CIHR STRATEGIC TRAINING PROGRAM.
“Innovative Technologies in Multidisciplinary Health Research Training”
Intermediate and advanced course (April 27 to May 11, 2006).
NOTE: The program is flexible and some changes can be done (coffee breaks will be included).
April 27.
8.00-8.30 Introduction and overview
S. Mai, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada
8.30-9.00 Students Introduction
9.00-10.00 Lecture 1: "Recent Improvements in Structured Illumination Microscopy
by Advanced Artefact Reduction and Deconvolution"
Lutz Schaefer, Advanced Imaging Methodology Consultation
Carl Zeiss, Canada.
10.00-11.00 Lecture 2: “Practical Considerations in the Selection and Application
of Fluorescent Probes”
Iain Johnson, Invitrogen
11:00-12:00 Lecture 3: “Introduction to optics: Waves, Rays, and Optical Imaging
Systems”
P. Jansson, Ph.D., Hockessin, Delaware, USA.
12:00-13:00 Lecture 4: “Three-dimensional reconstruction of fluorescent objects by
deconvolution”.
P. Jansson, Ph.D., Hockessin, Delaware, USA.
13:00-14:00 LUNCH
14:00-14:30 “Q-FISH protocol”
14:30-19:00 Imaging time at the Genomic Centre: “Q-FISH slides”
April 28.
9:00-10:30 Lecture 5: "Spectral imaging, methods and applications"
Light and optics, Optical detection methods and fluorescence,
Spectral imaging, spectral karyotyping, Other spectral imaging
methods, My current research.
Y. Garini, Ph.D., University of Delft, The Netherlands.
10:30-12:00 Lecture 6: “Imaging tissue with IR microspectroscopy”
Dr. Kathleen M. Gough, Department of Chemistry, University of
Manitoba
12:00-13:00 LUNCH
13:00-14:00 Lecture 7: "Quantitative Image Processing: part 1"
Bart Vermolen, M.Sc., University of Delft, The Netherlands.
14:00-15:00 Lecture8: "Quantitative Image Processing: part 2"
Bart Vermolen, M.Sc., University of Delft, The Netherlands.
15:00-17:00 Imaging time at the Genomic Centre: “Q-FISH slides”
17:00-19:00 Journal Club and Tutorial
(Dr. K. Gough)
April 29.
9:00-12:00 SKY experiment (Day1)
m-BAND experiment (Day 1)
12:00-13:00 LUNCH
13:00-14:30 Journal Club and Tutorial
(Dr. Y. Garini and Bart Vermolen)
14:30-18:30 Field Trip to the Virtual Reality Centre.
April 30.
Free Day.
May 1.
9:00-12:00 m-BAND experiment (Day 2- washes)
SKY experiment (Day 2-part 1-washes)
12:00-13:00 LUNCH
13:00-14:00 SKY experiment (Day 2-part 2-washes)
14:00- 18:00 SKY imaging and analysis
May 2.
9:00- 12:00 SKY imaging and analysis
12:00-13:00 LUNCH
13:00- 18:00 SKY imaging and analysis
May 3.
9:00-10:30 Lecture 9: “From the conception of the PRINS to its coronation”
Dr. Regen Drouin, University of Sherbrooke, Quebec.
10:30-12:00 Lecture 10: “m-BAND technology”.
U. Klingbeil. Ph.D., MetaSystems Group Inc., Boston. USA.
12:00-13:00 LUNCH
13:00-17:00 m-BAND imaging and analysis
17:00-19:00 Journal Club and Tutorial
(Dr. Ulrich Klingbeil)
May 4.
9:00-11:00 Lecture 11: Principles of Expression Analysis: Experimental Design,
Statistical Analysis and Biological Interpretation.
Marco Raposo, Field Applications Specialist,
AFFYMETRIX, INC.
Eric Leblond, Senior Account Manager, AFFYMETRIX,
INC.
11:00-12:00 Lecture 12: "Integrated Analysis of Cancer Genomes"
Dr. Wan Lam, Clinical Professor, Pathology, University of
British Columbia and Senior Scientist, Cancer Genetics and
Developmental Biology, British Columbia Cancer Agency
12:00-13:00 LUNCH
13:00-14:30 m-BAND imaging and analysis
14:30-15:30 Lecture 13: Oncogenomics research with high-density whole genome
and custom fine-tiling microarrays.
Luigi Vitiritti, Sr. Account Manager, Nimblegen Systems
Inc.
