What are the limitations of MLPA?
• MLPA reactions are more sensitive to contaminants (PCR inhibitors such as small remnants of phenol) than conventional PCR reactions. However, it will be quickly detected whether this has been the case, as it is predominantly those amplification products with lower average peak areas (usually the longer probes) whose signals will be reduced. Moreover, good results can be obtained on DNA extracted from formaldehyde-treated paraffin-embedded tissues. • Developing the type of MLPA probe sets sold by MRC-Holland is complicated, expensive and time-consuming. Each probe requires the design and preparation of a phage M13 clone, purification of its single-stranded DNA and subsequent digestion with expensive restriction endonucleases. Nevertheless, hundreds of different SALSA MLPA kits are already available from MRC-Holland and it is always possible to send in requests for new probe mixes. For research purposes, it is possible to design a small number of completely synthetic probes, resulting
