It is possible to use FFPE-extracted DNA for a limited number of MLPA assays. You can often find information about if a probemix is suitable for use with FFPE-extracted DNA in the intended use section of the probemix. Reactions on FFPE-extracted DNA often show higher standard deviations than reactions on DNA from other sources.
DNA extracted from FFPE tissue often contains impurities. In addition, FFPE-derived DNA is not only fragmented but is often also damaged by depurination, cross-links, and other base modifications. This usually results in a higher standard deviation than with non-FFPE-derived sample DNA. We therefore recommend comparing test samples to samples from healthy FFPE tissue to exclude that findings on test samples are due to the effects of the FFPE treatment.
If your FFPE samples are derived from tumours, please also keep the following in mind:
- Analysis on tumour samples provides information on the average situation in the cells from which the DNA sample was purified.
- Reference probes may not always be suitable, as they may frequently show copy number variations in the tumour.
- Gains or losses of genomic regions or genes may not be detected if the percentage of tumour cells is low in the sample, or if the tumour has subclonal aberrations.