Questions or concerns you have about your profile?
1. My MA thesis used qualitative method (interview+survey), would it be ok to use it as my writing sample? I have background in economics and big data analysis. Just wasn't sure if the committee may view the writing sample as ill-fit for the types of research I plan to do there (mixed-method).
2. How to differentiate myself with my training in qualitative methods from the applicant pool with most people with strong quant background?
I think 1 and 2 are closely linked. You show that you did an MA thesis with qualitative methods (interview+survey) but that you also have strong quant training.
You have a good profile. You are aiming for top schools, where everyone has top profiles, so there will be a bit of randomness to it, but I am sure you will get interviews. I would look and see who really does mixed methods at the places you go, though. It is good to have the tools in the toolbox, so to speak, but I don't know many scholars that truly do mixed methods.