Clinical Epidemiology Yellow Book

3.5 Thesis Guidelines

A. Introduction

Although didactic courses are an important part of the PhD/MSc program, conducting research and writing a thesis provides the main opportunities for developing both a broad perspective and in-depth knowledge of a particular area of research, either clinical or methodological (or both).

Earning a degree is more than simply completing a few courses, carrying out a piece of research and writing a thesis; it is the process of becoming a professional in a given area. A successful PhD/MSc means that the academic community accepts the candidate as a peer who has something worthwhile to say. The thesis demonstrates a wide and critical knowledge of the field, an ability to ask appropriate questions and set the research in its proper context, a mastery of the appropriate research techniques and an ability to communicate ideas and results have been communicated effectively to a group of peers. The thesis is about making an original contribution to a particular research field within a framework of research training. ‘Original contribution’ need not mean work worthy of a Nobel Prize. It does, however, mean finding a knowledge gap and answering the question(s) posed by that gap.

Original contributions in the area of clinical epidemiology may include:

  1. Scholarly enquiry into the theoretical foundations of clinical epidemiology, in areas such as study design, measurement of health or health care, and approaches to analysis and interpretation of the data derived from such studies.
  2. Development of new methods or tools pertinent to study design or measurement of health or health care.
  3. Significant advancement of existing methods or tools in study design, measurement or analysis.
  4. Application of existing methods or tools in such a way as to advance knowledge of health and health care.

B. Selection of a Thesis Committee

  1. CEHCR students will undertake a thesis under the supervision of a qualified IHPME faculty member whose interests lie primarily in Clinical Epidemiology and Health Care Research (CEHCR).
  2. All members must have an appointment at the University of Toronto. Temporary appointments are sometimes possible, but must be discussed with the CEHCR Director, Graduate Coordinator and IHPME Director.
  3. One other committee member must also have an IHPME appointment and an SGS appointment.
  4. The final member must have an SGS appointment but may be from outside IHPME.
  5. The supervisor must have an IHPME appointment and an Associate SGS appointment to supervise MSc students or a Full SGS appointment to supervise PhD students and must be approved to supervise Clinical Epidemiology students by the Director. Faculty who are appointed in other departments are not automatically approved to supervise students.
  6. The thesis committee should have a minimum of three members.
  7. Students should choose supervisors and committee members who are most helpful to them in the preparation of their thesis.

C. Role of the Thesis Supervisor

  1. The supervisor provides advice on all aspects of the thesis project. Specifically, he/she is responsible for providing direction to the student, advice on data sources and potential avenues of approach, instructions on the proper content and form of the thesis, review of the student’s progress, and serving as the first reader of the thesis. It is the responsibility of the supervisor to help the student think through methodologic issues and to raise questions about possible methodologic decisions faced/taken by the student.
  2. The supervisor and student are expected to read and sign a Statement of Agreement – [PDF] before undertaking thesis work.
  3. Additionally, the supervisor, in conjunction with the student, is expected to complete the Annual Student Study Plan by August 1 of each year the student is enrolled in the Program and return it to the CEHCR office.
  4. PhD students are required to meet with the CEHCR director or associate director and their supervisor before August 31 of each year to discuss the student’s progress.

For further information on supervisor role, please see the SGS website:  Find a Supervisor.

D. Types of Research Projects for a Thesis

A PhD thesis is one in which there is an element of originality (the work represents a unique contribution to the field) and the potential for 3 papers as a result (just a rough guideline).

Students can elect to analyse an ongoing study or design a new study. If analysis is the main focus of the thesis the student is not required to have designed the study. If the design is the main focus of the thesis, students must also do some data analysis related to the design of the study (e.g. pilot study, feasibility study, secondary data analysis). A study can involve a primary data collection (e.g. RCT, survey, observational study) or analysis of secondary data (e.g. administrative data, clinical database).

For full information on selecting a suitable topic for MSc or PhD, please refer to Section 1.2: Clinical Epidemiology – Selecting a Thesis Topic.

