Factors known to Significantly Affect Performance
Cytogenetic investigations require the culture of living cells and therefore multiple factors may result in failure to obtain a cytogenetic result;
- Bacterial contamination of the sample at source
- Exposure to temperatures above 38°C or below 0°
- Delays in transport (more than 3 days for blood samples, or 1 day for other sample types)
- Incorrect sample tube
- Insufficient sample volume
- Low cell count within sample
Cytogenetic Analysis
Cytogenetic analysis is the visual inspection of a series of bands along the length of the chromosomes. Generally blood samples give the best quality chromosomes and therefore provide the best chance of detecting small subtle chromosome abnormalities.
Chromosomes from other tissues (e.g. amniotic fluid, chorionic villus and products of conception) are generally shorter and have less banding detail, this therefore increases the risk of missing a subtle chromosome abnormality.
Some cytogenetic abnormalities may involve quite large segments of material being exchanged between chromosomes, however due to similarities in their banding patterns the resulting abnormality may remain cryptic. Some chromosome abnormalities are beyond the limits of resolution of the light microscope.
In some cases, parental blood samples will be required to help us interpret complex findings or to assess the implication of a cytogenetic result to the wider family.
Mosaicism
Cytogenetic mosaicism is the presence of more than one chromosomally different cell line. The likelihood of detecting mosaicism increases with the number of cell examined. Generally the karyotyping of a sample will involve looking at relatively small numbers of cells (less than 10) and so is not an effective way of detecting mosaicism. However, if there is an indication of suspected mosaicism, additional cells will be examined to exclude 10% mosaicism at a 95% confidence level.
Maternal Cell Contamination
Very rarely there may be a false negative result in prenatal samples due to the presence of maternal cell contamination.
Limitations of QF-PCR
In some cases, samples may be uninformative for all the markers on one or more chromosome.
Excessive maternal contamination of fetal samples can produce problems with the interpretation of tests. Samples of maternal blood are routinely requested to allow fetal DNA to be identified by its different genotype. If maternal cell contamination is found in a prenatal sample a second culture is checked by cytogenetic analysis.
Limitations of Microarray Testing
Microarray testing does not detect balanced rearrangements/low level mosaicism, or copy number variants smaller than 10Kb.
An Uncertainty of Measurement in Cytogenetic and Cytogenomic Tests Document is available on request
