Sample Submissions

TGL supports clinical genomics through integrated collaborative research networks within Canada, including the Princess Margaret Cancer Genomics Program (CGP) and Tumor Immunotherapy Program (TIP). TGL specializes in sequencing and analysis methods for low input Formalin Fixed Paraffin Embedded (FFPE) cancer tissues. Our expertise includes exome, RNA-seq, methyl-exome, and methyl-array (Illumina Infinium MethylationEpic) methods. If you have a project that is aligned with PM-OICR TGL’s strategic initiatives, and require more information about accessing TGL resources, please contact Dax Torti (dax [dot] tortiatoicr [dot] on [dot] ca) for further details. If your project is approved, please see below for general submission guidelines.

text for grant applications

We have summerized PM-OICR TGL's protocols, informatics, workflows, and lab overview into a document for easy "copy and paste" into grant applications, proposals and clinical research protocols. Please see our Manual for Grant Applications, Proposals and Clinical Research Protocols.

Research Ethics Board (REB) Approval

TGL is a joint collaborative workspace funded by PM and OICR. Various REBs exist in Ontario’s research community including but not limited to UHN, the University of Toronto, SickKids, The Ontario Cancer Research Ethics Board (OCREB), and the Toronto Academic Health Science Network. Please note PM-OICR TGL’s board of record is the University of Toronto. Please ensure that you have submitted an amendment to your respective REB, including TGL as part of your workflow and how our lab will assist in your research. For UHN collaborations, please review our UHN CAPCR submission workflow. TGL will require a copy of your amended protocol, consent template, REB approval notice and other relevant documentation. In all cases, TGL labs will submit an admin review to the University of Toronto. All projects must receive admin approval before initiating.

Multi-center trials submitted through OCREB that will involve TGL require a separate full application to the University of Toronto REB board. TGL will require all relevant REB documentation to formulate a submission.

REB approvals may take four to eight weeks for approval, please provide all requested documentation to expedite projects. Speak to your clinical research program manager, or call for further information.

Material, Intellectual Property & Data Transfer Agreements

The movement of biological samples and data between institutes is regulated by REBs and institutional legal departments. UHN projects may be covered under our UHN-OICR master agreement (MCA 2016-0694). For UHN collaborations, please review our UHN CAPCR submission workflow. If your research project is covered by MCA2016-0694 please review our Statement of Work form template. Other agreements and templates may apply to your project, please inquire. Please contact Dax Torti (dax [dot] tortiatoicr [dot] on [dot] ca), if assistance is required.

Required Research Acknowledgements

As a condition of collaboration, publications must acknowledge OICR funding as follows: “This study was conducted with the support of the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, Ministry of Research, Innovation and Science”. We ask that you also acknowledge the contributions of the PM-OICR Translational Genomics Laboratory in publications.

Tumor Tissue Recommendations (Pathology departments)

PM-OICR TGL recommends the following for pathology tissue lab requests: 10 micron sections, minimum n=12, 1 H&E at the top of the sectioning stack to establish tumor cellularity, 10 unstained slides cut onto uncharged slides (if study includes immunohistochemistry assays, charged slides are required), and 1 H&E at the end of the sectioning stack to verify tumor cellularity. If there are discrete areas of tumor, please request the pathologist to circle regions on the two requested H&E slides and score the % tumor cells, % necrosis for the circled region. If the entire tissue section is tumor, the entire tissue may be circled and scored. A tumor surface area >15mm^2 on a marked H&E slide (15mm^2*10 slides) will yield sufficient DNA and RNA for exome and RNA sequencing libraries. Tumors with a marked H&E surface area <15mm^2 may be extracted for DNA or RNA only, not both; 10 or more slides are recommended. This information may be detailed in PM-OICR TGL submission sheets. De-identified study codes must be used on all documentation.

Sample Submissions

All samples require a sample submission sheet. Samples may be dropped off in person at TGL labs between 10-4 p.m. on normal business days. Please note OICR is located on the fifth floor at 661 University Avenue. Take the elevator bank across from the west tower reception desk. Access to OICR is restricted. A receptionist at OICR will notify TGL of your arrival. For shipping instructions, see below.

TGL offers a select menu of sequencing and Illumina bead array technologies. See each of the options and sample requirements below:

Illumina Infinium Bead Array
Illumina MethylationEPIC BeadChIP (Fresh frozen or FFPE) 250ng minimum- 1ug recommended*

Sequencing
Illumina TruSeq Total RNA (FFPE) 200 ng minimum - 500ng recommended*
Agilent SureSelect XT Exome V6 + COSMIC (FFPE) 100ng minimum - 200 ng recommended*
Illumina TruSeq Methylation EPIC Exome (FFPE) 500ng minimum*

Recommended Read Depths
Exome 150X Tumor 50X Normal mean target coverage 125bpX125bp
RNA-seq (Total RNA) 80 million clusters, 75bpX75bp

*Recommended amounts assume material is DNase treated (RNA), or RNase Treated (DNA), and quantified with florescent dye such as Qubit. Nanodrop is not a suitable method for nucleic acid quantification. TGL will verify submitted quantifications. FFPE is routinely sequenced, however due to variability in sample age, storage, and fixation methods, results (including mean target coverage, duplicate rate) cannot be guaranteed.

Academic Costs*

Buffy Coat Extraction (Normal) $3
Tumor Tissue Extraction from Slides $18
Illumina TruSeq Total RNA (FFPE, Tumor) $920
Agilent SureSelect XT Exome V6 +COSMIC Normal (Buffy coat) $420
Agilent SureSelect XT Exome V6 + COSMIC (Tumor FFPE) $1,070
Illumina TruSeq Methylation EPIC Exome (FFPE, Tumor) $1,050
Illumina Infinium Methylation EPIC Array (Fresh frozen) $495
Illumina TruSeq Methylation EPIC Array (FFPE, Tumor) $590

*Pricing reflects reagent costs and may be used to estimate a project budget prior to requesting an official quote. PM-OICR TGL subsidizes labor costs for academic collaborations. Distinct recovery tiers and taxes apply to non-academic partnerships.


Procurement

Request a quote for the cost of your sequencing or array project. All sequencing and array requests should be submitted with a valid institutional Purchase Order (PO). Lab generated POs are not acceptable. Further instructions are provided on our quote. POs should be forwarded to dax [dot] tortiatoicr [dot] on [dot] ca.

Shipping

International shipments must include three copies of a commercial invoice form. If shipping from North America, ship no later than Wednesday for customs clearance. For international shipments, please ship on Mondays. Include an appropriate amount of dry ice based on your package’s expected transit time. Forward sample sheet in advance of shipment, including tracking ID.

Contact the PM-OICR Translational Genomics Laboratory

Dax Torti

Project Manager
PM-OICR Translational Genomics Lab

Email: dax [dot] tortiatoicr [dot] on [dot] ca

Phone: 647-260-7938

Ontario Institute for Cancer Research (OICR)
MaRS Centre
661 University Avenue
Toronto, Ontario M5G 0A3
Canada