Giner-Delgado, Carla, et al. described a variant of MLPA combining it with iPCR. They call these new method iMLPA and its procedure is the same as MLPA but there are necessary two additional steps at the beginning:
# First, a DNA treatment with restriction enzymes that cut on both sides of the region of interest is necessary.
# The fragments obtained from digestion are recircularized and linked
The probe design is quite similar. Each probe will be formed by two parts that have at least: a target sequence, which is a region that contains the sequence complementary to the region of interest, so that the correct hybridization can occur. And a primer sequence at the end, it is a sequence whose design varies and is what will allow the design of primers and subsequent fragment amplification. In addition, one of the parts of the probe usually contains a stuffer between the target sequence and the primer sequence. The use of different stuffers allows the identification of probes with the same primer sequences but different target sequences, that is key for multiple amplification of several different fragments in a single reaction.
The next step continues with the typical MLPA protocol.