E. Thesis Proposal Approval Process (Revised March, 2011)

Bound copies of theses by Clinical Epidemiology graduates are available in the CEHCR Program office for reference only and are also available online through the University of Toronto library system.There are two steps in the thesis proposal approval process:

Step I: Approval of the thesis question and the composition of the thesis committee

By the end of the first academic year of enrollment in the CEHCR program, the student is expected to have:

  1. Confirmed his/her supervisor (supervisor ideally identified at the time of application to the Program);
  2. Confirmed his/her thesis topic; and
  3. Confirmed his/her thesis committee membership. This information is to be submitted for approval to the CEHCR office by the end of May in the first year of enrollment.

Once the supervisor has been selected, the student should meet with his/her thesis supervisor to discuss the make-up of the remainder of the committee. It is important that the committee be balanced in terms of background/expertise and to include content experts, if relevant.

This information should be forwarded to the CEHCR Program where it will be circulated to the Program Director and Associate Program Director for approval.

Note: the main purpose of Step I is to approve your topic, the composition of the committee and its relevance to your selected topic.

Step II: Development of Full Thesis Proposal

Once the thesis topic and composition of the thesis committee (Step I) have been approved by the CEHCR Program Director (or Associate Program Director), students should work with their thesis committee to develop a more detailed proposal including the research design and procedures for data collection and data analysis.

The Supervisor (and student) must ensure that all members of the thesis committee are thoroughly familiar with the research proposal at an early stage of development and fully participate in all phases of the research. This is to avoid potential disagreements at a later stage.

The Thesis Supervisor should arrange for the proposal to be presented at one of the hospital or research institute based Clinical Epidemiology Rounds. The Supervisor and members of the Thesis Committee should be present for this preliminary presentation.

The Supervisor must inform the CEHCR Office of the time and date of the presentation at least 30 days in advance in order to adequately notify fellow students and clinical epidemiology faculty.

In addition, at the same time, the Thesis Supervisor and student should submit a 3-5 page outline of an MSc-quality thesis proposal including:

  • The research question(s)
  • Background and a brief literature review indicating the importance of the research
  • A preliminary research design, including the likely methods to be used
  • The data source(s), and
  • A preliminary analysis plan.

At least three additional IHPME faculty members are required to be present at this presentation. It is the responsibility of the supervisor to ensure that these committee members are present prior to the start of the presentation. If three additional IHPME faculty members are not present, the defence must be cancelled and rescheduled. The proposal defence should consist of a 20 minute presentation, followed by 20 minutes for questions and answers, followed by 20 minutes for the committee and additional IHPME faculty to meet.

PhD defence/transfer

The process for a PhD transfer defence and for a PhD Step II proposal are similar. The format is similar to that of a MSc proposal except that one of the additional faculty can serve as a reviewer of the proposal. The reviewer should be selected using the following the criteria:

  • The supervisor and the student should select the reviewer and inform the IHPME office of the reviewer’s name at least 2 weeks prior to the defense date.
  • Students are required to provide the reviewer with a copy of their written proposal at least 2 weeks in advance of their presentation.
  • The reviewer should be external to the committee but can be internal to IHPME
  • The reviewer should be someone who has sufficient expertise in the student’s area of research
  • The reviewer is expected to actively participate in questioning the student. Ordinarily, the reviewer will be the first questioner and will be given more time for questions than other attendees.
  • No formal written comments are required from the reviewer.
  • The reviewer need not have an SGS appointment, as long as they are external to the student’s committee and a recognized expert in the field
  • If the reviewer has an IHPME appointment, two additional IHPME faculty members must be present. If the reviewer does not have an IHPME appointment, three additional IHPME faculty member must be present.

Following this presentation, the student is excused and faculty who hold an IHPME faculty appointment and the thesis committee members will meet briefly to discuss and vote on the suitability of the thesis proposal.  Other faculty members should not attend this discussion.  The thesis supervisor will provide feedback to the student based on recommendations by the group.

After the Rounds presentation, the student must submit a revised proposal, incorporating feedback received at the proposal defence, to the CEHCR office for final approval. The proposal cannot exceed 5 pages in length, must be single-spaced and in 12-point Times New Roman font with 1 inch page margins.  The proposal should follow the format outlined in Section F.

