1. MBP 1018Y: Oncology Wednesdays, 10 a.m. – 12 noon January 11 – May 02, 2012 inclusive 610 University Avenue, Room 7-605

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

3. Contact Information Course Coordinator: Dr. Brad Wouters Course Coordinator: Dr. Brad Wouters –Room 10-116, Princess Margaret Hospital –610 University Avenue –Tel: 416-581-7840 –E-Mail: bwouters@uhnresearch.ca bwouters@uhnresearch.ca Teaching Assistant: Dr. Mahadeo Sukhai (Day-to-day contact person) Teaching Assistant: Dr. Mahadeo Sukhai (Day-to-day contact person) –Room 9-620, Princess Margaret Hospital –610 University Avenue –Tel: 416-946-4501 x 3498 –Email: m.sukhai@utoronto.ca m.sukhai@utoronto.ca

4. Significant Dates DateDeliverable January 11 Introductory session January 25 Submission of abstract of thesis project; term project groups identified and topics selected February 08 Submission of midterm assignment April 04 Last session April 11 Oral presentations – part 1 April 18 Oral presentations – part 2 April 25/May 02 Submission of final assignment

5. Course Schedule 2012 DATETOPICLECTURER JAN. 11 Introduction M. Sukhai JAN. 18 Imaged based monitoring of individual response to treatment G. Czarnota JAN. 25 The importance of genetic variation in oncology G. Liu FEB. 01 Novel models and methods for assessment of new targeted agents in oncology D. Hedley FEB. 08 Lung cancer genomics and patient individualization M. Tsao FEB. 15 Image guided personalized therapy D. Jaffray FEB. 22 Personalized Immunotherapy Approaches N. Hirano FEB. 29 Novel targeted drugs and their introduction in the clinic P. Bedard MAR. 07 Tumor microenviornment and metabolism in radiation oncology M. Milosevic MAR. 14 Novel risk factors N. Boyd MAR. 21 Breast cancer oncogenesis and new targets M. Reedjik MAR. 28 Imaging in oncology G. Stanisz APR. 04 Novel targets in leukemia M. Minden APR. 11 Oral Presentation Class APR. 18 Oral Presentation Class APR. 25 Oral Presentation / Optional Tutorial Session Class MAY 02 Final Assignment Due

6. 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.

7. Course Format Didactic lectures Didactic lectures –12 sessions, led by experts in the field (1 hr each) –Theme: Personalized medicine “Journal Clubs” “Journal Clubs” –12 sessions, held after each lecture (1 hr each) Group term project – development and presentation of “program project” grant proposal Group term project – development and presentation of “program project” grant proposal

8. Class Format Part 1: Didactic lecture, followed by discussion/Q&A (1 hr) Part 1: Didactic lecture, followed by discussion/Q&A (1 hr) Class discussion on 1-2 papers chosen by lecturer, led by students (“Journal Club” – 1 hr) Class discussion on 1-2 papers chosen by lecturer, led by students (“Journal Club” – 1 hr)

9. Journal Club Format Each lecturer (and their papers) will be assigned to teams of students (2-3 students per team) Each lecturer (and their papers) will be assigned to teams of students (2-3 students per team) Student teams to lead class discussions Student teams to lead class discussions

10. DO’s Focus on “big picture” – implications of the papers; integration with earlier concepts in the course; impact on personalized medicine; what comes next? Focus on “big picture” – implications of the papers; integration with earlier concepts in the course; impact on personalized medicine; what comes next? Engage all students in the discussion Engage all students in the discussion Spread the facilitation duties around among the team Spread the facilitation duties around among the team Keep discussion lively and interesting; be creative Keep discussion lively and interesting; be creative

11. How do we keep the discussion going? Facilitate! Facilitate! Be creative Be creative –Mock debates (pro/con) –Plant “ringers” –Play games with the audience –Snap group discussions –…The sky’s the limit For advice and assistance, contact the TA For advice and assistance, contact the TA

12. Do NOT’s Rely on Powerpoint presentations Rely on Powerpoint presentations Dissect/critique the papers, figure by figure Dissect/critique the papers, figure by figure Monopolize the discussion Monopolize the discussion Fail to engage your classmates Fail to engage your classmates

13. Every student’s responsibility Read the papers Read the papers –Even if you’re not presenting them! Come prepared with discussion questions to keep the “journal club” lively Come prepared with discussion questions to keep the “journal club” lively Evaluate the success of the discussion Evaluate the success of the discussion Integrate the knowledge gained/insights into your term projects and (beyond the course) research Integrate the knowledge gained/insights into your term projects and (beyond the course) research

14. Course Evaluation Participation (20%) Participation (20%) –Class attendance (if you are unable to attend with reason, please notify Dr. Sukhai in advance) –Leadership of journal club –Participation in journal club –NOTE that each week’s lecture/journal club will be evaluated through student survey feedback Midterm Assignment (15%) Midterm Assignment (15%) Term Paper (50%) Term Paper (50%) Oral Presentation (15%) Oral Presentation (15%)

15. Lecture Attendance MANDATORY MANDATORY If you are unable to attend (for e.g., ill; committee meeting; conference), please notify Dr. Sukhai 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

