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array comparative genomic hybridisation (aCGH)
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Array comparative genomic hybridisation (aCGH) is a microarray-based technique used to identify chromosomal copy number changes (deletions, amplifications, and micro-amplifications) genome-wide. aCGH can also be used to characterise various carcinomas and to identify and map disease genes involved with schizophrenia, depression, autism, and mental retardation. Another term for array CGH is matrix CGH. aCGH has been used successfully for analysis of tumour samples and cell lines and for analysis of single copy gains and losses in specific chromosomal regions, telomeres, and entire chromosomes.

aCGH services are available using the Agilent platform. Agilent has CGH arrays for a number of species, including human, mouse, rat, and chicken, and custom CGH arrays for other species are also available.

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How much sample is required for hybridisation to CGH arrays?

The amount of sample required for hybridisation depends on the platform. For example, most oligonucleotide arrays require at least 100 ng of DNA and some have developed a PCR amplification procedure that allows as a little as 10 ng of input genomic DNA. Most labelling protocols for cDNA and BAC arrays require 1-3 μg of genomic DNA for hybridisation, which may limit the use of these arrays to large tumours and cell lines.

What is the difference between disease-specific, chromosome-specific and genome-wide CGH arrays?

As the names suggest, disease-specific arrays survey regions of the genome that are often altered in certain disease states and chromosome-specific arrays contain elements specific to a particular chromosome. The disadvantage of these arrays is that they require a priori knowledge of the regions of interest. Genome-wide arrays cover the entire genome allowing for identification of chromosomal changes in suspected and novel regions.

What are the advantages of aCGH over traditional methods?

aCGH provides rapid genome-wide analysis at high resolution and the information provided by aCGH experiments can be directly linked to physical and genetic maps of the human genome. Traditional CGH has limited resolution and data analysis requires expertise in cytogenetics.

What are SeGAs?

SeGA stands for Segmental Genomic Alterations and it is SeGAs that aCGH is used to detect. Identifying these genomic alterations will yield molecular targets for diagnosing diseases and treating patients.

What is spotted on aCGH arrays?

In terms of the spotted elements, there are two main types of aCGH arrays. One type is spotted with PCR amplified cDNA or bacterial artificial chromosome (BAC), that are usually in the range of 150 to 200kb. Another type is spotted with synthetic oligonucleotides in the range of 25-85 bp in length.

What is a marker-based CGH array?

A marker-based array is one that consists of elements that do not sequentially overlap. The resolution of this type of array is dependent on the distances between the clones and the size of the clones.

What is a tiling CGH array?

A tiling array is one that contiguously covers the genome using overlapping clones. The very high resolution of this type of array allows gains or losses of 40-80 kb regions to be detected.

What is a SMRT array?

SMRT stands for Sub-Megabase Resolution Tiling array.

What is a genome complexity reduction step?

A genome complexity reduction step is a measure that amplifies the genomic sequences of interest, and thus minimises the inherent "noise" generated by the remaining sequence of the genome. In terms of experiments involving microarrays, genome reduction can improve hybridisation kinetics and signal-to-noise ratios and reduce cross-hybridisation of the array elements to multiple genomic loci. Genomic complexity reduction can be achieved by target amplification by PCR and by strategies that use polymerase extension and probe ligation.

What is ROMA?

ROMA stands for Representative Oligonucleotide Microarray Analysis. This method reduces the complexity of the genomic DNA sample to about 2.5% of the genome by a restriction enzyme digest and linker-mediated PCR amplification.

Can cDNA arrays be used for array CGH?

cDNA arrays can be used to identify high level segmental genomic alterations, however, because of low signal-to-noise ratio and variable signal intensities, it is difficult to detect copy-number alterations using cDNA arrays. When hybridising to cDNA arrays, larger quantities of sample genomic DNA is required in order to generate a strong signal. The one advantage of using cDNA arrays for aCGH is that genomic data and expression data can be easily linked.

What are some of the advantages and disadvantages of BAC clones versus oligonucleotide arrays?

BAC clones are used for aCGH because of their high resolution and the fact that they provide stronger signal intensities than cDNA clones (due to their large size). However, arrays made from BAC clones (or cDNA) are subject to PCR contamination and BAC array data may contain mapping inaccuracies of the clones to the human genome.

The advantage of oligonucleotide arrays is that the arrays themselves are easier to make (PCR and clone management is not required). However, oligonucleotides are likely to cross-hybridise with multiple genomic loci. To increase the signal-to-noise ratio, assays (which involve PCR amplification of sample genomic DNA) have been developed to reduce the genomic complexity of the sample prior to hybridisation.

How are deletions and duplications confirmed?

Fluorescent in situ hybridisations (FISH) experiments are done to confirm deletions and duplications identified by microarray analysis.

Does the UHNMAC manufacture arrays for aCGH?

We do not make arrays for specifically for aCGH, however, our Hum19k cDNA and Yeast 6.4K arrays have been used for aCGH experiments. For details, please review the publications by Pandita et al. and Gerstein et al. who used Hum19K and Yeast 6.4K arrays, respectively, for aCGH.