Preliminary Qualifying Exam (PQE)

In the spring of the second year, BPH students take a preliminary qualifying examination (PQE). The purpose of the PQE is to assess the student’s preparation and ability to embark on original scientific investigation. The primary goal of the PQE is to evaluate the student’s ability to identify and articulate a clear hypothesis for the thesis topic based upon familiarity with relevant literature, to propose critical experiments designed to prove or to disprove the hypothesis, and to interpret experimental outcomes in a manner that indicates awareness of the limitations of the methods used.  It is not expected that preliminary data will be presented to support the hypothesis. The exam includes a written proposal and oral defense of that proposal on a topic related to the dissertation research.

Preparing for the PQE: Student Timeline

  • Complete the BPH Preliminary Qualifying Exam Course Form, listing the coursework taken to fulfill program requirements. The BPH Program must approve of satisfactory progress before the student proceeds in the PQE process.
  • The PQE committee will consist of three BPH program faculty* with relevant expertise for each student’s area of research, chosen by the student in consultation with the advisor and Faculty Director. Students may also name faculty with appointments in BPH-affiliated departments, who themselves might not be BPH members. The PQE committee chair, who will act to moderate and document the proceedings and outcomes of the exam, in addition to serving as an examiner, will be assigned from the ranks of the PQE Steering Committee, which is comprised of experienced examiners with collective expertise that cuts across the scientific spectrum covered within the program.  The research/dissertation advisor is not part of the student’s PQE committee. The student must complete the PQE Committee Form and have it approved by the BPH Faculty Director.
      For students in dissertation labs outside of BPH (HILS-affiliated labs), one member of the student’s PQE committee can be from the HILS-affiliated lab’s department.
  • The student is required to send the PQE Committee Form and the PQE Course Form to the BPH Office as soon as they are complete along with the date, time and location of the exam. NOTE: It is critical for students to work with the BPH Office in scheduling PQEs so as to not conflict with other BPH academic endeavors such as Dissertation Defenses.
  • Topic and content: Students are expected to choose a topic for their exam that is ordinarily related to the topic of the student’s dissertation. While it is fully expected that the advisor would help guide the student toward their current topic of dissertation research and provided technical advice, the advisor and PQE committee are not allowed to assist the student in developing the scope and aims of the proposal. However, students are encouraged to get feedback and critical comment from their peers in the laboratory and program.
  • Preparation Period and Guidelines: During the preparation of the proposal, students may consult with faculty and other students. Consultation on general issues (clarification, technical advice, etc.) is appropriate, but solicitation regarding ideas for specific aims or experimental design is inappropriate. Faculty members, including dissertation advisors, should not read written drafts of the proposal in order to provide extensive help. Further, students should not seek feedback from the members of their exam committee.

The written component is submitted to the PQE committee at least 10 calendar days before the oral exam. A copy of the proposal should also be provided to the BPH program office and the dissertation advisor. The proposal should be single spaced, following the form of an NIH post-doctoral fellowship application on the topic chosen (Ariel, 11 pt. font, 6-page maximum, excluding specific aims page and references). The proposal should include the following sections:

  • Specific Aims – Listing the objectives of the specific research proposed (e.g., to test a stated hypothesis, create a novel design, solve a specific problem, challenge an existing paradigm or clinical practice, address a critical barrier to progress in the field, or develop new technology). One page or less is recommended.
  • Background and Significance– Briefly sketch the background leading to the proposal, critically evaluate existing knowledge, and specifically identify the gaps that the project is intended to fill. State concisely the importance and health relevance of the research described in this application by relating the specific aims to the broad, long-term objectives. If the aims of the application are achieved, state how scientific knowledge will be advanced. Describe the effect of these studies on the concepts, methods, technologies, treatments, services or preventative interventions.  Summarize your preliminary work, and work of others, that support the proposed research. Two pages are recommended.
  • Research Design and Methods – Describe the research design conceptual framework, procedures, and analyses to be used to accomplish the specific aims of the project. Briefly summarize how the data will be collected, analyzed, and interpreted. Describe any novel approaches, tools, technologies, or methods you may develop, and advantages over existing methodologies. Describe any novel concepts, approaches, tools, or technologies for the proposed studies. Discuss the potential challenges, difficulties, caveats, and limitations of the proposed procedures and alternative approaches to achieve the aims. Highlight anticipated outcomes, alternative interpretations, and potential pitfalls. Four pages are recommended.
  • References: (author, title, journal, inclusive pages, year)

The oral portion of the exam is built around a defense of the written proposal. At the outset of the exam, the student leaves the room for the PQE committee to discuss the merits of the written proposal and identify key areas they want to test the student on.  Additionally, the Dissertation Advisor will be asked to attend the PQE exam at the very beginning to review the student’s preparation for the exam with the committee, but will not be present during the oral examination.

