User blog comment:DeadDATA/Cerberus In ME3: How They've Grown/@comment-1221773-20110818030837

I've seen this idea raised on BSN as well. Cloning is probably the most plausible explanation for Cerberus' new-found strength. It stands to reason that if Saren and Okeer could make armies of cloned krogan, the Illusive Man could clone a human army too.

As for the clones being of Shepard or using some of Shepard's genetic code, it would be an interesting twist. What if other major ME characters were also cloned, like Miranda and Jacob? Each class of Cerberus trooper might be comprised of a different character.