Collaborative Research Resources
OICR is making its technology infrastructure, expertise and resources available to the Ontario cancer research community through collaborative cost-sharing arrangements. Click on the links below to learn more about each platform:
Diagnostic Development (tissue-based research)
OICR's Diagnostic Development program, located at the MaRS Centre, focuses on tissue-based analysis with expertise with human samples in formalin-fixed, paraffin-embedded (FFPE) and a breadth of associated technologies for complex genome analysis, nucleic acid and protein extraction, tissue microarray construction, NanoString technologies, automated immunohistochemistry and quantitative molecular pathology analysis.
- DNA extraction (FFPE or frozen tissue).
- RNA extraction (FFPE or frozen tissue).
- Dual DNA and RNA extraction (FFPE and frozen tissue).
- Histology - Tissue sectioning (FFPE and frozen tissue).
- Histology - Laser capture microdissection.
- Histology - routine H&E stain.
- Low-density tissue microarray construction (50-100 cores).
- High-density tissue microarray construction (200 cores).
- Multiplex qPCR (FFPE compatible).
- Library preparation for targeted sequencing (FFPE compatible).
- FISH (FFPE compatible).
- Quantitative FISH analysis.
- Multiplex CNV analysis (e.g., Multiplex ligation dependent probe amplification -MLPA).
- NanoString-based technologies.
- Automated immunohistochemistry (whole sections and TMA).
- Single or multiple labeling (Chromagenic and FITC).
- Antibody optimization and validation.
- Automated quantitative IHC image analysis.
- Slide scanning and archiving.
OICR's Drug Discovery program, located at the MaRS Centre, supports the synthesis of small molecules, low to medium throughput screening, SAR analysis and hit triaging, a range of in vitro and in vivo assays to fully characterize ADME, pharmacokinetic profiles and maximum tolerated dose of candidates, including help with biochemical or cell based assay development and optimization for profiling and screening small molecule libraries.
- Plasma or blood stability - single time point.
- Microsomal stability - single time point or time course and half-life determination.
- Microsomal stability - metabolite ID.
- Primary hepatocyte stability - single time point or time course and half-life determination.
- Caco-2 permeability - bi-directional (papp and efflux ratio).
- Caco-2 permeability - efflux transporter (P-gp MRP2 etc.) inhibition.
- CYP450 inhibition - P450 inhibition percent inhibition one concentration -1 isoform.
- Plasma or protein binding - single time point.
- MTD determination - IV, PO or IP (three dose, two time point study) – mouse, rat or only sample analysis.
- PK study - IV, PO or IP (single dose, nine time points) - mouse, rat or only sample analysis.
- PK study - IV plus one other route (for F% determination) - mouse, rat or only sample analysis.
- Prep HPLC use - purify compounds.
- 500 MHz NMR use - analyze compounds.
- Assay development and optimization (guidance and execution).
- Low to medium through put screening.
- Expertise with state-of-the-art equipment (SPR/ HP dispenser/FACS etc)
- Medicinal chemistry and synthetic expertise.
- SAR analysis and hit triaging.
- Surface plasmon resonance (SPR) use.
OICR's Genomics and Informatics programs, based at the MaRS Centre, offer comprehensive next-generation sequencing (NGS) and analysis services using the HiSeq 2500, MiSeq and PacBio platforms. The sequencing project workflow involves consultation before and throughout the project, sample preparation, library preparation, sequencing and analysis (see Informatics section for more detail). Extensive quality checks are conducted throughout the workflow. Applications include whole genome, exome, transcriptome and custom targeted library construction with a focus on low-input and FFPE samples.
- DNA extraction
- RNA extraction
- Whole genome library preparation and sequencing (FFPE compatible)
- Standard human coverage (30X)
- Deep human coverage (50X)
- Human whole exome library preparation sequencing (FFPE compatible)
- Stranded whole transcriptome
- Stranded transcriptome capture (FFPE compatible)
- Custom genome solutions and capture panels (FFPE compatible)
- PacBio library preparation (20kb insert library)
- PacBio sequencing, per SMRTcell (P6/C4 chemistry)
OICR's Informatics program, based at the MaRS Centre, offers tools and workflows for sequence analysis and quality control, with extensive expertise in a wide variety of cancer sequence data types. Using highly automated and reproducible workflows, OICR provides both primary and secondary analyses, and can also perform bespoke analysis using specific cutting-edge software. The analysis team provides assistance with experimental design, as well as the interpretation and the publication of experimental results. Data storage and secure transfer or sharing options can also be provided. In support of these analysis and data access activities, OICR’s Research IT infrastructure hosts custom servers and virtual machines (VM). OICR’s Web Development team develops custom web designs, web services and web applications.
