Call me crazy, but I've got an itch I can't scratch. I read a lot in school and one of the books I remember from Junior High (early 2000's) was a book about some children that were being experimented on in a lab. I think I recall they had powers and the boy's eyes glowed blue as he was able to read minds/move objects with his mind etc. I'm pretty sure he was trying to escape the lab and the doctors.
Yes, Mind Trap is definitely the book. Thank you Mithrandir.
Scott's identity as a telepathic alien from another planet may be exposed when he's imprisoned in a research institute for psychic children run by a mysterious doctor.