CIHR STRATEGIC TRAINING PROGRAM.
“Innovative Technologies in Multidisciplinary Health Research Training”
Intermediate and advanced course (April 5-17, 2004).
April 5.
8.00-8.30 Introduction and overview
S. Mai, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada
8.30-9.15 Lecture 1:“Introduction to optics: Waves, Rays, and Optical Imaging Systems”
P. Jansson, Ph.D., Hockessin, Delaware, USA.
9.15-9.30 Coffee
9.30-10.15 Lecture 2: “Three-dimensional analysis of fluorescent objects”.
P. Jansson, Ph.D., Hockessin, Delaware, USA.
10.30-12.00 Q-FISH (part 1)
12.00-13.00 Lunch
13.00-13.45 Journal Club and Tutorial
S. Mai and P. Jansson
14.00-16.00 Q-FISH (part 2)
16.00-16.15 Coffee
16.00-18.00
Group 1: Image acquisition (3D) – Zeiss AxioVision
Group 2: Image analysis (3D) – Zeiss AxioVision
Group 3: Image acquisition (2D) – AI and MetaSystems
Group 4: Image analysis (2D) - DAKO
Group 5: Image analysis (2D) – MetaSystems
18.00-18.30 Discussion
April 6.
8.30-10.30
Continued imaging
Group 5: Image acquisition (3D) – Zeiss AxioVision
Group 1: Image analysis (3D) – Zeiss AxioVision
Group 2: Image acquisition (2D) – AI and MetaSystems
Group 3: Image analysis (2D) - DAKO
Group 4: Image analysis (2D) – MetaSystems
10.30 -11.30 Lecture 3: “M-FISH and related technologies”.
U. Klingbeil. Ph.D., MetaSystems Group Inc., Boston. USA.
11.45-12.45 Lunch
13.00-15.30 M-FISH
15.30-15.45 Coffee
15.45-17.45
Group 4: Image acquisition (3D) – Zeiss AxioVision
Group 5: Image analysis (3D) – Zeiss AxioVision
Group 1: Image acquisition (2D) – AI and MetaSystems
Group 2: Image analysis (2D) - DAKO
Group 3: Image analysis (2D) – MetaSystems
April 7.
8.30-9.15 The Canadian Institute of Health Research (CIHR)’s Strategic Training
Program: “Innovative Technologies in Multidisciplinary Health Research
Training”
S. Mai, Ph.D. Manitoba Institute of Cell Biology, Winnipeg, Canada
9.15-10.30 Getting to know your fellow trainees and their research.
10.30 Coffee
10.30-12.30
Group 3: Image acquisition (3D) – Zeiss AxioVision
Group 4: Image analysis (3D) – Zeiss AxioVision
Group 5: Image acquisition (2D) – AI and MetaSystems
Group 1: Image analysis (2D) - DAKO
Group 2: Image analysis (2D) – MetaSystems
12.30-13.30 Lunch
13.30-15.30
Group 2: Image acquisition (3D) – Zeiss AxioVision
Group 3: Image analysis (3D) – Zeiss AxioVision
Group 4: Image acquisition (2D) – AI and MetaSystems
Group 5: Image analysis (2D) - DAKO
Group 1: Image analysis (2D) – MetaSystems
15.30-16.00
Discussion of the day
16.00-18.00
Presentation of images by each group (one representative/group)
April 8.
8.00-10.00
M-FISH washes
10.00-10.15 Coffee
10.15-11.00 Lecture 4: “Affymetrix GenChip® Technology: overview and applications.”
E. Leblond, Senior Account Manager, Affymetrix Inc.
11.00-11.45 Lecture 5: “Practical considerations - designing a microarray experiment –
example of published applications”
Kimberly Woller, Field Application Specialist, Affymetrix Inc.
11.45-12.00
Discussion
12.00-13.00
Lunch
13.00-19.00
Imaging and analysis of M-FISH.
13.00-15.00: Groups 1 and 2: MetaSystems workstations 1 and 2
15.00-17.00: Groups 3 and 4: MetaSystems workstations 1 and 2
17.00-19.00: Group 5: MetaSystems workstation 1.
19.00-19.30 Discussion of M-FISH imaging
S. Mai and U. Klingbeil
April 9.
9.30-11.30 Presentation of imaging data by each group (one person per group)
11.30-12.30 Lunch
12.30-13.30 Journal club.
13.30-15.30 Continued imaging and analysis on selected stations.
15.30
Introduction to spectral karyotyping (SKY) protocol
S. Mai, Ph.D., Manitoba Institute of Cell Biology, Winnipeg,
Canada
April 10.