- Experimental design.
- Quality control.
- Primary analysis (alignment, variant calling (e.g., SNV, indel, Structural rearrangements, CNA).
- Secondary analysis (mutational signature, pathway analysis, functional consequence analysis).
- Tertiary analysis (data integration).
- Storage and sharing of sequence data.
Other Informatics Services
Imaging: Engineering Services and MRI/Ultrasound
OICR's Imaging program offers image processing, 3D visualization, mechatronics design, systems design through CIMTEC and access to MRI/ultrasound scanning through The Centre for Imaging Technology Commercialization (CIMTEC) and Robarts Research Institute.
- Image processing: Customized, clinically-validated image processing algorithms for rapid segmentation, registration and classification.
- 3D visualization: Clinical graphical user interface (GUI) development, multi-modal 3D imaging and real-time quantification.
- Mechatronics Design: Design and manufacture of prototypes with expertise in motion control and image-guided interventions.
- Systems Design: Ensure that systems integrate smoothly into clinical workflow with attention to training requirements, impacts of pathology process developments and optimizing performance for time savings.
- 3-Tesla GE 750 whole body imager.
- Siemens 3-Tesla Siemens Tim Trio whole body imager.
- 7-Tesla Varian/Siemens human head MRI System/ 7T.
- 9.4-Tesla 31cm bore Varian animal MR imager with a range of rf coils.
Contact the OICR team at Robarts for more information about services available or to request a quote for your project: http://www.oicr-itp.ca/resources.
For commercialization services contact CIMTEC: http://www.cimtecimaging.com/
Imaging: Probe Development
OICR's Imaging program offers probe development and characterization services, including radiopharmaceutical probes through the Centre for Probe Development and Commercialization (CPDC) and Sunnybrook Research Institute.
- Cytometer for sorting ligand bound beads (peptide library).
- Gamma counter.
- Biotage microwave.
- Biotage V10 for rapid evaporation.
- Biotage SP1 for rapid purification.
- Advanced ChemTech peptide synthesizer.
- Zetasizer Nano ZS dynamic light scattering based particle sizer.
- Particle size and protein mobility analyzer, Zetasizer Nano ZS.
- GMP hot cell.
- 50 MW nuclear reactor.
- RDS 112 cyclotron.
- Nanoparticle dispersion and cell disruption ultrasonic stysten, Misonix Sonicator 3000\.
- Lyposome formulation system, Lipex Extruder.
- Automated synthesis unit, Modular-Lab Exkert & Ziegler.
- HPLC with gamma detectors.
- Agilent LC/MS and GC/MS.
- Waters LCT Premier MS System.
Contact CPDC for more information about the services available at McMaster or to request a quote for your project: http://www.imagingprobes.ca/
Contact the OICR team for more information about services available at Sunnybrook: http://www.oicr-itp.ca/resources
Imaging: Quantitative Imaging and Centralized Storage
OICR's Imaging program offers services and tools to support the acquisition of robust imaging data from multi-centre clinical trials through the Quantitative Imaging for Personalized Cancer Medicine (QIPCM) program. Support services include scanner validation and QA; imaging protocol development; novel image analysis; tools development; image analysis; storage; archival and remote image review.
- Scanner QA.
- Image analysis.
- Central data repository.
- Virtual machine remote access.
- Image anonymization and transfer.
Contact Techna (an institute of the University Health Network in collaboration with the University of Toronto) for more information about services available or to request a quote for your project: http://technainstitute.com/
Imaging Pathology Validation
OICR's Imaging program offers access to imaging pathology validation services/tools and tools through Sunnybrook Research Institute and Robarts Research Institute/CIMTEC in the following areas:
- Whole-mount tissue processing and advanced immunohistochemistry (whole mount and conventional) and cross-platform image registration for validation of new imaging techniques, clinical trials and pilot projects.
- Biomarker panel development and validation using multiplexing technologies in combination with molecular profiling (primarily for collaborative research projects).
