She has been thinking about some top schools. She lives and works relatively close to Harvard. She and I have signed up to attend a talk on cancer research at MIT which is connected to the upcoming alumni events. She also has legacy status at Stanford and Columbia (both of which apparently do look at legacy at least a little bit for graduate programs).
Otherwise I do not think that she has figured out where she wants to apply. She has dual US/Canadian citizenship which might help a bit with McGill and/or Toronto but she has not talked about either.
My understanding is that when applying to graduate programs either “get a job” or “keep working at your current job” is in many cases the safety. Given what she is currently working on, continuing to work for another year or two seems like a very reasonable option (assuming that funding continues).