Karyotyping is a test to examine chromosomes in cultured cells using a microscope. It may identify genetic problems as the cause of a clinical problem. As the cells have to be cultured we can only carry out a karyotype test on viable (living) cells. In the laboratory, trained staff count the chromosomes within a cell and look for structural changes.
Karyotyping gives a whole genome overview and a skilled cytogeneticist would detect most chromosome rearrangements above 5~10Mb of DNA depending on tissue type. Karyotyping is used for prenatal, haematological and constitutional referrals.
Fluorescence in situ hybridisation
Fluorescence in situ hybridisation (FISH) is a targeted technique that allows the presence, absence or location of specific DNA sequences to be detected. The technique uses DNA probes tagged with fluorescent labels that hybridise to specific DNA regions of interest. It can be used to detect specific deletions, duplications and rearrangements and can be applied to prenatal, haematological and constitutional samples.
QF-PCR: Quantitative Fluorescence-Polymerase Chain Reaction
In this laboratory this technique allows several small parts of DNA from regions on chromosomes 13, 18, 21, X and Y to be amplified and measured for copy number. It is used as a rapid method to detect extra copies of these chromosomes in amniocentesis samples without having to wait for the cells to be grown in culture.
Microarray can detect whether a patient has regions of DNA that have been lost (deletions) or gained (duplications) which may be associated with their clinical problems. It is a higher resolution test than karyotyping and significantly increases the rate of detection of regions of copy number change compared to karyotyping. Microarray allows us to identify the genes which have been gained, lost or possibly disrupted. On some occasions parental blood samples may be requested to help interpret some findings. At present this technique is applied to patients referred for neurodevelopmental disorders, congenital heart disease, dysmorphism and hypotonic infants; as well as samples from pregnancy loss and a subset of prenatal referrals. Prenatal microarray referrals should be accompanied with parental EDTA bloods. A subset of haematological malignancy referrals also undergo array analysis to look for regions of imbalance, loss of heterozygosity as well as a high resolution analysis of disease-specific target genes.