10.00-13.00 SKY (day 1)
13.15-14.00 Lunch
14.00-15.00 Introduction to SKY software.
Free afternoon and evening
April 11.
Free day
April 12.
9.00-10.00 Lecture 6: “Introduction to spectral imaging”. Y. Garini, Ph.D., University
of Delft, The Netherlands.
10.00 Coffee
10.15-11.00 Lecture 7: “New imaging and analysis tools”. Y. Garini, Ph.D., University
of Delft, The Netherlands.
11.15-12.00 SKY washes (day 3, part 1)
12.15-13.00 Lunch
13.00-15.00 Continuation of SKY (day 3, part 2).
15.00 Coffee
15.15-17.15
SKY imaging and analysis
Group 1 and 2 on SKY workstations
17.15-19.15
SKY imaging and analysis
Groups 3 and 4 on SKY workstations
April 13.
8.30-10.30 SKY imaging and analysis
Group 5
10.30 Coffee.
11.00-12.00 Journal Club
12.00-13.00 Lunch
13.00-14.00 Lecture 8: “Molecular cytogenetics in cancer”.
J. Squire, Ph.D., Ontario Cancer Institute, Toronto, Canada.
Probes, mapping, applications of advanced molecular cytogenetics in
leukemias and solid tumors. Paraffin interphase FISH. Tissue arrays.
Integration with other genomic technologies.
13.00-15.00 Continued imaging and analysis on selected workstations
15.10-16.00 Lecture 9: “Use of microarrays in tumor classification”.
J. Squire, Ph.D., Ontario Cancer Institute, Toronto, Canada
Microarray types. CGH arrays and expression arrays. Quality controlnormalization, scanning etc. Analytical methods. Validations. Integration
with other newer profiling technologies such as SNPs, epigenomics and
proteomics. Bioinformatics and discussion on copy number dependent
expression and sequences/pathways that may facilitate genomic
alterations.
16.00 Coffee
16.30-17.30 Journal club on two selected papers (J. Squire).
April 14.
9.00-12.00 Lecture 10: “Functional genomics” (class 1 and 2)
G. Hicks, Ph.D., Manitoba Institute of Cell Biology, Winnipeg,
Canada and S. Liu, Ph.D., Manitoba Institute of Cell Biology,
Winnipeg, Canada.
Class 1: “Functional Genomics”- large scale functional analysis and
annotation of the mammalian genome.
Class 2: “Understanding sequence analysis tools foe mining the genome”.
12.00-13.00 Lunch
13.00-17.00 “Functional genomics” (workshops 1 and 2)
G. Hicks, Ph.D., Manitoba Institute of Cell Biology, Winnipeg,
Canada and S. Liu, Ph.D., Manitoba Institute of Cell Biology,
Winnipeg, Canada
Workshop 1: “The single query”.
Workshop 2: “Functional annotation”.
April 15.
9.00-12.00 Lecture 11: “Functional genomics” (class 3 and workshop3)
G. Hicks, Ph.D., Manitoba Institute of Cell Biology, Winnipeg,
Canada and S. Liu, Ph.D., Manitoba Institute of Cell Biology,
Winnipeg, Canada
Class 3: “Database management”
Workshop 3: “Analysis of large sets of sequence data”.
12.00-13.00 Lunch
13.00-14.00 Lecture 12: “Introduction to Array CGH”
Timothy Stenzel, MD, Ph.D., Vysis.
14.00-15.00 Lecture 13: “Practical Applications of Array CGH in Research and
Diagnostics”
Ekaterina Pestova, Ph.D., Vysis.
15.00-15.30 Coffee
15.30-16.30 Lecture 14:“Clinical Array CGH”
Valia S. Lestou, Ph.D., BC Cancer Agency.
16.30-17.30 Discussion and journal club. Assigned Array CGH Papers (led by Drs.
Lestou, Pestova and Stenzel).
April 16.
The 20 workshop participants will be divided into two groups of 10 for the microarray
training.
8.00-5.00pm: Parts I and II: label DNA, denature DNA, check quality of labeling by gel
electrophoresis, hybridize sample to the array, perform washes,
and counter-stain with DAPI. During the down time between steps,
the participants will learn about chip analysis. (Please note that the
hybridization step is truncated to fit within the time frame of this
workshop).
NOTE: 12.00-13.00 Lunch
April 17.
8.00-12.00 CGH array analysis and training.
12.00-13.00 Lunch
13.00-15.00 Studying time.
15.00-17.00 TEST
18.30 Dinner