Genetics

Genetics Student Handbook

ACADEMIC REQUIREMENTS: COURSES (9/12)

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. Courses not taken for a letter grade do not count toward the total of nine courses.

Core Requirements
GENE 200 (Training Camp)
BIOS 200 (Foundations in Experimental Biology)
GENE 205 (Advanced Genetics, Win)
GENE 210 (Genomics and Personalized Medicine) Class URL
GENE 211 (Genomics) Class URL
GENE 215 (Frontiers, Fall & Spr) – must register each quarter
MED 255 (The Responsible Conduct of Research, Aut, Win, Spr) – register early, fills up fast
bHRP 258 (Introduction to Probability and Statistics for Clinical Research, Spring) Or
bSTAT 141 (Biostatistics, Fall)

Other Electives (at least 2 required) such as
GENE 214 (Representations and Algorithms for Computational Molecular Biology, Spr)
GENE 244 (Introduction to Statistical Genetics, Aut, alternate years)
GENE 245 (Computational Algorithms for Statistical Genetics, Spr, alternate years)
GENE 233 (Biology of Small Modulatory RNAs, Fall, alternate years)
GENE 206 (Epigenetics, Win, not every year)
GENE 218 (Computational Analysis of Biological Information: Intro to Python for Biologists, Smr, alt yrs)
BIO 244 (Molecular Evolution, Spr)
GENE 210 (Personalized Medicine, Spr)
BIO 222, BIO 237, BIO 258, CBIO 275, CS 278, PATH 210, DBIO 201, DB 210, GENE 221, GENE 234, GENE 235, IMM 230, STAT 202.
GENE 267 (Molecular Mechanisms of Neurodegenerative Disease, Win, alternate years)

aCourses outside the medical school (e.g., CS, STAT) are encouraged and can be applied to the minimum requirement of nine courses.

bThe statistics requirement counts towards the minimum of nine courses. Students may petition the Graduate Program Director to receive approval for any course, including statistics, that they have completed elsewhere and that may substitute for a required Genetics course. All such petitions must be submitted no later than Friday of the second week of classes during the quarter in which the course that is the subject of the petition is taught.

Example first year curriculum

Fall – 10 units
GENE 200 – Training Camp
BIOS 200 – Foundations in Experimental Biology
GENE 215 – Frontiers in Biology Rotation

Winter – 10 units
Genetics 211 – Genomics
GENE 203 – Advanced Genetics
GENE/MED 255 – The Responsible Conduct of Research Rotation

Spring – 10 units
GENE 215 – Frontiers in Biology
HRP 258 – Introduction to Probability and Statistics for Clinical Research Rotation and Electives

Your Individual Development Plan and Annual Planning Meetings

Your Individual Development Plan (IDP) and annual planning meeting with your advisor are intended to help you:

As of March 31, 2014, the Committee on Graduate Admissions and Policy (CGAP) has adopted a new policy requiring all Biosciences PhD candidates and their mentors in the Schools of Medicine and H&S to create and discuss their Individual Development Plans (IDPs) on an annual basis.
Students and their advisors share responsibility for completing the IDP, as well as the consequences of not completing the IDP by the deadlines below. Failure to comply with IDP requirements will

Key Deadlines

Action

First Year Students

All Other Students

Schedule a planning and mentoring meeting with your advisor

Within 30 days of joining your thesis lab

Before June 1

Download and complete the appropriate IDP form. (Ideally, share the completed form with your advisor in advance.)

Before your meeting

Before your meeting

Hold your annual planning/ mentoring meeting with advisor

Within 30 days of joining your thesis lab

By August 1

Verify that you and your advisor met to discuss your IDP

Within 30 days of joining your thesis lab

By August 1

See http://biosciences.stanford.edu/current/idp/ for more information and IDP forms, including extensive FAQs and resources for both faculty and students.

Questions? Please email somcareers@stanford.edu

ACADEMIC REQUIREMENTS: QUALIFYING EXAMINATION

Students in the Genetics Graduate Program take the Qualifying Examination in the Fall 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.

Qualifying Exam Topic

The research topic of the Qualifying Exam should be within the same general area as the expected dissertation work, but should not be specifically on their current work in the lab, projects being done by others in the lab, or a project that the PI has written about in a grant proposal. For example, a Qualifying Exam for a student in a lab that studies aging should be in the general area of aging but address questions not actively investigated by the lab. A goal of this ‘in area, off thesis topic’ approach is to give students the opportunity to master necessary background knowledge for their dissertation, while providing the opportunity to think independently and creatively beyond the constraints of model organism(s), resources, and technical expertise present in their thesis lab.

Purposes of the Qualifying Exam

The purposes of the Qualifying Exam are for students to:

  1. demonstrate understanding of the fundamentals of genetics, genomics, and molecular and cellular biology.
  2. learn the essential background knowledge for their expected thesis area.
  3. demonstrate the capacity for independent, creative thinking within their chosen topic area.

In the Qualifying Exam, the student should:

  1. identify interesting unanswered questions and pose hypotheses concerning those questions.
  2. design experiments that test the hypotheses or answer 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.
  3. anticipate possible outcomes that might be obtained from the proposed experiments and interpret the results to draw appropriate conclusions.
  4. suggest alternative experimental approaches if an initial approach fails to answer a question.
  5. consider subsequent questions, which may depend on the results obtained in the initial experiments.

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 set up their committee in the Spring quarter to schedule their exam date for the Fall quarter. The committee should include:

  1. the 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.

