Stanford School of Medicine
Genetics–

Genetics Student Handbook

ACADEMIC REQUIREMENTS: COURSES (9/07)

Course Requirements For Ph.D. or M.S. Degree

All students must take a minimum of nine medical school coursesa divided into three general categories (see below) and register for exactly 10 units each quarter (including summer). Students must earn a minimum grade of B- in all nine courses and maintain at least a B average for continuation in the program.

Category I: Core Requirements
GENE 203 (Advanced Genetics, Fall, 4 units)
GENE 215 (Frontiers, Fall, 1 unit)
GENE 222 (Method & Logic, Win, 3 units)
MED 255 (The Responsible Conduct of Research, Win, Aut, Spr, 1 units)
bSTAT 141 (Biostatistics, Fall, 4 units)

Category II: Genetics Electives (At least one of the following)
GENE 211 (Genome Biology, Win, 3 units)
GENE 214 (Representations and Algorithms for Computational Molecular Biology, Spr, 4 units)
GENE 244 (Introduction to Statistical Genetics, Fall, 3 units)

Category III: Other Electives such as
BIOCHEM 241 (Biological Macromolecules, Fall, 3 units)
CSB 210 (Signal Transduction Pathways and Networks, Win, 4 units)
DBIO 210 (Developmental Biology, Spr, 5 units)
MCP 256 (Molecular Physiology of Cells, Spr, 4 units)
GENE 233 (Biology of Small Modulatory RNAs, Fall, 2 units alternate years, not in 2006)
GENE 235 (C. elegans Genetics, Spr, 2 units, alt. years)
aCourses outside the medical school (e.g., CS, Stat) are encouraged, but can only be applied to the minimum requirement of nine courses with permission from the Graduate Program Directors.
bThe statistics requirement counts towards the minimum of nine courses. Students may petition the Graduate Program Directors to receive approval for any courses, including statistics, that have been completed elsewhere and that may substitute for required courses in the Department of Genetics Graduate Program, but such students must still take nine courses.

Possible first year curriculum

Fall
GENE 203 (Advanced Genetics)
GENE 215 (Frontiers in Biology)
GENE 260 (rotation)
STAT 141
Winter
GENE 222 (Method & Logic)
GENE 255 (The Responsible Conduct of Research)
GENE 260 (rotation)
GENE 211 (Genome Biology)
Spring (pick and choose)
GENE 260; GENE 214, DB210, MCP256 or other electives

ACADEMIC REQUIREMENTS: QUALIFYING EXAMINATION

Students in the Genetics Graduate Program take the Qualifying Examination in the Winter Quarter of their second year of study. There are two parts to the exam, a written research proposal and an oral examination. Students must pass both parts of the exam to qualify for doctoral studies.

The Qualifying Exam research topic must be distinct from other research conducted by the student so that the student can become thoroughly familiar with a new area of investigation. For example, a Qualifying Exam topic should be different from a student’s undergraduate research and not be closely related to the student's likely area of dissertation research.

Qualifying Exam Committee
A student’s Qualifying Exam Committee is composed of four or more faculty members. It is the student's responsibility to arrange faculty for the committee and to set a time and place for the exam.Because it may be difficult to get all committee members together at the same time, it is recommended that a student begin in early December to set up their committee and schedule their exam date. The committee should include:

  1. Student’s advisor (s/he generally does not ask questions or comment during the exam).
  2. At least two members of the Genetics Faculty (a complete list of faculty is available on the departmental web site).
  3. At least one other faculty member. If a student’s advisor is not affiliated with the Genetics Department, this ‘other’ member must be affiliated with Genetics. All other students can fill out their committee with faculty from any relevant department, including Genetics.

A member of the Genetics Department Curriculum Committee (GCC) will attend and chair the exam. If a student has not already chosen a member of the GCC in 2-3 above, a member will be assigned to their committee.

Purpose of the Qualifying Exam
The purpose of the qualifying exam is to demonstrate that a student has begun to master the following:

1. Learning the background knowledge and experimental basis for a particular biological system, such as cell cycle regulation, gene expression regulation, neurobiology of a particular process or phenomenon, etc.
2. Identifying interesting unanswered questions concerning the biological system, and posing hypotheses concerning those questions.
3. Designing experiments that test the hypotheses or answers the questions. This means that the student needs to understand what types of experiments are feasible, how to execute them, what their limitations are, and the types of data that result from particular types of experiments.

  1. Anticipating possible outcomes that might be obtained from the proposed experiments and interpreting the results to draw appropriate conclusions.
  2. Suggesting alternative experimental approaches if an initial approach fails to answer a question.
  3. Considering subsequent questions, which may depend on the results obtained in the initial experiments.
  4. An understanding of the fundamentals of genetics, genomics, and molecular and cellular biology.

