Karyotype analysis is suitable for the analysis and detection of large structural and numerical chromosomal abnormalities. Further details of DNA dosage imbalances and LOH, can be characterized using array comparative genome hybridization (CGH) and array genome hybridization (AGH). Array CGH and AGH can be performed for the assessment of acquired DNA copy number variation (CNV) with a genome-wide resolution of ~200 kb.
Cell Guidance Systems offers two levels of service for human samples: array CGH and AGH.
Array CGH is performed on the Agilent 8x60K platform, where two differentially labeled DNA samples are co-hybridized to an array with ~60,000 oligonucleotide probes simultaneously.
There are two levels of service for array CGH:
a single sample is hybridized against control DNA sample provided by ourselves
two samples, both provided by the customer, are co-hybridized to assess acquired differences in CNV
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. This assay will assess for acquired loss of heterozygosity (LOH).
What type of abnormalities will or will not be reported? Please find our comments as follows:
Benign constitutional (heritable) CNVs will not be reported and the assessment of normal variation will be performed using ~5000 normal control samples and a database of ~10,000 clinical samples.
Acquired CNVs and LOH present in at least ~15-20% of cells will be reported.
Balanced rearrangements and low level (10 – 20%) of mosaicism will not be detected using either array CGH or AGH.
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.
Both G-banding and arrays analysis should be used in combination when culturing cells to check that the cell line remains chromosomally normal.
The array CGH / AGH services are only available for human 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 where used).
At present, Cell Guidance Systems also provides G-banding analysis. No SKY services is available.
FISH services are available upon request. Please ask for further details.