They're connected to MCT, and tied to a research facility that is located in the old East Coast Stock Exchange building in Boston. Lockdown mentions experiments being done on the effects of Dissonance on Technomancers, and in Lockdown, it mentions that for each point of Dissonance a Technomancer acquires (it is not explained how this is done) they get the benefit of one level of submersion, allowing them to gain power very rapidly, though it also drives them insane.
Putting all these together, I would imagine that MCT chromes out their Technomancers, then has them start to rack up Dissonance points to make up for their lost Resonance. Given that Dissonant Technomancers are the matrix equivilant of blood mages and toxic shaman, it isn't really a PC-friendly option.