aCGH service for human cells
aCGH (array comparative genomic hybridization) refers to our oligonucleotide array service, where the DNA samples will be run on the Agilent 8x60k platform.
This array contains approximately 55,000 oligonucleotide probes, however, unlike our AGH (array genomic hybridization) platform, it does not contain SNP probes. Consequently, only DNA copy number changes can be detected using this array. The genome-wide resolution for detection of DNA copy number losses or gains is about 500 kilobases in size.
The sample DNA and control DNA are differentially labelled and hybridized to a single array to determine the relative DNA copy number differences between these two samples. If the two samples have the same DNA copy number change, this will not be detected using this platform, only the DNA copy number changes which are different between the two co-hybridized samples will be detected.
aCGH requires the use of a control DNA sample. The options for this are listed below:
- A single sample is hybridized against control DNA sample provided by ourselves (cat code K20).
- Both test and control samples are provided by the customer and are co-hybridized to assess acquired CNV. We recommend that both the control and test DNA samples are isolated from the cells at the same time (cat code K21).
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 firstname.lastname@example.org to schedule your samples for arrival.