Both G-banding and arrays analysis are complementary and should be used in combination to check that a cultured cell line remains chromosomally normal. Karyotype analysis is suitable for the analysis and detection of large structural and numerical chromosomal abnormalities > 30 Mb. Karyotype analysis can also detect balanced translocations which frequently occur in cultured cells. However, karyotype analysis provides low resolution. A much higher resolution of DNA dosage imbalances and LOH can be characterized using array comparative genome hybridization (aCGH) and array genome hybridization (AGH). aCGH and AGH can be performed for the assessment of acquired DNA copy number variation (CNV) with a genome-wide resolution of < 200 kb and as little as 2 kb.
Cell Guidance Systems offers two services for human samples based on different array platforms: aCGH and AGH.
aCGH is performed on the Agilent 8x60K platform. This system utilizes two differentially labeled DNA samples co-hybridized to an array with ~55,000 oligonucleotide probes. The relative abundance of DNA binding to each probe provides a direct measure of relative copy number of the two samples.
There are two service options for aCGH:
A single sample is hybridized against control DNA sample provided by ourselves.
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.
AGH is performed using Affymetrix CytoScan 750K platform, where the hybridization data from a single test DNA is compared with a series of controls hybridizations in silico. The array has 750,486 distinct features. The AGH assay is particularly useful for assessing for acquired loss of heterozygosity (LOH).
What Types of Abnormalities are Reported?
Acquired CNVs and LOH present in at least ~15-20% of cells will be reported.
For the CytoScan platform (AGH), an assessment of normal variation is made with reference to ~5000 normal control samples and a database of ~10,000 clinical samples. 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 an analysis of 20 cells.
Karyotype analysis 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 only by using G-banding analysis. Marker chromosomes and additional material on a chromosome from unknown origin will require array analysis.
Sample Types Accepted
The array CGH / AGH services are only available for human samples. We will provide precise instructions on preparation of samples
Reports will be provided by Cell Guidance Systems within 15 – 17 business days after the DNA samples have been received by us (please allow additional time for transport from distributors when used).
FISH services are available upon request. Please ask for further details. No SKY service is available.