Once the student is asked back into the room, the exam starts with a short presentation by the student (no more than 10 slides) of the background, specific aims, rationale, preliminary data, and proposed approach. The examiners, having read the proposal in detail, then ask questions that are both directly relate to and tangential to the proposal. Students must defend and explain the hypothesis, methods, and anticipated results, while also recognizing alternative approaches and interpretations. The committee will invariably test the student’s understanding of the core principles that underlie the scientific problem and their origins. Students may be asked to draw models or experimental flowcharts on the board for clarity. The exam is usually completed in about 2 hours, at which time the committee deliberates an outcome with the student out of the room. The PQE Chair will serve not only as an examiner, but will also oversee the administering of the exam and arbitrate problems. The Chair will also see that the PQE Report Form is completed and on file in the BPH Program Office at the completion of the exam.


The PQE committee evaluates the individual sections and overall content of the written proposal, with an emphasis on the rationale and feasibility of the aims and whether the aims are interdependent or not. Often, deficiencies in the written proposal are satisfactorily addressed in the oral exam. However, a critique of the proposal will be provided and students may be asked to rewrite specific sections or, on occasion, the entire proposal.

For the oral exam, the committee will deliberate on the student’s preparedness as it relates to:

1) Broad background knowledge of the chosen field and related literature;
2) The ability to deconstruct and think critically about the research project and field (i.e., what are the established first principles and how were they established and what assumptions have been made, but not proven, that impact the proposed study?);
3) The application of specific methods, including strengths, limitations, alternatives, and statistical considerations;
4) The capacity to interpret specific outcomes and define an appropriate course of subsequent experiments;
5) Presentation skills and clarity.

Specific comments on these areas of competency and others will be provided on the PQE Report Form.

Based on the performance of the student, the committee will make constructive recommendations or require specific actions related either to the written proposal or for improving in specific competency areas recognized from the oral exam.

The Potential Outcomes of the PQE are:

1) PASS – a constructive critique and list of recommendations for improvement is provided.

2) CONDITIONAL – This is a qualified pass. In addition to recommendations, a specific list of required changes to the written proposal or actions needed to improve competencies (e.g., through coursework, online modules, article reading, working with a tutor or faculty member on a specific area of deficiency, etc.) will be given and discussed with the student, along with a timeline for completion. For example, a student might be asked to write an additional one or two-page report on a specific area of importance to their project that they displayed insufficient knowledge of, which would be done after further reading of the literature and/or additional coursework. The satisfactory completion of these required actions within the set timeline will be overseen by the PQE chair, laboratory mentor, and Faculty Director.

3) RETAKE – If it is felt that both the written proposal and oral exam are inadequate, with substantial deficiencies being recognized in multiple areas, then the student will be asked to retake the exam. The PQE Report will delineate these deficiencies and make clear recommendations to the student on what needs to be improved. A decision to require a retake of the PQE must be signed off on by the Faculty Director and PQE steering committee after reviewing the case.

A meeting is then held with the PQE chair, Faculty Director, Advisor/PI and student to discuss the case and the specific improvements needed. Resources available to the student and a strategy to employ them for improvements in scientific understanding and reasoning, critical thinking, proposal writing, or presentation will be provided to the student. The student must retake the exam, including submission of a revised written proposal, within six months. Unless aspects of the previous exam were deemed potentially unfair to the student, the same PQE committee will administer the retake, and the Faculty Director or a representative of the PQE steering committee will attend as an observer. In rare circumstances, the student may be counseled to consider leaving the program at this stage.

4) FAILThe outcome of the retake exam is either pass or fail, and a student can only fail the PQE at the retake stage. Failing the PQE would occur if a combination of the revised proposal and second oral exam are again found to be insufficient and demonstrating a lack of preparedness and qualifications to move forward in the program. If after final considerations by the Faculty Director, PQE steering committee, and mentor, it is concluded that the student is best served by leaving the Program to pursue other interests, the student will be asked to leave the program at the end of the semester.

Upon satisfactory completion of their PQE, BPH students advance to become PhD candidates.