By the end of the first year of the program, each student will focus on a research project for his or her Master's thesis under the guidance of a supervisory committee. The thesis project may be based on research involving primary data collection, or may be a secondary analysis of data from a completed genetic epidemiologic study by investigating a research question not yet considered in that study.

The thesis committee chair is chosen by the student and must be a member of the IPHG Faculty. The full Master's thesis committee will consist of at least two members of the Graduate Faculty. No more than four members can serve on a master's committee. Each MSGE student must write a thesis proposal and obtain approval of the proposal by his or her thesis chair before beginning research and before earning thesis credits. A copy of this proposal should be turned into the IPHG office before registering for thesis credits.

As with all graduate programs, the thesis must be completed and approved by the thesis committee before the student can complete his or her degree program.