16. Term Projects Group-developed “program project” grant application Group-developed “program project” grant application –Midterm: Individual letters of intent –Final: Group project proposal –Oral: Group presentation of project proposal In these types of grants, often three to four linked initiatives are submitted as part of a larger overall program of research. In these types of grants, often three to four linked initiatives are submitted as part of a larger overall program of research. –For example, a program project grant in head and neck cancer may involve biomarker identification and validation; imaging; and new therapy development, all linked by common themes and integrated with one another. Demonstrates “team science” and the ability to integrate concepts and ideas in a collaborative environment Demonstrates “team science” and the ability to integrate concepts and ideas in a collaborative environment

17. Term Projects Groups of 3-4 Groups of 3-4 Each group identifies an overall topic or theme Each group identifies an overall topic or theme –MUST be approved by Dr. Sukhai –No two groups can do the same topic –Topic choice is made on a first come-first served basis What’s a topic/theme? Examples: What’s a topic/theme? Examples: –A given tumor site –Multiple approaches to biomarker discovery/validation –Novel target discovery/experimental therapeutics –Combinations of the above –Anything you can think of!

18. Midterm Assignment “Letter-of-intent”/Statement of Research Interests “Letter-of-intent”/Statement of Research Interests –INDIVIDUAL SUBMISSION –2 pages –Single spaced –Not including any necessary references or the title page Contents Contents –Clearly stated research question –Well-defined hypothesis –Two clearly-stated aims/objectives –Translational relevance –Human impact –Integration with overall group project “Set the Stage” for your final assignment “Set the Stage” for your final assignment Each group is also expected to submit an overall group abstract, outlining the parts of the group project application Each group is also expected to submit an overall group abstract, outlining the parts of the group project application

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

20. Midterm Assignment: Research Plan “Set the Stage” “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 You may outline your proposed study design, but don’t make this the focus of your discussion

21. Midterm Assignment: Research Plan Why are we making you do this? 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 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 Good practice to solidify your ideas before launching into the more complex – and technical – grant writing exercise

22. Term Paper “Medical Biophysics Translational Research Program Project Grant” “Medical Biophysics Translational Research Program Project Grant” Full research proposal Full research proposal –4 pages per group member –Single spaced –Not including figures, tables, references, title page This grant is to be built around the translational research aim(s) you designed for the Midterm Assignment This grant is to be built around the translational research aim(s) you designed for the Midterm Assignment

23. Final Assignment: Grant Proposal Longer and more complex than the research plan 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 Meant to be a “window into your thought processes” if well written

24. Term Paper Components Components –Abstract of overall project (1 page) –Introduction and statement of relevance (2 pages) –Rationale and outline of objectives/hypotheses (1 page) –Each group member’s specific research proposal (4 pages, max, each – including a review of preliminary data from the literature, 2 aims, and a statement of translational implication) –A section on integration and an overall conclusion (1 page)

25. Oral Presentation Group (~25-30 minute) oral presentation outlining your research proposal Group (~25-30 minute) oral presentation outlining your research proposal Focus on translational aims and impact Focus on translational aims and impact “Interview” for grant proposal “Interview” for grant proposal

26. Assignment Notes Late papers will not be accepted Late papers will not be accepted Electronic submissions are preferred Electronic submissions are preferred Your research question CANNOT be derived from your own work 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

27. 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 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: 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: You CANNOT use for this purpose: –Mice or other animal models –Cell lines derived from patients –Other cell culture systems

28. But I Don’t Do Translational Research! Don’t worry! Fewer of us than you might think do purely 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 Objective of MBP 1018 is to develop your ability to conceive of and integrate translational concepts into your thinking If you do: 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! …There are translational applications in the future – just think about them!

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

30. Tutorial Scheduling and Purpose Tuesdays, 4-5 p.m. Tuesdays, 4-5 p.m. –610 University Avenue, room 7-605 Purposes: Purposes: –Forum for learning to improve your scientific writing –Forum for dealing with necessary course business –Whatever else you want them to be –My formal “office hours”

31. Tutorial Schedule DATETOPIC Jan. 17 Effective group facilitation – getting the most out of the journal club discussions Jan. 24 Q&A around term project topics Jan. 31 Short-form proposal abstract/Letter of Intent writing Feb. 07 Q&A on Midterms Feb. 14 Topic of students’ choice Feb. 21 Topic of students’ choice Feb. 28 Midterm Feedback Mar. 06 Writing long-form proposals I Mar. 13 Writing long-form proposals II Mar. 20 Requirements for the Oral Presentation Mar. 27 Writing long-form proposals III April 03 Q&A on Orals April 25 Q&A on Final Assignments

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

33. CRITICAL READING 2 Rules

34. Rule 1 Read the paper

35. Rule 1b Read all of the paper

36. Rule 2 Look at the data

37. Critical Points Understand the details of the research 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?

38. Discussion Points Understand the details of the research 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?

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

40. “The Matrix” GOOD WRITING GOOD SCIENCE GOOD WRITING BAD SCIENCE BAD WRITING GOOD SCIENCE BAD WRITING BAD SCIENCE

41. Questions?