Okay guys, let me clear this up.
Paul is genuine, he was a ordinary human and he had/has real parents, he is the original Denton*.
Now if Paul Denton was a genuine kid, how the hell did they get hold of him for experimentation? -- the answer is simple: forced donation.
This could work 2 ways, one: he was adopted/kidnapped by Page Industries for their experiments. But lets be serious here, what if his parents were employees of MJ12?, high ranking employees?
In the mix of Deus Ex you get alot of lies and rumors lusting you to do something you shouldn't do. Alot of deceit exists so what if Paul Denton got lied to just to join the NSF?
My theory is Mr and Mrs Denton were in one of the highest positions on the MJ12 job ladder -- but say they screw over Bob Page... Bob Page doesn't like this so the ginger orders his men to assassinate them while they're out driving as a couple (A very young Paul being present.) and make it look like a car accident.
All goes well but Paul survives, one of the assassination goons (that certain MiB) talks with Bob Page over his codec (I had to) and says that a child survived, Bob gets the evil idea to keep the kid and run his experiments on him, as a test dummy.
Anyway clones are born from Paul's DNA strands at one point, memory also altered at some point, gets tutored somewhere (iirc, a different country) and is sent straight to Unatco training.
One of the clones have started to be near completion, he is released at a certain date 5 years prior to the game he will go major memory alteration and hibilation.
That clone is JC Denton.
*Source: Deus Ex Bible
** Source: Deus Ex, Area 52 Boss