FAQs

The Centre for Phenogenomics (formerly "Toronto Centre for Phenogenomics").

The Centre for Phenogenomics is a $69 million, state-of-the-art facility that enables groundbreaking research and discovery with the goal of advancing human health. Using mouse models, the TCP seeks cures and treatments in areas such as diabetes, cancer, musculoskeletal disease, neurodegenerative disorders, cardiovascular and renal disease, and stem cell and regenerative medicine. TCP is jointly owned and operated by Mount Sinai Hospital and The Hospital for Sick Children and serves local, national and international users.

TCP is located at 25 Orde Street, in the heart of Toronto’s Discovery District, (close to University Avenue and College Street).

Construction was completed in July 2007

Construction of TCP was funded by the Canada Foundation for Innovation (CFI), the Ontario Innovation Trust (OIT), Mount Sinai Hospital, The Hospital for Sick Children and in-kind funding from industry.

TCP is the largest vivarium in Canada with 110,000 gross sq ft of custom-designed laboratory space on four floors: two below ground and two above.

Mice are the most efficient, cost-effective and easily genetically manipulated mammalian research model. With over 95% genetic similarity to humans, mice are ideal for modelling human diseases and drug efficacy testing.

TCP LIMS is our custom laboratory information management system that allows you to request cost estimates, make service requests, submit mouse line passports, manage your cages and mice, view AUPs, SOPs, reports and forms , book equipment and safety training among many other things. To create an account go to LIMS and click the “Register New User” link. Note that if you are not the Principal Investigator (PI), either have your PI sign up for the account, listing you in his/her contact information OR set up an account on your PI's behalf, listing yourself as the contact person.

To create an account go to LIMS and click the “Register New User” link. Note that if you are not the Principal Investigator (PI), either have your PI sign up for the account OR set up an account on your PI's behalf, listing yourself as the contact person.

We provide a range of services to design and generate genetically modified mouse models using ES cell and endonuclease mediated (CRISPR/Cas9) as well as classical transgenic approaches. We also offer services to generate genetically modified rat models using endonuclease mediated (CRISPR/Cas9) approaches. For the full list of services and their description, see Model Production Services

For the complete fee schedule, see Model Production Service Fees

See Request. Clients are strongly encouraged to first contact the Services Coordinator at services@phenogenomics.ca to discuss your needs.

We prioritize all service requests on a "first-come, first-serve" basis. The timeline varies depending on other requests in the queue at the time but typically try to schedule the request within 2-3 weeks after its submission provided all required material and the paperwork (e.g approved Animal Use Protocol for investigators housing animals in TCP) are ready. It takes approximately 2 months from the scheduled experiment to weaning chimeras or founders.

ES cell clones ordered from international repositories can be shipped directly to TCP. Through our participation in the NorCOMM2 and KOMP2 (DTCC) projects (coordinated by the International Phenotyping Consortium (IMPC) ), we have obtained extensive experience in generating mouse model for phenotyping. We recommend ordering at least 2 clones for each gene of interest.

We do not require a pathogen test report for the cells from ES cell facilities at The Hospital for Sick Children (SickKids), Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, TCP and certain international repositories as samples from these facilities are regularly tested. All cells originating from or propagated in other laboratories must be tested prior to generation of chimeras. We can expand untested cells and submit them for testing on a cost-recovery basis.

Based on our experience since the early 1990s we continue to offer outbred albino morula aggregations as a primary method to generate chimeras from locally derived clones from following parental ES cell lines: R1 (129X1 x 129S1), G4 (129S6/SvEv x C57BL/6NTac) and C2 (C57BL/6NTac). We have been successfully using aggregation method with targeted C57BL/6 ES cells from international repositories in combination with specific culture conditions, for more details see http://www.ncbi.nlm.nih.gov/pubmed/20582321 . We use microinjection into C57BL/6 host embryos for external 129 ES cell lines.

The contribution of tetraploid embryos is primarily restricted to the extraembryonic tissues. Complementation of tetraploid embryos with ES cells capable of contributing to embryonic lineages results in the production of embryos, nearly 100% derived from ES cells. This approach can be used to study and bypass extraembryonic defects of mutations, to produce mutant embryos directly from ES cells without breeding for the analysis of their phenotype.

