MBP 1018Y: Oncology
Wednesdays, 10 a.m. – 12 noon
January 11 – May 02, 2012 inclusive
610 University Avenue, Room 7-605
Outline
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Introductions
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Course Contact Information
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Significant Dates
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Course Schedule
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Course Overview – Goal, Format
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Course Evaluation
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Tutorial Schedule
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Tutorial
Contact Information
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Course Coordinator: Dr. Brad Wouters
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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)
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Room 9-620, Princess Margaret Hospital
610 University Avenue
Tel: 416-946-4501 x 3498
Email: m.sukhai@utoronto.ca
Significant Dates
Date
Deliverable
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
Course Schedule 2012
DATE
TOPIC
LECTURER
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
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.
Course Format
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Didactic lectures
– 12 sessions, led by experts in the field (1
hr each)
– Theme: Personalized medicine
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“Journal Clubs”
– 12 sessions, held after each lecture (1 hr
each)
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Group term project – development and
presentation of “program project”
grant proposal
Class Format
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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)
Journal Club Format
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Each lecturer (and their papers)
will be assigned to teams of
students (2-3 students per team)
Student teams to lead class
discussions
DO’s
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Focus on “big picture” – implications of the
papers; integration with earlier concepts in
the course; impact on personalized medicine;
what comes next?
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Engage all students in the discussion
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Spread the facilitation duties around among
the team
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Keep discussion lively and interesting; be
creative
How do we keep the
discussion going?
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Facilitate!
Be creative
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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
Do NOT’s
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Rely on Powerpoint presentations
Dissect/critique the papers, figure by
figure
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Monopolize the discussion
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Fail to engage your classmates
Every student’s
responsibility
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Read the papers
– Even if you’re not presenting them!
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Come prepared with discussion questions to
keep the “journal club” lively
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Evaluate the success of the discussion
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Integrate the knowledge gained/insights
into your term projects and (beyond the
course) research
Course Evaluation
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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
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Midterm Assignment (15%)
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Term Paper (50%)
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Oral Presentation (15%)
Lecture Attendance
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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
Term Projects
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Group-developed “program project” grant application
– Midterm: Individual letters of intent
– Final: Group project proposal
– Oral: Group presentation of project proposal
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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.
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Demonstrates “team science” and the ability to
integrate concepts and ideas in a collaborative
environment
Term Projects
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Groups of 3-4
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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
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What’s a topic/theme? Examples:
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A given tumor site
Multiple approaches to biomarker discovery/validation
Novel target discovery/experimental therapeutics
Combinations of the above
Anything you can think of!
Midterm Assignment
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“Letter-of-intent”/Statement of Research Interests
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Contents
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INDIVIDUAL SUBMISSION
2 pages
Single spaced
Not including any necessary references or the title page
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
Each group is also expected to submit an overall group
abstract, outlining the parts of the group project application
Midterm Assignment
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What is NOT necessary
– Detailed methodology
– Discussion of experimental plan
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DO NOT make this about your
research directly!
Midterm Assignment:
Research Plan
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“Set the Stage”
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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
Midterm Assignment:
Research Plan
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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
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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
Term Paper
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“Medical Biophysics Translational Research
Program Project Grant”
Full research proposal
– 4 pages per group member
– Single spaced
– Not including figures, tables, references, title page
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This grant is to be built around the
translational research aim(s) you designed
for the Midterm Assignment
Final Assignment: Grant
Proposal
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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
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Meant to be a “window into your
thought processes” if well written
Term Paper
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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)
Oral Presentation
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Group (~25-30 minute) oral
presentation outlining your
research proposal
Focus on translational aims and
impact
“Interview” for grant proposal
Assignment Notes
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Late papers will not be accepted
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Electronic submissions are preferred
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Your research question CANNOT be derived from your own work
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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
What is Translational
Research?
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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
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You CANNOT use for this purpose:
– Mice or other animal models
– Cell lines derived from patients
– Other cell culture systems
But I Don’t Do
Translational Research!
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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
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…There are translational applications in the
future – just think about them!
But I Don’t Do Oncology
Research!
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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.
Tutorial Scheduling and
Purpose
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Tuesdays, 4-5 p.m.
– 610 University Avenue, room 7-605
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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”
Tutorial Schedule
DATE
TOPIC
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
Tutorial 1: Analysis of
Primary Papers
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Rules of Reading a Paper
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Things to look for
CRITICAL
READING
2 Rules
Rule 1
Read the paper
Rule 1b
Read all of the paper
Rule 2
Look at the data
Critical Points
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Understand the details of the
research
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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
Discussion Points
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Understand the details of the
research
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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
Things to look for
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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?
“The Matrix”
GOOD WRITING
GOOD WRITING
GOOD SCIENCE
BAD SCIENCE
BAD WRITING
BAD WRITING
GOOD SCIENCE
BAD SCIENCE
Questions?