The first priority after completing a FISH assay is to assess the quality of the control slide. It is essential that a positive control slide is performed with each FISH assay.
The positive control slide may be of several types. A cell line control may be used. This control slide may be manufactured at the site of testing, as long as it has been prepared into a pellet and formalin-fixed, paraffin-embedded (FFPE) in the same manner as the sample tissues. Some manufacturers offer a positive control slide that can be purchased in addition to the probe set. These are most often cell lines as well. A tissue control known to contain the abnormality can be used as a positive control. This is an optimal situation because the tissue is the most like the test samples. However, they can be hard to find and keep enough on hand for long term purposes.
The control slide enumeration range must be determined by the laboratory performing the FISH assay. Typically, laboratories will use a control cell line that has a range of 4.0 +/- 1 standard deviation (SD). If the cell line control is purchased from a manufacturer, the manufacturer will provide a control range, but the laboratory must verify the control range and determine their in-house standard deviation.
If the control slide enumeration does not come into the pre-determined quality control range, the entire assay must be rejected and repeated.