Non-PI recs (non-science & science)

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If the MD program requires it, submit it. Generally (not always) MD/PhD programs are structured so that they require the MD application plus whatever additional things the MD/PhD program wants.
 
It's often specific to the program, but most of the time you get to choose which letters to assign to a specific school when you list them on AMCAS. You'll have to check school-to-school to make sure that the letters you've assigned meet their criteria (for instance, the MSTP at Indiana U requires one research letter, one science professor letter, and one non-academic letter). It sounds like you've got a good collection together, just make sure that the letter writers know what qualities you'd like them to emphasize (i.e., that you have great potential as a physician-scientist).
 
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