004 | title = High resolution microarray comparative genomic hybridization analysis using spotted oligonucleotides | journal = J Clin Pathol | volume = 57 | issue = 6| pages = 644–646 | doi=10.1136/jcp.2003.013029| pmid = 15166273 | pmc = 1770328 }}</ref> It is also possible to use arrays which have overlapping probes so that specific breakpoints may be uncovered.