Student Handbook

Admission to Candidacy ("A") Exam

See GGD Handbook for more details.

To qualify as a Ph.D. candidate, each graduate student must pass an “Admission to Candidacy” exam (or A-exam) before the start of the fifth semester. The examiners are the members of the student’s Special Committee and one other faculty member (to be chosen jointly by the student and thesis advisor). The purpose of the exam is to test the student’s level of knowledge and ability to design research strategies.

Some procedural details

The examination consists of a written proposal for a research project on a student’s thesis project or on an unrelated project, and the student’s oral defense of the proposal (the actual A-exam). The format of the proposal should be either that of an NSF or an NIH grant request (15 double-spaced pages of text, 12-point type or larger-see below for details). It should explain how the research will answer some important scientific question, or (at least) how the research will rule out some possible answers to an important question. Individual members of the Committee may add special requirements to be included in the proposal; for example, a detailed protocol for mapping a gene involved in the proposal, etc. The major professor is permitted one reading of the proposal prior to submission to the exam Committee. The student must deliver a copy of the completed proposal to each exam Committee member no later than one week before the A-exam. At the A-exam, the Committee will question the student about various aspects of the proposal; but their questions need not be limited to the proposal and should assess the student’s ability to analyze and plan experiments in genetics or development, and their knowledge of genetics or development.

Satisfactory defense of the proposal and related questions at the A-exam leads to admission of the student to candidacy for the Ph.D. Failure of the exam leads to one of the following: A one-time rescheduling of the exam; a decision to terminate the student at the Master’s degree level upon completion of a Master’s thesis; or dismissal from the program (at the discretion of the student’s committee).

The A-exam must be taken by the beginning of a student’s fifth semester in graduate school (September 15 of your third year). To ensure that the exam will be completed within this time frame, students will be asked to set an exam date in the summer after their fourth semester (June 15). Students who have not set a date by this time will have one set by the Director of Graduate Studies.

Genetics, Genomics and Development graduate students have the option in their second year to take BioMG8380, Methods and Logic II (or SOS, Skills of a Scientist), taught by David Shalloway. This course provides a good preparation for the A-exam because assignments are given in which students write and critique grant proposals relevant to their thesis work. In addition, students are taught analytical and statistical skills and are introduced to career paths that are pursued by many of our graduates.

Remember that, in addition to your Special Committee members, you need to ask one additional faculty member to join to read your proposal and attend the examination. This person is not officially a member of your committee, and should not sign the Schedule of Examination form or the Results of Examination Form. The additional faculty member does not necessarily have to be in the Field of Genetics, Genomics and Development; but if you decide to invite someone other than a Field member, please check first with your major professor.

You should give a copy of your proposal to each member of your examination committee at least a week before the exam.

It is essential that the Graduate School and the Graduate Field Assistant receive a signed copy of the Schedule of Examination form at least 7 days prior to the A-exam. That form must be signed by the three members of your Special Committee and the Director of Graduate Studies. You must turn in the Results of Examination form within 3 business days after the exam to the Graduate School and the Graduate Field Assistant (GFA). These forms can be downloaded from the Graduate School web site at

In addition to the required forms from the Graduate School, the Field has a new “GGD A-exam Evaluation Form” that should be filled out by your advisor following the exam. The completed form should be turned into one of the GFAs along with the Results of A-exam form.

The written proposal

The total length of the proposal, including figures, is 15 pages. Literature cited is not included in this page limit. The proposed work should be on the research that you intend to accomplish as a graduate student. The proposal should be well-formulated and presented in sufficient detail so that it can be evaluated for its scientific merit. Your proposal should be written following the format specified below which is based on the guidelines for NIH grant proposals.

A.  Abstract  (< 1 page).  This is a summary of the proposed work, with enough of an introduction to allow someone not expert in the field to understand what is planned and to appreciate its importance.

B. Introduction or background and significance (< 6 pages). This section introduces the topic and system, and summarizes what is already known. The review should be comprehensive but not simply be a chronology of events; it should represent a critical appraisal of developments in the field and an evaluation of the present state of affairs. You should cite review articles as well as original research articles that are relevant. End this section with a clear statement of the overall goal of the work. State succinctly why your results will be of importance for answering fundamental questions, or that they will lead to avenues of inquiry, or that they will be of practical relevance to medicine or biotechnology (for example).

C. Specific Aims. (< 1 page). This section states crisply the hypothesis you are testing, or the questions you will try to answer.  It also provides a list of each separate approach (aim) you will use to reach the overall goal.

D. Experimental Design and Methods (< 10 pages).  This is the meat of your proposal and should be organized according to the specific aims and presented clearly.  Critical experiments should be described so that examiners appreciate your mastery of the subject. Experiments, important controls and contingency plans need to be fully described. Give enough detail so the reviewer can judge if the experiment is likely to work. The reviewer is looking for indications that you have carefully thought out every step in the proposed procedure.  If you are not sure every step is feasible, so indicate and describe what you will do if the step doesn't work.  An important part of the "Experimental Design and Methods" section is a description of how data will be interpreted.  This is especially true for quantitative data. What is the meaning of the data you hope to collect?  At the end of the "Experimental" section, it is wise to put in a paragraph or two about possible pitfalls.  Nothing is guaranteed to work.  If you let the reviewer know what you think the major limitations are, then you make clear the fact that you have thought about them.  If you anticipate a potential problem, then you should indicate what alternative procedures you will use to get around it.