The development of new microarray applications, such as
chromatin immunoprecipitation (ChIP) and comparative genomic hybridization (CGH), are rapidly being adopted to complement gene expression microarray experiments. Integration of a full suite of experimental tools will provide a more
comprehensive view of abnormal cellular activities and accelerate the field
of oncogenomics research. Our maskless array synthesis (MAS) platform
enables the use of long probes for increased sensitivity and high density
for high resolution coverage of the whole genome or a subset of genomic
regions. Further, the technology enables rapid development of new arrays,
enabling the researcher to customize their experiments using either a
gene-centric or tiling-path approach. Data will be presenting demonstrating
the use of ChIP chips for genome-wide analysis of binding sites for
DNA-binding proteins such as transcription factors and RNA polymerase; and,
array CGH for analysis of copy number changes (e.g., DNA amplifications and
deletions).
15:30-16:30 Lecture 14: Probing genome structure and function using high-density
oligonucleotide microarrays.
Rebecca Selzer, PH.D., Sr. Product Manager, NImblegen
Systems Inc.
NimbleGen has developed “tiling” microarray designs that space probes evenly across the genome covering both coding and non-coding regions. Using these array designs allow unbiased analysis of DNA copy number changes, DNA protein interactions, and gene expression profiles. Data will be presented
from studies mapping active promoters in the human genome, copy number
changes involved in both disease pheneotypes and normal copy number changes,
and experimental annotation of human chromosome 12 gene expression.
16:30-17:30 Lecture 15: Data Analysis Utilizing SignalMapTM Data Visualization
Software.
Rebecca Selzer, PH.D., Sr. Product Manager, Nimblegen
Systems Inc.
SignalMap uses GFF files as an input for visualizing NimbleGen array data and provides the capability to handle large data sets for graphically-based browsing, rescaling, analysis, and export of graphical files for publication. We will present detailed analysis of Comparative Genome Hybridization and Chromatin Immunoprecipitation (ChIP-chip) Promoter array data.
17:00-19:00 Journal Club and Tutorial
(Dr. R. Selzer and Luigi Vitiritti Nimblegen Systems Inc.)
May 5.
9:00-12:00 Lecture 14: “Functional genomics”
G. Hicks, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada and S. Liu, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada.
(Large scale functional analysis and annotation of the mammalian genome. Understanding sequence analysis tools foe mining the genome. Database management).
LUNCH 12:00-12:45
13.00-18.00 “Functional genomics” (continuing)
G. Hicks, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada and S. Liu, Ph.D., Manitoba Institute of Cell Biology, Winnipeg, Canada
(The single query. Functional annotation. Analysis of large sets
of sequence data).
May 6.
9:00-12:00 Lecture 15: “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.
LUNCH 12:00-12:45
13:00-16:00 Lecture 16: (continuing) “Use of microarrays in tumor classification”.
J. Squire, Ph.D., Ontario Cancer Institute, Toronto, Canada
Microarray types. CGH arrays and expression arrays. Quality control-normalization, 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.
16:00-18:00 Journal Club and Tutorial
(Dr. J. Squire)
May 7.
Free Day.
May 8.
8:00-8:30 Introduction and welcome: Kathryn B. Becker, Ph.D. and Alex Mathews,
Vysis/Abbott
8:30-9:30 General Session: CGH Microarrays: Overview & Applications - Kathryn
B. Becker, Ph.D., Vysis/Abbott
9:30-10:15 Assay Lecture (first group) Kathryn B. Becker and Alex Mathews,
Vysis/Abbott
10:15-11:00 Software 1
11:00-11:45 Practice and review
12:00-13:00 LUNCH
13:00-13:45 Software 2
13:45-14:45 Practice and review
14:45-15:00 Coffee break
15:00-15:30 Q&A/review
15:30-15:00 Journal Club and Tutorial
Kathryn B. Becker and Alex Mathews, Vysis/Abbott
May 9.
9:00-9:45 Assay Lecture (first group)
9:45-10:30 Software 1
10:30-11:30 Practice and review
12:00-13:00 LUNCH
13:00-13:45 Software 2
13:45-14:45 Practice and review
14:45-15:00 Coffee break
15:00-15:30 Q&A/review
15:30-16:30 Lecture 18: “Tissue Microarrays”
Dr. Peter Watson, Department of Pathology, Faculty of
Medicine, University of Manitoba.
May 10.
9:00-12:00 Representative images from each group.
Discussion of selected images per group.
12:00-13:00 LUNCH
13:00-15:00 Studying time.
15:00-17:00 TEST
18:30/19:00 DINNER