The full proposal must be accompanied by a letter from the supervisor (email correspondence is acceptable) including the following:

  • the date and location of the thesis proposal
  • the committee members who were present
  • a statement that the proposal has been approved by the thesis committee and that it incorporates feedback received at the presentation

The student cannot proceed with the study until this documentation has been received by the CEHCR office.

All students must obtain University of Toronto research ethics approval for their research in addition to any approvals required at their home institutions or those of their supervisors.  Applications for approval can only be submitted after the proposal has been approved by the CEHCR director.  Students must be listed as a researcher or investigator with the relevant Research Ethics Boards.  While the University of Toronto sometimes exempts student research from full ethics review, students must apply for such exemptions and supply the appropriate documentation to the IHPME graduate office.  Students must never assume that their research is exempt from ethics approval.  Students who not have documented University of Toronto ethics approval will not be allowed to proceed to their defense.

F. Format of Full Thesis Proposal for Submission to CEHCR Office

Note: SGS guidelines for formatting a thesis that is ready for defense can be found at the end of this Section.

Objective: The exact question(s) to be addressed by the thesis proposal.
The deficit in current knowledge to be addressed and the importance of the question.
Research Design: The nature of the study architecture (descriptive or analytic; retrospective or prospective; experimental or observational; randomized or non-randomized; cross-sectional or longitudinal; etc.)
Setting: The location of the study and the nature of the patient population.
The clinical disorder and key sociodemographics, the number and selection of participants.
Research Procedure: The intervention, exposure or investigational manoeuvre and proposed monitoring.
Main Outcome Measures: The primary and secondary outcome measures(s), their frequency and measurement characteristics (particularly in settings and populations similar to those proposed in the study)
Sample Size/
The number of subjects needed for the key outcome measures and the proposed plan of analysis.
Feasibility: The availability of data or subjects and the expected participation rate; resources available for the completion of the research.
Ethics Approval: Proposal should indicate that it will be submitted for ethics approval.

Students may wish to refer to the following references:

Naylor C.D., Williams I.J., Guyatt G. Structured Abstracts of Proposals for Clinical and Epidemiological Studies; J Clinical Epidemiology Vol. 44 pp. 731-737, 1991.

AD HOC Working Group for Critical Appraisal of the Medical Literature. A Proposal for More Informative Abstracts of Clinical Articles. Annals of Internal Medicine Vol. 106 pp. 598-604, 1987.

G. Reading of the Thesis

Committee members must read the thesis and each member must conclude that it is an acceptable piece of work. Typically, a student will provide each reader with a completed first draft, and the readers will make whatever recommendations they feel are necessary for revision so that a final draft will be acceptable. It is the responsibility of the supervisor to get committee members and the student together to obtain a common understanding of what changes in the first draft are necessary for an acceptable subsequent document. If the recommendations for change are at all contentious or detailed, the student is entitled to a written statement from the committee outlining exactly what has to be done.

When you choose to defend your thesis may have bearing on the academic fees that you will have to pay. Please note the dates below. The deadline for submission of completed thesis means that all revisions suggested at the defense must be completed, signed off and delivered to the School of Graduate Studies by that date.

Deadlines – SGS Sessional Dates

Deadline Request for Defense Last Scheduled Defense Deadline for Submission of Completed Thesis to SGS Expected Convocation
July 7, 2020 August 18, 2020 September 15, 2020 (PhD)
October 2, 2020 (MSc)
November mid-December January 15, 2021 (PhD)
January 22, 2021 (MSc)
March (in absentia)
or June
January 29, 2021 April 2, 2021 April 16, 2021 (PhD & MSc) June

H. Process For Setting Up Thesis Defense

It is necessary to give considerable lead-time in setting up the oral defense. Two months (eight weeks) prior to the requested date of defense, the student and/or thesis supervisor should contact the CEHCR program office 416-946-3486. At this time, an Oral Defense Membership Form (this can be obtained from the CEHCR program office; please do not use the general HPME form) requesting information about the composition of the committee, names of potential external and internal reviewers, and preferred oral defense dates is completed and sent to the CEHCR program office.

Important! – The thesis supervisor must ascertain the written agreement from all the thesis committee members that the thesis is ready for final and formal defense. The thesis committee will need a minimum of two weeks for final approval before beginning the thesis defense process.

