Dark YA book/possibly series about boy who is sent to a secret spy(?) school

Here's what I remember -boy lives with his parents and brother. They all don't like him and are mean to him -at one point he uses sugar to mess up his brother's comic collection by attracting ants -his family knows he's going to a weird school but he keeps it a secret exactly what kind of school it is -his fellow classmates keep disappearing. I think one of them starts acting weird and then it later turns out he's been replaced by a robot wearing his skin or something -at some point he realizes (or at least thinks) that his family are also actually spies and not his real family. He wonders if they go back to their real families when they're off duty -there is a disabled girl that he's very close with. I think she has cerebral palsy? At one point they're captured together and he has to change her diaper and the captors make gross comments about it. -I read it in 2013 I believe

Any help is greatly appreciated! Thank you!!!