We prioritize all service requests on a "first-come, first-served" basis.

To work with mice at TCP you will first need a study plan and an approved Animal Use Protocol. Please contact the Services Coordinator at services@phenogenomics.ca to learn more about how to start a project at TCP.

TCP adheres to the Canadian Council on Animal Care (CCAC) “Care and Use of Experimental Animals Guidelines.” TCP has been granted the status of Compliance and maintains a current CCAC Certificate of GAP – Good Animal Practice®. We also maintain a current Certificate of Registration of Research Facility under the Animals for Research Act and Regulations granted by the Ontario Ministry of Agriculture, Food and Rural Affairs.

TCP is staffed with both full-time and part-time animal care staff (Veterinary Technicians and Animal Care Attendants) many of whom are certified by the Canadian Association for Laboratory Animal Science (CALAS). There is a full time Veterinarian at TCP who has specialized training in the care and use of animals for research and is board certified by the American College of Laboratory Animal Medicine (ACLAM). All animals are observed on a daily basis by trained Animal Care Attendants for signs of illness, injury or abnormal behaviour.

TCP strictly ensures that all animals are appropriately housed in compliance with the CCAC Guidelines and the OMAFRA Animals for Research Act. Mice are housed in individually ventilated cages and are fed a standard, high quality, commercially available diet that is irradiated off-site. Water is delivered to the animals through an automated system and undergoes reverse osmosis, acidification and UV irradiation to prevent microbial contamination. All mice in the facility receive environmental enrichment to improve their well-being by encouraging species-specific behaviour. All animal rooms are supplied with 100% fresh air and receive 10-15 air changes per hour. Room temperature is maintained at 20-22⁰C.

TCP is a bioexclusion mouse barrier facility and the mice are specific pathogen free (SPF). TCP operates an animal health surveillance program for all rodent colonies. “Sentinel animals" are maintained for this purpose, and regular serology, PCR, parasite and bacteriology evaluations are conducted to ensure all animals maintain a normative health status.

TCP is a specific pathogen free (SPF) facility. For these reasons, mice from other institutions must be rederived into the facility. For rederivation services see Rederivation section of Model Production. TCP will accept mice from approved commercial suppliers who meet the SPF requirements of the facility.

TCP is a secure animal facility and visitor access is limited. Visitors may be approved by management on a case-by-case basis. Please contact Betty-Jo Edgell at bettyjo.edgell@phenogenomics.ca to explain the nature of the visit.

To obtain a TCP access card you must complete and submit the Request for TCP Security Access Card form listed here . Access will be granted to those users who have completed the required training courses.

TCP is a secure facility with entry via electronic access card only. Access cards are active from 6:00am – 8:00pm, seven days a week, including holidays. If access is required outside of the times specified, please contact the Animal Care Coordinator at acc@phenogenomics.ca

Changes to AUP documents are requested by filling out the appropriate forms . The changes will be reviewed by the veterinarian and/or TCP Animal Care Committee and you will be notified once the changes have been approved.

To order mice you must complete and submit this form . Forms must be submitted before noon on Wednesday to ensure delivery the following week. Mouse strains must be listed on an approved AUP before they can be ordered.

TCP veterinary technicians can provide a variety of services to assist you with the following: colony maintenance, breeding and weaning, ear notching, tissue sampling for genotyping, blood sampling, surgical procedures, compound delivery (intraperitoneal, subcutaneous, intravenous injections), and oral gavage. Please contact Tanya Cini-Kirk at tanya.cini-kirk@phenogenomics.ca to discuss and schedule the services you require.

TCP offers customized training for a variety of surgical and technical procedures. Please contact Tanya Cini-Kirk at tanya.cini-kirk@phenogenomics.ca to discuss the training you require and we will schedule a date.

We prioritize all service requests on a "first-come, first-served" basis.