E. Figures and Tables.  Figures and tables are often useful as an aid to the text.  It is quite appropriate to reproduce figures from a review or other important article (state clearly from where taken).  Figures may also be useful to show the reader what data you expect and how the data will be interpreted.  Key figures and tables should be placed in the appropriate positions in the text and they count toward the page limits.

F.  References.  These should be in the regular journal format, with titles.

The oral exam

The oral component of the A-exam is a defense of the written proposal (please see the GGD handbook for details regarding the written proposal). It is presented to an Exam Committee of 4 faculty: the student’s Special Committee plus one additional faculty member. It is expected that the majority of questions that the exam committee will ask the student will directly relate to the proposal and to areas that are considered off-shoots of it; however no area is off-limit.  The Exam Committee will likely ask the student to explain, in more detail than the written format permits, background material, logic and rationale for choice of aims, and experimental protocols.

The Committee will likely also ask broadly-based questions on basic concepts, to ensure the student has strong command of foundational knowledge in GGD.  The committee member representing the minor subject area is particularly responsible to ascertain that the student has achieved competency in that area.

Although the Exam Committee may run the A exam in whatever way it deems appropriate, the Field recommends that during the exam, the mentor (thesis advisor) should not ask questions or make comments except when asked by other committee members or when clarification is needed. The intended goal of this policy is to dissuade the mentor, who may have a vested interest in the outcome of the exam, from stepping in to justify the research or the particular experimental approach being used.  The student is expected to fully defend the proposal by him/herself.  However, the mentor should participate fully in the discussion of the student’s performance, during the evaluation discussions once the student has left the room. 

In addition to evaluating the written proposal, its oral presentation and defense, and the student’s knowledge of basic concepts, the A exam is the time when the Committee will discuss and evaluate the potential of the student to accomplish significant dissertation research in a timely manner. In its evaluation discussions (carried out in camera, with the student out of the room) the Exam Committee will discuss the student’s course work and course performance, the student’s performance in the laboratory, as well as the motivation of the student for research.  

Some factors that may be judged in evaluation of the A-exam are:
- Course work
- Performance in research project  
- Breadth of knowledge   
- Ability to respond to questions
- Communication / presentation skills
- Regarding the A-exam proposal:
importance of the problem chosen
      demonstrating a command of the field.
      evidence of creativity in formulating experimental approaches
      feasibility of the proposed experiments
      whether a range of different approaches are brought to bear on the problem
      whether the scope of the proposed experiments is feasible for a 3-4 year project
      adequacy of control experiments
      clarity of the proposal

Possible outcomes

Possible outcomes of the A exam are listed below.  While one of these outcomes will apply in most cases, it should be noted that the final outcome is determined by the Exam Committee and they are not limited to the examples given below. 

1.  Pass. When the committee decides that the overall proposal, defense and progress are satisfactory. There may still be some small areas for improvement and these can be stated to the student verbally at the defense.

2.  Conditional Pass.  This option will be exercised when the committee judges that SOME aspect of the proposal and/or defense and/or the student's progress in the program needs substantial improvement.   In this case, the committee will specify the “condition” that must be met within a certain time-frame, before the student can receive a pass.  

      Some options for Conditional Pass:

      (a) The committee may specify that the entire proposal or that parts of it need to be revised within a certain time frame.  The extent to which the major professor wants to be involved in the rewriting is up to him/her.
      Some reasons for revision are:
            - The writing needs to be improved (for example, grammar, clarity, or logical flow of ideas).
            - Some aspect of the science needs to be rethought (for example, better controls, more cautious interpretation, or more detailed description).
            - An additional section needs to be incorporated into the proposal.
      (b) The committee may specify that the student carries out additional literature review, e.g. weekly written report of a paper, participation in journal clubs, etc.  This might be particularly helpful when the student appears to have weaker command of the literature surrounding an area.  

      (c) The committee may specify that the student complete a piece of research / a particular sub aim within a certain time-frame.  This is particularly relevant when the committee has some concerns about the ability and/or motivation of the student to complete the proposed research.   

      (d) Any other options that the committee deems to be helpful for the further training of the student.  

3.  Fail.  This option will be exercised when the committee judges that MOST of the proposal and/or defense and/or the student's progress in the program is inadequate

In the case of exam failure, the committee will usually recommend one of two actions.  If the committee has confidence in the overall ability of the student to complete the Ph.D. program,  they may recommend that the student retake the A exam.  In this case, they will specify whether an entirely new proposal on a different topic is to be written or whether they expect a major rewriting of the original proposal.  Note that the rules of the Graduate School specifies that a second A exam cannot be scheduled earlier than 3 months after the first.


If the committee feels that the gap between the student’s ability/motivation and the expectation of the program is too wide to be bridged, it may recommend dismissal of the student from the program.