1. Defense Committee

The initial process for the defense is to select the members of the defense committee.

a. The Final Defense Committee

The final defense committee includes at least 4 but no more than 6 voting members.  IHPME strongly encourages selecting a date and time that accommodates the entire defense committee.

The defense committee includes:

  • The student supervisory committee.  Up to 3 committee members may vote at the examination.
  • An external examiner / appraiser.  IHPME strongly prefers that the external appraiser be a voting member of the committee.
  • An internal examiner who is a voting member of the committee.
  • For PhD examinations only, a departmental representative is a voting member of the examination committee.

b. Examiners and Appraisers

All examiners and appraisers must have:

  • An appointment with a graduate department (for examiners at the University of Toronto, this is the School of Graduate Studies).
    Note: Internal examiners may be granted a temporary appointment for the purpose of the thesis examination if sufficient advance request (greater than 2 months) is made to the Program Director (who in turn makes the request to the IHPME appointments committee).
  • Recognized expertise in the field being examined.

For an MSc thesis defense:

Internal Examiner:

  • The MSc internal examiner should be internal to the department of IHPME
  • The MSc internal examiner should have an arm’s-length relationship with the student and supervisor.  The criteria for judging whether a relationship is arm’s-length will generally be similar to that of an external examiner but the CEHCR director and the graduate coordinator will have flexibility in judging the nature of the relationship on an individual basis and may, for example, approve individuals from the same research institute or hospital division at their discretion.

External Examiner:

  • The MSc external examiner should be external to IHPME.  The examiner can be from the University of Toronto or another accredited academic university
  • The MSc external examiner should have an associate professor rank or higher
  • The MSc external examiner should have an arm’s-length relationship with both student and supervisor, defined as follows:
    • No publications or grants with the student or supervisor for the last 6 years
    • The external examiner should not have served in a student/supervisor relationship in the past six years;
    • The examiner should not be in the same research institute or hospital division as the student or supervisor.

For a PhD thesis examination:

It is the responsibility of the Supervisor and Student to nominate a suitable External Examiner/Appraiser.  The supervisor recommends the External Examiner to the CEHCR director and the Graduate Coordinator for approval.

Internal Examiner:

  • The PhD internal examiner should have an associate professor rank or higher
  • The PhD internal examiner should be internal to the University of Toronto. Preference is for an examiner who is external to IHPME, however this is not a strict requirement and those who are internal to the department of IHPME are eligible
  • The PhD internal examiner should not be in the same research institute or hospital division as the student or supervisor
  • The PhD internal examiner must have an arm’s-length relationship with the student and supervisor as defined by the same criteria as the external examiner.

External Appraiser:

  • The PhD external appraiser should have an associate professor rank or higher
  • The PhD external appraiser should be external to the University of Toronto
  • The PhD external appraiser should have an arm’s-length relationship with both student and supervisor, defined as follows:
    • No publications or grants with the student or supervisor for the last 6 years
    • The external appraiser should not have served in a student/supervisor relationship in the past six years;
    • The appraiser should not be in the same research institute or hospital division as the student or supervisor.

Although the external appraiser need only fulfill the role of Appraiser and need not, ultimately vote, IHPME, strongly encourages Appraisers to act as External Examiners and to vote at the examination committee. The External Examiner can participate in person or by teleconference.

c. The student/supervisor is responsible for:

  • Securing the members of the defense committee;
  • Setting the date/time of the defense; and
  • Forwarding the thesis proposal to all members as well as a copy to the Clinical Epidemiology program office.

d. The Clinical Epidemiology Office is responsible for:

  • Securing the Chair;
  • Booking the room and AV equipment; and
  • Confirming the arrangements with the Defense Committee.

2. Supervisor’s Role

  • When all members of the candidate’s supervisory committee agree that the thesis is complete and ready for defense, contact the CEHCR Program office. Submit a completed and signed PhD or MSc Thesis Committee Meeting Report to the Graduate Assistant.
  • Complete the PhD Final Oral Examination Booking Request form or MSc Oral Defense Membership form according to the guidelines below in consultation with the Graduate Coordinator and/or Graduate Assistant.