Blood must be collected for hematological analysis in 200 ul EDTA-coated capillary tubes (Drummond Microcaps, Drummond Scientific Company, Broomall, PA).  The analyzer requires a volume of 20 ul of whole blood for a successful measurement. Therefore, we collect 50-60 ul of whole blood so that we may repeat the measurement if necessary. The collected blood is dispensed immediately into a 0.5 ml microtube. The tube is then capped and the contents of the tube gently mixed by flicking the side of the tube to be sure all the blood is mixed with the anticoagulant and no clots form. The blood sample is kept at room temperature for at least 15 minutes prior to measurement in order for the cells to stabilize. The sample may be analyzed up to several hours after collection. The presence of clots within the sample or the storage of the sample on ice will greatly lower platelet counts. When it is not possible to test the blood on the day of collection, the blood samples can be stored at 2-8°C for up to 24 hours. Long term storage of whole blood is not recommended. All samples are allowed to come to room temperature prior to analysis.

In order to bring mice into TCP we require:

• One year’s worth of health testing from the room the animals are currently housed in – this is exchanged between your animal facility and our animal facility so that it may be assessed by the veterinarian
• If the health reports are satisfactory, then the animals are shipped to TCP.  A van service can be hired (enquire for fee) for transport from local animal facilities. Mice can be returned to the originating facility by van if the facility is local and the receiving facility permits this.
• The animals then undergo a second health test where feces is collected and sent for testing to confirm they are not positive for any banned pathogens (set charge/10 cages/import)
• The secondary testing takes 10-14 days and cage  per diems apply during this period
• If the animals pass this health test then they can be tested in the Clinical Phenotyping Core.

See Pathology Sample Prep Guide

See Pathology Fees

Please contact the Services Coordinator for antibody availability. We have tested over 300 antibodies and can help guide you in selecting antibodies for IHC. When searching for IHC antibodies look for commercially available ones that have been tested by the vendor or reported in the literature to work on paraffin and/or frozen sections and are cross-reactive with the test species. If website information is not available contact the vendor directly. Some vendors often provide or sell control peptides that can be useful in confirming staining specificity. It is highly recommended that you provide positive and negative control slides when possible.

The volume of plasma/serum required for each test are indicated in the "Clinical Chemistry" section of the Pathology Service page. Add an additional 10μl (min.) for each sample to account for dead volume (dead volume requirement may vary if clots are present or hemolysis has occurred).

• plasma EDTA sample submission (PDF)
• plasma Heparin sample submission (PDF)
• serum sample submission (PDF)
• panels and volume requirements (PDF)

To obtain specific protocols for sample preparation and submission, please contact the services coordinator.

See Pathology Services

Our veterinary pathologists will provide gross tissue examinations and necropsy results, a full histopathology report on prepared tissues including screening, H&E staining (the gold standard for diagnosis), special stains, immunohistochemistry interpretation and marker localization, diagnoses and a summary with recommendations. Additionally, they will interpret tissue changes due to age related, strain related or experiment related conditions within the context of all biological systems. This information can be critical in understanding mechanisms of disease and is often needed for publication of results from animal model studies.

All anatomical systems are interrelated functionally and physiologically thus necessitating the integration of information from each system by an expert. A full body necropsy assesses all organ systems, identifies any abnormalities, and interprets and interrelates findings in all tissues. Often in genetically engineered mice, lesions can be found in organs that were not expected to have any changes.

We prioritize all service requests on a "first-come, first-served" basis.

The Canadian Mouse Mutant Repository, CMMR, is Canada’s national mouse cryopreservation and recovery facility. It is located in The Centre for Phenogenomics and is dedicated to the preservation and distribution of mutant mouse lines, samples, and ES cells.

The Depositing Investigator (DI) should start the process by registering for an account in TCP LIMS. IF desired, his/her designate can also establish an account in the DI’s name (with the designate as the Contact) and provide the information requested for the completion of the service request. The first step is to create a Mouse line passport for the strain(s) to be deposited in TCP LIMS. These passports provide information about the derivation, specific mutation(s), genetic background, genotyping protocol(s), coat colour, phenotype and health status of the strain. Guidelines naming transgenic and mutant strains can be found in Rülicke et al. (2007) Laboratory Animals 41:301-311 or http://www.informatics.jax.org/mgihome/nomen/index.shtml . Mouse line passport information will be checked for accuracy and completeness.

