Preliminary Qualifying Exam (PQE)

The preliminary qualifying exam (PQE) format is a written proposal and potential dissertation project to be presented, discussed and defended by the student. The proposal is written in the format of an NIH post-doctoral application with a slightly longer page limit of 10 pages not including references. The goal of the PQE is to evaluate the student’s potential and ability to think independently and creatively about experimental design. The student must demonstrate solid knowledge in the background of their proposed topic and an overall knowledge of the immune system. The written proposal, in conjunction with the oral defense, will be evaluated in this light.

Students should plan to complete the PQE between December and March of the second year of graduate study. Before scheduling the examination, students should email their list of proposed PQE Committee members to Shiv Pillai ( and Wendy Garrett ( Along with their proposed PQE members, they should also include a brief description (2-3 sentences) on the topic of their project. One week prior to the exam, students must email their written proposal to each member of their PQE Committee and the immunology program administrator. 

PQE Committee

The PQE Committee must include at least one faculty member of the Immunology Graduate Committee, who will also serve as the Chair. PQE Committee members most often become the Dissertation Advisory Committee (DAC) members, though this is not required, and changes may be made following the PQE. Collaborators should not be on the PQE Committee. Once the Committee has been approved by the program heads, students may schedule their PQE exam. Students should contact the immunology program administrator as soon as they arrange a date for their PQE or if they need any assistance with the scheduling process. Using or similar tools to schedule the PQE is highly recommended.


The proposal should be a description of the student’s proposed dissertation project. It is important to clearly convey: (1) what the scientific questions are, (2) why they are significant, and (3) whether the approaches and techniques proposed are the most appropriate. Students may include relevant preliminary data from their own work or from others in the lab, but this is not a requirement

Students are encouraged to initially discuss the overall aims and format of the proposal with their dissertation advisors. However, the proposal must be authored solely by the student. Once a student and dissertation advisor are in agreement on the aims and format of the proposal, the student should receive no further input or feedback from faculty members in writing the proposal or preparing for the oral defense. Students can seek input from graduate students and postdoctoral fellows on their written proposal and presentation for the oral defense.

Guidelines for the Written Proposal
The written proposal should be no longer than 10 pages in length, single-spaced, with 0.75” margins all around, and with size 12 Arial font. The references do not count towards the page limit.  Organization of the report should be as follows:

A. Specific Aims (limit 1 page): The Specific Aims page should stand alone, is separate from the proposal, and counts towards the 10-page limit. Provide a paragraph on the knowledge gaps in the field that builds to a clearly articulated overarching hypothesis.  Propose two or three Specific Aims. Each aim should broadly represent a question that you seek to answer. No aim should depend on a prior aim. If possible, include a schematic on this page summarizing your Aims and include an Impact Statement. There should be no references on this page.

B. Background and Significance (~2 pages):  Summarize what is known about the field, emphasizing how your proposed research will fill in gaps in our knowledge and advance our understanding of the biological processes involved.  After a succinct literature review, structure this section as follows: (1) x is not known, (2) it is important to know it because, (3) a good system and appropriate reagents are available (or could be developed) to answer this question, and (4) how we will answer it is summarized in specific aim y.

C. Preliminary Results: This section should describe the experimental system, which will most likely be established to some extent in the lab or in other labs working in the field.  Preliminary data is useful but not required. Relevant work from others in the lab may be included.  If a proposal is based on developing an entirely new system in the lab, specific data/experimental information from the literature that would not be appropriate to include in the background section may be included here.

D. Experimental Design and Methods:  Organize these according to your specific aims.  For each aim, provide a brief rationale for the experimental approach and then provide a conceptual description of the techniques involved (no lists of buffers, please!) with a discussion of what controls will be performed and how the data will be analyzed.  Next, summarize what the different experimental outcomes might be and how you would deal with each. Remember, the best experiments are those in which every outcome provides interpretable information; occasional yes or no experiments will be tolerated but you should try to avoid experiments in which the likelihood of an interesting outcome is remote. Identify potential pitfalls of your proposed experiments and alternative strategies. Mention these at the end of each Aim in this section. It is acceptable to incorporate the Preliminary Results into the Experimental Design section, incorporating data related to each Aim prior to the actual proposed experiments.   

You are expected to work with your dissertation advisor and seek his or her advice in the preparation of the aims and format of your proposal. However, the writing must be completely executed by the student. To reiterate, once the student and dissertation advisor are in agreement on the aims and format of the proposal, the student should receive no further input or feedback from faculty members including the dissertation advisor. Students are encouraged to seek input from graduate students and postdoctoral fellows on their written proposal and presentation for the oral defense.

Final copies of your written proposal must be emailed to all members of your PQE Committee and the immunology program administrator at least one week prior to the date of the PQE. 

Oral Examination

For the PQE meeting, students prepare a presentation of their proposal, including an abbreviated Background section with a focus on the Specific Aims, Preliminary Results and Experimental Design and Methods (10-15 slides should be sufficient). Plan for about 20 minutes of actual presentation and expect to be interrupted by the examiners. Schedule 2 hours for this exam.

Be prepared to discuss in depth and answer questions regarding all aspects of the proposal during the oral examination. Be familiar with all pertinent or related techniques, concepts and areas of research. Exam questions will not necessarily focus on just the proposal itself.  

Before the exam, see the immunology program administrator for the PQE evaluation form to be completed by examiners during the exam. This form must be returned to the coordinator (by the PQE Chair) immediately following the exam.


The PQE chair will share the results (pass, conditional pass, or fail) with the student at the end of the meeting.

  • Pass.  No further work on the PQE will be required.
  • Conditional Pass. A student will receive a conditional pass if the committee thinks that the student would benefit from additional preparation. The additional preparations may include:

1. A re-write of the proposal - a deadline for the submission of the re-written proposal must be provided to the student as well as clear suggestions for improvement.

2. Additional coursework - specific coursework that will address the individual student’s required areas of growth must be assigned. Coursework must be scheduled at the earliest possible opportunity.

3. Additional study - specific articles/journals that will address the individual student’s required areas of growth must be assigned.

Terms of the conditional pass, as well as a completion due date, must be set during the PQE meeting and included on the evaluation form. Once this work is completed to the satisfaction of the PQE Committee, the Chair will notify the student and the immunology program administrator that the student has fulfilled the requirements and the result is changed to a “pass.”

  • Fail.  A student will receive a fail if there are serious concerns based on the written proposal and the oral exam. The student will be given the opportunity to rewrite the proposal and retake the oral exam following completion of additional recommended work.

It is expected that the work will be done in parallel with your thesis project.

Next Steps

After passing the PQE, the student will assemble a Dissertation Advisory Committee (DAC). PQE Committee members most often become the DAC members, though this is not required, and changes may still be made at this time or if the project changes direction. The first DAC meeting should take place within 3-4 months of passing the PQE, and no later than 6 months after the PQE. At each DAC meeting, the DAC members will suggest a date for the next meeting to take place, keeping the Timeline to Degree  in mind.


Timeline to Degree

G-1 Year: Coursework and Lab Rotations

G-2 Year: Lab declaration, Teaching Requirement, Complete PQE & Set up DAC

G-3 Year: DAC meeting by the end of August of 3rd year

G-4 Year: DAC meeting by the end of May of 4th year

G-5 Year: DAC meeting by the end of December or within 6 months of previous DAC.

G-6/Above: Meet every 6 months with DAC

Final DAC Meeting: 

Any year, but typically 4/5 years total enrollment & no more than 6/7 years: The DAC decides when student should begin writing the thesis. A suggested endpoint for graduation, though this is at the discretion of the individual DACs, is two submitted manuscripts