3. Student’s Role

  • After approval of the thesis defense committee, the candidate and/or the supervisor will contact all members of the thesis defense committee and propose at least two potential dates.
    (Please note that your choices for internal and external examiners must be approved by the Program Director before you can set a firm defense date. Your PhD or MSc Thesis Committee Meeting Report, MSc Oral Defense Membership or PhD Final Oral Examination Booking Request form, must be received by the CEHCR office before a final defense date will be set.)
  • Ensure that the thesis follows the format indicated by the University of Toronto and the National Library.
  • Distribute the thesis to all defense committee members at least four weeks for MSc (six weeks for PhD) prior to the defense.
  • All CEHCR MSc defenses and PhD oral examinations are held at the Health Sciences Building, 155 College Street, 4th Floor. They are held Monday through Thursday (between 9 a.m. and 5:00 p.m.) or Friday (between 9 a.m. and noon).

4. Graduate Coordinator’s Role

  • Ensure that student has completed all other degree and course requirements. (Note: No defense can be scheduled if there are any outstanding grades.)
  • Finalize composition of thesis defense committee in consultation with the Supervisor and Graduate Chair.

5. Graduate Assistant’s Role

  • Inform the internal and external examiner of their role including the need to prepare a written confidential critique; copies should be available at the time of the defense.
  • Arrange for a meeting room and A/V equipment; distribute notices, and appoint an independent, non-voting chair for MSc students only (SGS appoints a chair for PhD defenses).
  • Familiarize the student with the examination process and expectations.

I. What to Expect at the Defense

  • A quorum of the Defense Committee must be present.
  • The Chair appointed by the Graduate Department follows clearly established Examination procedures.
  • Student is asked to leave the room.
  • The Defense Committee discusses the internal and external reviews.
  • The student is recalled and presents his/her thesis within 20 minutes.
  • One or two rounds of questions are posed to the student. (*Note: Questions can be asked about both the oral and written presentations.)
  • Student is asked leave the room.
  • The Defense Committee votes on the acceptability of both the thesis and the oral defense.
  • The Supervisor informs the student if modifications are required.

J. After the Defense

  1. Student makes modifications to the thesis as required. These are reviewed by the faculty member(s) designated at the end of the oral defense.
  2. Supervisor informs the Graduate Department in writing that the student has made revisions/corrections.
  3. As of September 1, 2009, the School of Graduate Studies will ONLY accept the submission of theses in electronic format. Please view SGS – Producing your Thesis webpage for information on electronically submitting your thesis.
  4. If the student wishes to publish a hard copy, it is the student’s responsibility to prepare the final manuscript for binding according to the guidelines, and to submit the thesis for binding. Binding should be hard cover, buckram, with gold lettering and a dark colour binding. IHPME would welcome a hard copy of a student’s thesis.
  5. The Graduate Department prepares the Degree Recommendation for the School of Graduate Studies for MSc students. (Note: Students who have not paid their fees will not be granted a degree.)
  6. Students failing to complete all steps by the SGS deadlines will be required to register and pay fees for another term.
  7. The School of Graduate Studies notifies students about convocation arrangements 4 – 6 weeks in advance.

K. Summary

The Thesis Defense Process should follow this schedule:

  1. At least two months prior to the expected defense date
    1. Thesis supervisor or student to contact the CEHCR office (416) 946-3486 to initiate the process;
    2. CV’s of internal & external reviewers sent to graduate assistant for review;
    3. An email containing the Oral Defense Membership form, Committee Meeting form and defense guidelines will be sent to the student.
  2. At least 6 weeks for MSc (8 weeks for PhD) prior to expected defense date
    1. Student to give copy of the thesis to the supervisory committee for final review and approval;
    2. Thesis supervisor obtains written thesis committee agreement via Thesis committee Meeting Report form;
    3. Once the Oral Defense Membership form is completed, the student send the form back to the CEHCR program office for finalization of defence details.
  3. 4 weeks for MSc (6 weeks for PhD) prior to defense date
    1. Student to distribute hard copies and PDF of thesis to the CEHCR office and all defense committee members including internal and external reviewers.