Once a Mouse line Passport has been completed, the DI or designate should complete the appropriate service request form in TCP LIMS. Once a service request is submitted, a Material Transfer Agreement (MTA) provided by the CMMR is executed between The Hospital for Sick Children (the legal entity of the CMMR) and the DI and/or his/her institution to clearly outline the obligations of each party and disposition of samples. Once the MTA is complete, the service will be scheduled. The CMMR will receive, process, cryopreserve, and archive the mutants or samples per our fee schedule. The DI will have the option of making his/her mutants or samples available to other investigators.

The method of cryopreservation depends on the specific mutation(s) in your mouse lines, the genetic background, and the fertility and fecundity of the line.

Sperm cryopreservation cryopreserves only the male germline and is a terminal procedure. Choose Sperm Cryo when you can recover the line using commercially available donor oocytes. At least one generation of subsequent breeding will be required to generate homozygous mice.

Speed embryo cryopreservation cryopreserves the mutation(s) from the male germline after IVF with wild-type donor oocytes. Choose Speed Cryo when you want to dedicate a small number of mice from your colony for cryopreservation, you do or can maintain your mutation(s) of interest on a commercially available background, and you can accept one generation of mating after cryorecovery to produce homozygous mutant mice.

Basic embryo cryopreservation cryopreserves both the male and female germlines using embryos from naturally mated males and females from a given mouse line. This method enables the preservation of specific genetic backgrounds, homozygous alleles and/or strains with multiple alleles that would segregated if bred to wild-type mice.

Choose Basic Cryo when you have good fertility and plug rates in your colony and have at least 8 stud males to dedicate to mating for embryo harvest. While females will be transferred for embryo harvest, males may be maintained in the Requester’s colony, provided females are available there. Basic Cryo may also be performed with wild-type females when males cannot be euthanized for the purposes of cryopreservation.

Investigators can search our catalogue of mice and ES cells http://www.cmmr.ca/gene-list.html . Detailed information about gene mutations, alleles, or genetic background can be found through MGI and the International Mouse Phenotyping Consortium .

The Withdrawing Investigator or Institution (WI) initiates the process by registering for an account in TCP LIMS. Once registered, the WI completes a Service Request form to recover or withdraw their mutant of interest. If necessary, a Material Transfer Agreement (MTA) provided by the CMMR will be sent to the WI for completion prior to shipment of samples. The MTA describes the conditions associated with the use of mutants and samples and confirms the rights of the Depositing Investigator/Institution (DI).

Frozen samples are normally shipped on dry ice or in dry shippers via overnight courier at the WI’s expense. Dry shippers must be returned to the CMMR as soon as possible, at the WI’s expense, to enable their repeated use. Requests for live animals require recovery from cryopreserved samples (if applicable) and coordination of animal shipments between the CMMR and the WI’s animal facility.

Most recipients will be associated with a recognized biomedical or genetics research institution. Depositing Investigators and/or their institutions may restrict the distribution of their strains and samples.

The Depositing Investigator or Institution (DI) retains ownership of the sample(s). The CMMR acts with the DI to distribute sample(s) and notifies the DI before releasing samples from the archive. The DI may prohibit access to an archived sample. All DIs will receive updated inventories of their mutants and samples at the CMMR, along with a list of all Withdrawing Investigators/Institutions (WIs) who have received their mutants and/or samples. The DI will be responsible for the authenticity of the mutants and samples and any relevant documentation.

It is the responsibility of the WI to ensure that any executed MTAs enable their research goals and to obtain appropriate licenses for any relevant patents or other uses. Further it is the responsibility of the WI to ensure that the WI signatory(ies) on any MTA has(have) the legal authority to sign the MTA.

International WIs must conform to their country’s rules and regulations for importing or exporting biological samples and/or live animals. It is the WI’s responsibility to inform the CMMR of any regulations pertaining to or special documentation required for the shipment of requested samples or animals.

All WIs must agree to conform to the relevant governing regulations concerning the use of biological reagents and the ethical treatment of animals.

Investigators can order mice from virtually any repository. A good place to start your search is MGI and the International Mouse Strain Resource . Samples are shipped from the originating repository to the CMMR for recovery as live mice and distribution to the Requesting Investigator. Shipping gametes and cells across international borders is often less restricted than shipping live mice. The CMMR has considerable experience in the recovery of mutant mice from both sperm and embryos.

We prioritize all service requests on a "first-come, first-served" basis.