- Multimodality image processing, algorithm development and image registration for digital pathology and imaging applications.
- Research strategy, study designs, selection of biomarkers, optimization of immunostaining, clinical quality control, specimen and image repository and database, pathology consultations and assessment of results.
- 3D pathology lab, tissue sectioning/staining/digitized imaging.
- Whole mount tissue slide preparation: large format (2"x3"-5"x7") microtomy.
- Automated whole mount tissue processing, both regular and rapid (microwave).
- Automated immuno and special staining for regular and whole mount tissue slides.
- Large format (up to 5"x7") slide scanning and digitization, including multispectral.
- Development of image processing algorithms, quantitative image and histology analysis tools, 2D and 3D viewers and software programs.
- Pathology consultations, biomarker analysis, quality control and clinical trials assistance.
Contact OICR team for more information about services available at Robarts or Sunnybrook or to request a quote for your project: http://www.oicr-itp.ca/resources
Ontario Health Study (population-based health data)
The Ontario Health Study (OHS) is an innovative population-based health study serving as an integrated platform to investigate the environmental, lifestyle, clinical and genetic factors associated with risks of chronic diseases. Over 230,000 participants have been recruited to date, and consented to i) active follow-up (e.g., additional questionnaires, sample collection); ii) passive follow-up through record linkage (e.g., Ontario Cancer Registry, vital statistics, insurance claims); and iii) receive invitations to participate in other health-related research studies. The intent is to follow participants both actively and via linked administrative health data for their entire lifespan.
Scientists may submit proposals for access to the following data and samples collected by the Ontario Health Study:
- Baseline questionnaire responses, including socio-demographic information, personal and family medical histories, screening activities, health behaviours, medications, and self-reported anthropometrics;
- Physical measures collected from a subset of participants, including standing and sitting height, weight, bioimpedance, waist and hips circumferences, and grip strength;
- Biological specimens, including cell-free blood serum and plasma, red blood cells, buffy coat, DNA and urine;
- Glycated hemoglobin and complete blood count from a subset of participants; and
- Genotyping data from a subset of participants.
Ontario Tumour Bank
The Ontario Tumour Bank is a province-wide biorepository and data bank focused on collection of tumour-related human biospecimens. It provides academic and industry cancer researchers with a diverse selection of high quality tumour-related specimens and derivatives accompanied with de-identified annotated clinical data. Currently, four academic teaching hospitals across Ontario are participating in the OTB: Kingston General Hospital, London Health Science Centre, St. Joseph’s Healthcare Hamilton and The Ottawa Hospital. Dedicated tumour bank staff at each hospital collect samples and clinical data from participating donors while following a stringent set of procedures and ethical guidelines.Learn more
- Tumour tissue;
- Normal adjacent tissue;
- Peripheral blood.
- Fresh frozen tissue (250mg/vial);
- Paraffin-embedded formalin-fixed tissue;
- Cryopreserved plasma (1 mL/vial), buffy coat (250uL/vial) and circulating nucleic acid plasma (1 mL/vial).
- Tissue Microarrays
Please visit our website at www.ontariotumourbank.ca for immediate access to inventory of thousands of biospecimens and related clinical data. For more information or for assistance with a detailed search for samples, please contact us by email at firstname.lastname@example.org or by phone at 416-673-6658.
Platform for Advanced Cell Engineering
The Platform for Advanced Cell Engineering (PACE) provides collaborative access to genetic reagents, technologies, data analysis pipelines and expertise required for functional genetic screens and cell line engineering. The PACE has advanced their genetic tools to include CRISPR-Cas9 based genome editing systems. We offer access to the recently developed Toronto Knockout (TKO) genome scale CRISPR-Cas9 editing system which facilities high resolution functional genomics, in addition to the previous RNAi and human ORF collections.
- Engineered Cas9 or knockout cell lines
- Access to Guide-RNA portal/database
- Design and construction of CRISPR-Cas9 plasmids and libraries
- Access to TKO CRISPR-Cas9 libraries
- Lentivirus production
- Access to the RNAi consortium collection in arrayed or pooled format
- Access to the Human ORFeome 8.1 collection (entry clone collection)
- Access to the human and mouse TCAC collection (Origene TrueClone expression constructs)
- Assistance with pooled-genome wide screening in cell lines and assay development