The Written Proposal
The Qualifying Exam proposal should demonstrate a student’s ability to think critically and write well. The experimental strategies covered in GENE 222 and the required final research proposal should provide excellent preparation for formulating and writing a Qualifying Exam proposal. The proposal should have the following format:

The Qualifying Exam proposal is a maximum of 15 (usually 10-15) pages of 1.5-spaced text, not counting the references. The volume written is not the point, obviously; it is the content that is important. Students should strive to ask questions that can be experimentally tested by one or two people over a three- to four-year period. For instance, a proposed set of experiments that would abruptly end if a particular result were obtained early in the process is neither a good Qualifying Exam proposal nor a good NIH grant proposal. Likewise, proposing a set of experiments that requires the entire output of a 10-person lab for five years is way too much and would be perceived as “overly ambitious”, a common criticism of first-time grant applicants. The student is allowed to rely on reagents and knowledge from other laboratories, but most of the student’s proposal must be based on work that s/he (and, optionally, one more person) could do in a few-year period.

Students have sole responsibility for the content and form of their proposal. The biological system, questions to be asked, and experimental approach must be devised by the student. However, students are encouraged to seek, as needed, the advice of their thesis advisor and other students to refine their ideas. One or more practice oral exams (see below) are also encouraged, if needed.

Important Qualifying Exam Due Dates
An abstract describing the specific aims of the Qualifying Exam Proposal must be given to the Graduate Program Directors and thesis advisor by the first Monday in December in the Fall Quarter of the student's second year. This deadline serves to ensure that students start working seriously on the proposal in time to complete the qualifying exam within the specified period (see below). Inform the Graduate Program Administrator of the composition of your committee, date and time of your exam no later than the first week of Winter Quarter. Students must provide a copy of the Qualifying Exam Proposal to all faculty members on their Qualifying Exam Committee at least one week in advance of the exam date, and earlier if requested by the Committee. The Exam should be taken between January 15 and February 15 of the Winter Quarter of the second year. If it is not possible to schedule a meeting within this time period because of prior faculty commitments, the exam can be scheduled in the last two weeks of February. Under no circumstances should the exam be taken later than the last day in February without the prior approval of the Graduate Program Directors.

Oral Examination Format
The Qualifying Exam usually lasts about an hour-and-a-half, so the student should schedule the faculty and the room for two hours to play it safe. The will student will begin with a 5-10 minute introduction summarizing their proposal in as succinct a way as possible. No more than 2-3 slides per aim should be used. The student should state the problem, any specific hypotheses, and the general experimental approach that will be used. The student does not need to go into specific experimental detail in this introduction, as this will be probed later with questions from the faculty. The student may also use this time to bring up any changes they decided to make in their proposal after they submitted it to the faculty. The written proposal will serve as a starting point for a broader discussion of biological principles and knowledge.

Outcome of the Exam
Prior to the exam, each student is responsible for providing her/his committee with an "Outcome of Qualifying Exam" form (Appendix). These forms can be copied from the Appendix of this document or obtained from the Genetics Graduate Program Administrator. Immediately after the exam, the faculty will give the student feedback on this "Outcome of Qualifying Exam" form regarding how the student did and their evaluations about their strengths and areas that need work. There are three potential outcomes of the Qualifying Examination:

  1. Unconditional pass - no additional work is required.
  2. Conditional pass - specific work is required to receive a passing grade. This would usually be additional written work or separate meetings with individual faculty to demonstrate that the student has mastered an area that needs improvement.
  3. Incomplete - exam must be taken over to receive a passing grade.

Regardless of the grade, the "Outcome of Qualifying Exam" form, with signatures from the committee, and a copy of the Qualifying Examination must be filed with the Genetics Graduate Program Administrator, so it can be added to the student’s Ph.D. Progress file.

If the Qualifying Exam Is Not Passed

Student Responsibilities
If the student receives an incomplete grade on their Qualifying Exam, they must retake the exam and earn a passing score by the end of Spring Quarter of that same year in order to be admitted to candidacy for a doctorate from the Department of Genetics (see below). Students should consult with faculty members and their committee for advice on how to prepare for the second exam.

Committee Responsibilities
Faculty members on a Qualifying Exam Committee should plan to offer the student advice on how to prepare for the second exam. Faculty should also be aware and remind the student that the second qualifying exam must be completed and passed by the end of Spring Quarter of that same year.

ACADEMIC REQUIREMENTS: APPLICATION FOR CANDIDACY

In the quarter after the Qualifying Examination is successfully completed, students are Admitted to Candidacy by the Department of Genetics. When a student submits an Outcome of Qualifying Exam form to the Genetics Graduate Program Administrator indicating that they have passed their exam, the student’s candidacy will be entered into the computer system. Students who are admitted to candidacy should register for GENE 399 (instead of GENE 260) under their advisor’s section for subsequent quarters until achieving terminal graduate registrant status (TGR) in the spring quarter of their fourth year.

Admission to candidacy for the Ph.D. program is an acknowledgment of the Student’s potential to complete successfully the requirements for the Ph.D. The University requires that students in the Ph.D. program be admitted to candidacy by the end of the second year of study.

Once a student has been admitted to candidacy, the status is valid for five years subject to termination by the Department of Genetics if progress is unsatisfactory. In special circumstances it may be renewed by the submission and approval of a new application or extended upon the Graduate Program Directors’ recommendation. Any interruption of graduate work must be by official leave of absence.

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