MBP 1018Y: Oncology

1. MBP 1018Y: Oncology Wednesdays, 10 a.m. – 12 noon January 12 – May 04, 2011 inclusive 620 University Avenue, Room 7-709 (CFIBCR Seminar Room)

2. Outline • Introductions • Course Contact Information • Significant Dates • Course Overview – Goal, Format • Course Evaluation • Course Schedule • Tutorial

3. Contact Information • Course Coordinator: Dr. Brad Wouters • Room 10-116, Princess Margaret Hospital • 610 University Avenue • Tel: 416-581-7840 • E-Mail: bwouters@uhnresearch.ca • Teaching Assistant: Dr. Mahadeo Sukhai (Day-to-day contact person) • Room 9-620, Princess Margaret Hospital • 610 University Avenue • Tel: 416-946-4501 x 5036 • Email: m.sukhai@utoronto.ca

4. Significant Dates • January 12 - Introductory session • January 26 - Submission of abstract of thesis project • February 09 - Submission of midterm assignment • February 26 - Last date to drop Y/S courses without academic penalty • April 6 - Last session • April 13 - Oral presentations – part 1 • April 20 - Oral presentations – part 2 • April 27 - Oral presentations – part 3 (if necessary) • May 4 - Submission of final assignment

5. Course Goals To expose graduate students to the concepts of translational oncology (“from bench to bedside”) through a series of seminar-type presentations highlighting recent advances of translational research; And, To motivate graduate students to apply the concepts of translational oncology to their own research through a series of written and oral assignments.

6. Course Format • Didactic lectures • 12 sessions, led by experts in the field • Theme: Personalized medicine • “Journal Clubs” • 12 sessions, held after each lecture • Independent term project – development and presentation of grant proposal

7. Class Format • Part 1: Didactic lecture, 45-50 minutes in length; followed by discussion/Q&A • Class discussion on 1-2 papers chosen by lecturer, led by students (“Journal Club”)

8. Course Evaluation • Participation (20%) • Class attendance (if you are unable to attend with reason, please notify Dr. Sukhai in advance) • Leadership of journal club • Midterm Assignment (15%) • Term Paper (50%) • Oral Presentation (15%)

9. Lecture Attendance • MANDATORY • If you are unable to attend (for e.g., ill; committee meeting; conference), please notify Dr. Sukhai • “My experiment got in the way” is not an acceptable excuse (speaks to time management skills) • “I needed to finish my assignment for X course” is also not an acceptable excuse

10. Journal Club • All students are expected to read the assigned papers in advance of the class • Papers will be posted 1 week in advance of the lecture where possible; this depends on when we get them from the lecturer • 2-3 students will be assigned to lead the journal club discussion in class • Leaders will be notified in advance • Come to the session with prepared questions and/or discussion topics that arise from the selected manuscripts • You are not expected to present the paper, figure-by-figure, but instead to come prepared to discuss it and its implications to translational oncology and personalized medicine • Be creative with the discussion period! Leaders can feel free to coordinate with each other and develop ways to engage their fellow students and the lecturer in discussion • A straight PPT show will be frowned upon

11. Midterm Assignment • “Letter-of-intent”/Statement of Research Interests • 2 pages • Single spaced • Not including any necessary references or the title page • Contents • Clearly stated research question • Well-defined hypothesis • Two clearly-stated aims/objectives • Translational relevance • Human impact • “Set the Stage” for your final assignment

12. Midterm Assignment • What is NOT necessary • Detailed methodology • Discussion of experimental plan • DO NOT make this about your research directly!

13. Midterm Assignment: Research Plan • “Set the Stage” • Background of your question • Clinical and translational relevance • Rationale for your choice • What models and systems will you be using • You may outline your proposed study design, but don’t make this the focus of your discussion

14. Midterm Assignment: Research Plan • Why are we making you do this? • Experience with a different style of scientific writing • Grad students, post-docs and people applying for faculty positions have to write these statements of research interest in applying for fellowships/positions • Write for a general audience – OK to be nontechnical • Good practice to solidify your ideas before launching into the more complex – and technical – grant writing exercise

15. Term Paper • “Medical Biophysics Translational Research Grant” • Full research proposal • 5 pages • Single spaced • Not including figures, tables, references, title page • This grant is to be built around the translational research aim you designed for the Midterm Assignment

