(FOUND) YA fantasy about dragons and magic.

Pretty general huh? The book is about a brother and sister on the run from an army because they or their parents had magic. I think they are eventually captured and taken to a castle or something where they find other kids like them being killed for their magic. I remember the magic coming from where dragons once lived and their scales contaminated the soil and water. The cover of the book had 2 children waking into the mother of a cave that looked like a dragon skull. The book also felt like it should have had a sequel but I don't think the author ever wrote one. Also the author is male.