AGH service for human cells

Code Description Price Qty
K22 AGH £605.00

Service Description

AGH (array genomic hybridization) refers to our SNP array service, in which the DNA samples will be run on the Affymetrix 750k 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 hybridization of the labelled sample DNA, the amount of hybridized DNA to each of the array probes is measured and compared in silico to a set of ~10,000 control hybridizations.

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 (Affymetrix CytoScan 750k platform), 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.

Balanced rearrangements and low level (10 – 20%) of mosaicism will not be detected using either array CGH or AGH. In practice, this level of mosaicism is statistically similar to the level which can be detected by karyotype analysis of 20 cells.

We recommend array analysis for identifying marker chromosomes and additional material on a chromosome of unknown origin. Karyotype analysis alone can detect certain acquired abnormalities, e.g. gain in the small arm of a chromosome, but the precise nature of certain unbalanced chromosomal abnormalities is difficult to establish by only using G-banding analysis.

Sample types accepted

The aCGH and AGH services are 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. 

Frequently Asked Questions (FAQs)

For any additional questions, please refer to FAQs document below.

 

Please do not send any samples without booking in advance. Please contact us by email at info@cellgs.com to schedule your samples for arrival.

aCGH vs AGH

                 

Comparison of aCGH and AGH methods.

For aCGH, (a) the sample and a normal control are labelled with fluorophores which fluoresce at different wavelengths. (b) The relative intensities of these wavelengths are compared. (c) The probes are plotted against their chromosomal origin.  Duplication events are indicated by clusters of probes that show an increase in the relative intensity of test vs control fluorophore. Deletion events are re indicated by clusters of probes that show a decrease in the relative intensity of test vs control fluorophore.    

For AGH, (a) only the sample is labelled with a fluorophore. (b) The intensities of the signals are read and (c) compared in-silico to a database of thousands of normal and disease-specific cells (d) The probes are plotted against their chromosomal origin. (Duplication events are indicated by clusters of probes that show an increase in the relative intensity of test vs control samples database. Deletion events are re indicated by clusters of probes that show a decrease in the relative intensity of test vs control sample database.