16. Final Assignment: Grant Proposal • Longer and more complex than the research plan • Similar to grant and fellowship proposals you will be writing as a graduate student • Similar to the design for a reclass/qualifying exam proposal • Intended to give you a sense of the form and function in a scientific proposal • Meant to be a “window into your thought processes” if well written

17. Term Paper • Components • A brief introduction to the research area, including literature review and rationale for your proposed study • A clearly stated research question, and summary of the preliminary data for the project (this can be derived from the literature, with the appropriate references) • A clearly stated hypothesis • At least two specific aims of your research, including at least one clear translational research aim • The experimental approach, availability of samples, methodologies, anticipated outcomes and potential pitfalls of each aim should be laid out • A clear description of the translational nature of the aim should also be presented • A statement of clinical relevance/impact

18. Oral Presentation • Short (~10-12 minute) oral presentation outlining your research proposal • Focus on translational aims and impact • “Interview” for grant proposal

19. Assignment Notes • Late papers will not be accepted • Electronic submissions are preferred • Your research question CANNOT be derived from your own work • To verify this, we ask for a copy of your research abstract (e.g., your project proposal abstract from your first committee meeting or qualifying/reclassification exam; or your student seminar abstract) • Failure to abide by this rule will result in an automatic failing grade in the course; there will be no opportunity for a make-up assignment • You may stay within the same disease, but you must choose a different aspect of it (for e.g., if you are working on a particular signaling pathway, you cannot do that, but you can do something based on imaging modalities in the same disease, or experimental therapeutics, etc.) • You cannot work on the same protein • You may apply a technique you’re learning or working on currently to your research question, but remember that a research question isn’t based around a technique • You can, also, if you like, extrapolate from your research if it is very basic, and consider how you would apply it 5 or 10 years from now, in the clinical setting • If you have any questions, please do not hesitate to contact Dr. Sukhai

20. What is Translational Research? • For the purposes of this grant, “Translational Research” is defined to be use of clinically obtained samples in at least one major aim of the proposal • Specifically, use of: • Human subjects (with malignancy or disease) • Primary tissues/fluids (e.g., bone marrow samples or tumour biopsies) derived from patients with malignancy or disease • You CANNOT use for this purpose: • Mice or other animal models • Cell lines derived from patients • Other cell culture systems

21. But I Don’t Do Translational Research! • Don’t worry! Fewer of us than you might think do purely translational research • Objective of MBP 1018 is to develop your ability to conceive of and integrate translational concepts into your thinking • If you do: • Basic research (with cell lines or animal models) • Structural research • Photonics or imaging research • …There are translational applications in the future – just think about them!

22. But I Don’t Do Oncology Research! • That’s OK – think about the pathways you work on. • Do they have application to cancer in some way? • Can you draw connections outside of your own immediate sphere of research? • If you can, write about those connections.

23. Course Schedule

24. Tutorial 1: Analysis of Primary Papers • Rules of Reading a Paper • Things to look for

25. CRITICAL READING 2 Rules

26. Rule 1 Read the paper

27. Rule 1b Read all of the paper

28. Rule 2 Look at the data

29. Critical Points Understand the details of the research Initial observations/background Formulate the question/problem Is there a hypothesis? Is the methodology valid? Is the experiment appropriate? Are the data of high quality? Are the appropriate controls present? Are the data consistent with other data?

30. Discussion Points Understand the details of the research Initial observations/background Formulate the question/problem Is there a hypothesis? Is the methodology valid? Is the experiment appropriate? Are the data of high quality? Are the appropriate controls present? Are the data consistent with other data?

31. Things to look for • Was the methodology appropriate for the question being asked? • Were the data consistent with the methodology? • Were the data internally consistent? • Do the data make sense? • Were the controls appropriate? • Can you conclude what the authors concluded from their data? • Do you agree/disagree with the authors’ interpretation? • Do you agree with the “big picture” the authors present?

32. “The Matrix”

33. Hypotheses

34. Hypotheses • Are supposed to be falsifiable • Can be specific • It’s OK if they end up being WRONG! • Hypotheses MUST agree with the objectives under investigation

35. A Bad Hypothesis • Objective: • To determine the association between Gene X and patient outcome in AML • Hypothesis: • Gene X is associated with AML • Gene X is involved in the DNA damage response • AML patients that demonstrate impaired DNA damage have a poor prognosis

36. A Good Hypothesis • Objective: • To determine the association between Gene X and patient outcome in AML • Hypothesis: • Expression of Gene X is associated with poor prognosis in AML

37. Optional Writing Tutorials …Will arrange if enough students are interested

38. Questions?