I was the same way at that age, and it definitely didn't help that I wore glasses and was on the heavy side. I had my couple of friends and hardly ever strayed outside my "circle." However, in 7th grade, I decided I was done with all that and tried out for my junior high volleyball team. I made the team, but what gave me the courage to do something I loved so much was 2 of my friends played volleyball with me. My 8th grade year was the ultimate turning point for me. Now, I'm 33 and while I'm not an A-type personality by any means, I'm outgoing in my own way. There are sometimes I still have to make an incredible effort to put myself out there (I'm a Mary Kay consultant), and it's made my business suffer.
My recommendation is to find something she loves and have her join a club (or form a club) associated with that love. Once she meets people who have the same interests, she may be a little less shy around them, which could help translate to the rest of her life :) And be patient. It could take a few more years!