Because the Qualifying Exam topic is in the same general area as a student’s expected dissertation, there should be substantial overlap between the examiners for the Qualifying Exam and the expected composition of the Dissertation Committee. As a result, most examiners will have expertise in the general area of the proposal and one or more examiners should have specific expertise on the topic of the Qualifying Exam proposal. Students should ask their advisor for suggestions regarding examiners/thesis committee members.

The Written Proposal

The Qualifying Exam proposal should reflect the student’s thinking and writing and demonstrate her/his ability to think critically and write well. The proposal must have the following format:

Title Page: just that – proposal’s title and student’s name.

Abstract: a summary of the entire proposal, 1-2 paragraphs and about 250-400 words long. Put this on a separate page just after the title page. The abstract should include a statement of the specific aims.

Specific Aims: one page, describing the major goals of the proposal in clear, concise language. The aims page should answer several questions. What is the overall conceptual framework for the studies? What is the rationale for constructing the framework? What does the investigator plan to do or test (without going into a lot of detail)? Proposals should have 3 logically connected specific aims, the third of which should be a higher risk, pioneering idea. For purposes of clarity, some proposals will contain subaims for one or more aims. Each aim or subaim should be described in one or two pithy sentences. An aims page often ends with a description of how achieving the proposed aims will advance the field.

Background and Rationale: up to 4 pages describing the system and problem the student wants to understand, including published knowledge that bears on the problem and the facts and hypotheses that led the student to propose their particular set of experiments.

Research Design and Methods: this is the meat of the proposal, where the student describes the design of the research that s/he expects to do, the experiments themselves, the interpretation of possible results s/he will obtain, and where s/he will go with the results. It is important to structure this section such that each specific aim or subaim is a distinct subsection. Re-listing the aim or subaim at the beginning of each subsection can improve clarity.

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 (wet and/or dry) 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 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 specific topic, questions to be asked, and experimental approach must be devised by the student. S/he may seek help from peers (e.g., a practice presentation to classmates), but input from the advisor, other senior lab members and faculty should be limited to general suggestions.

Important Qualifying Exam Due Dates

Exams will usually be taken during a 6-week period in the Fall quarter of the second year, starting in early October and ending the Friday before Thanksgiving. An abstract describing the specific aims of the Qualifying Exam Proposal must be given to the Graduate Program Director and thesis advisor early in the Fall Quarter, prior to the start of the exam period. This deadline serves to ensure that students start working seriously on their proposal in time to complete the Qualifying Exam within the specified period. Inform the Graduate Program Administrator of the composition of your committee, date and time of your exam as soon as you can and no later than the start of the exam period. Students must provide a copy of their 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.

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 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, provided by the 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 Winter 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 Winter Quarter of that same academic year.

ADMISSION TO CANDIDACY

When a student has successfully completed her/his Qualifying Examination, s/he should submit an Outcome of Qualifying Exam form to the Genetics Graduate Program Administrator indicating that they have passed their exam. Once a student has passed their qualifying exam, successfully completed all required courses (exclusive of electives), and had his/her first Dissertation Committee meeting, s/he can be “Admitted to Candidacy” by the Department of Genetics, a process done by the Graduate Program Administrator.

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 their second year of study.

Once the 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 Director’s recommendation.

Any interruption of graduate work longer than one month must be by official leave of absence.

ACADEMIC REQUIREMENTS: DISSERTATION ADVISORY COMMITTEE

The dissertation is expected to be an original contribution to scholarship, to exemplify the highest standards of the discipline, and to be of lasting value to the intellectual community. The work for the dissertation will be in progress from the time a student chooses a permanent laboratory in which to work. Before defending her/his dissertation, every student must have submitted for publication or published at least one first author or co-first author manuscript arising from their thesis work.

Dissertation Advisory Committee

The Dissertation Advisory Committee is a critical aspect of a student’s graduate training. Preparing for the first meeting will stimulate a student to think deeply about potential thesis projects and apply knowledge gained from coursework and the Qualifying Exam to their project of choice. This and subsequent meetings provide a regular forum for a student and their thesis advisor to receive advice from other faculty members. The Dissertation Advisory Committee serves as the core of a student’s Dissertation Reading and Thesis Exam Committee. At the time of the thesis defense, it is important and useful for students to have examiners who are familiar with their work. Moreover, the relationships developed with committee members over the years will serve students well when transitioning to positions after graduation.

A student should select the Dissertation Advisory Committee in consultation with her/his advisor. At least three Genetics faculty members must serve on the committee, including a student’s advisor if s/he is a member of the Genetics Department. If a student’s advisor is not a member of the Genetics Department, three Genetics faculty members must be recruited for a total of four faculty. If desired, additional faculty members can be added from any appropriate department at Stanford, including Genetics. Generally, members of the Dissertation Advisory Committee must also be members of the Academic Council. Changes to the Dissertation Advisory Committee are allowed, but must be reported promptly to the Genetics Graduate Program Administrator.

A student’s first committee meeting should be no later than the end of the Spring quarter of their second year. The first meeting will consist of a thesis project proposal and include a three-page (minimum length) written summary. A student and her/his advisor should agree on an appropriate format for the summary, which should be provided to the committee a week in advance. Students are not required to present results from their experiments at the first meeting. Subsequent meetings will be held at least once every twelve months thereafter. Students should fill out the attached "Dissertation Advisory Committee Meeting Form" after each meeting and submit a signed form to the Genetics Graduate Program Administrator so that the Department has a record of their meetings. Failure to provide evidence of a committee meeting according to the schedule described above may result in withholding of a student's stipend payments until the requirement is met.

FORMS:

Outcome of Qualifying Exam
Dissertation Advisory Committee Meeting Form

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