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AGH analysis

Cambridge Bioscience offers access to a SNP array service from Cell Guidance Systems for human samples based on AGH array platforms.

AGH (array genomic hybridisation) refers to the SNP array service, in which the DNA samples will be run on the Affymetrix 750k/Infinium Global Screening Array v3.0 platform.

This array uses a combination of copy number probes and single nucleotide polymorphisms (SNPs) to enable determination of DNA copy number changes as well as the detection of regions with absence of heterozygosity (AOH) or the acquired loss of heterozygosity (LOH). The genome-wide resolution for the detection of DNA copy number losses or gains on this platform is about 200 kb.

This array contains 750,486 distinct probes. Following the hybridisation of the labelled sample DNA, the amount of hybridised DNA to each of the array probes is measured and compared in silico to a set of ~10,000 control hybridisations.

What types of abnormalities are reported?
• Acquired copy number variations (CNVs) and loss of heterozygosity (LOH) present in at least ~15 – 20% of cells will be reported.
• For the AGH analysis, an assessment of normal variation is made with reference to ~5,000 normal control samples and a database of ~10,000 clinical samples. However, benign constitutional (heritable) CNVs will not be reported unless requested.
• Balanced rearrangements and low level (10 – 20%) of mosaicism will not be detected using AGH. In practice, this level of mosaicism is statistically similar to the level which can be detected by karyotype analysis of 20 cells.

Sample types accepted
The array service is only available for human samples. Requirements for the samples are as listed below:
Sample type: isolated DNA
Concentration: >50 ng/µl
Minimum total volume: 1 µg
Purity: A260/A230: 1.8 – 2.2, A260/A280: > 1.8 

Service description and reporting
A summary report of the results will be issued following completion of the analysis. This will include the array profile overview, details of any abnormalities detected, and a description of the analysis carried out. This will be emailed to you in PDF format, along with a TIFF file containing an image of the genome overview.

The results are returned by email within 15 – 17 business days after the DNA samples have been received at our laboratories. Please note that lead times can be longer during busier periods. If this applies to your order, our team will keep you updated.

To discuss a project, please contact our Cell Guidance Systems specialist

Material available for download:
Requisition form and instructions to send samples

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