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

If you are writing a grant or need general guidance on liquid biopsy, archival tissue, fresh frozen tissues, protocols, informatics, workflows, ethics, contracts or a general lab overview, please review our Manual for Grant Applications, Proposals and Clinical Research Protocols (updated 180911).

Research Ethics Board (REB) Approval

TGL is a joint collaborative workspace funded by the Princess Margaret Cancer Foundation and OICR by the Government of Ontario, Ministry of Research, Innovation and Science. Various REBs exist in Ontario’s research community including but not limited to UHN (CAPCR), the University of Toronto (MHRP), SickKids, The Ontario Cancer Research Ethics Board (OCREB), and the Toronto Academic Health Science Network. PM-OICR TGL may utilize the University of Toronto's MHRP or UHN's CAPCR ethics approval board depending on the study sponsor. 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. TGL requires a copy of your protocol, consent forms, REB approval notice/letter and other relevant documentation. All projects must receive ethics 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. Review our Manual for Grant Applications, Proposals and Clinical Research Protocols (updated 180911) and 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). 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

PM-OICR TGL follows authorship guidelines for the International Committee of Medical Journal Editors (ICJME), see our Manual for Grant Applications, Proposals and Clinical Research Protocols (updated 180911) for full details. As a condition of collaboration, publications must acknowledge TGL's 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 and the Princess Margaret Cancer Foundation”. 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 parameters for tissue requests: 10 micron sections, minimum n=10, 1 hematoxylin and eosin (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. Please notify the consulting pathologist to circle tumor regions on H&E slides and the section’s % total tumor area relative to normal tissue, and within the tumor area, the % viable tumor and % necrotic tumor for the circled region. Circled tumor regions should have a minimum cellularity of 40%. Please provide a de-identified pathology report containing this information to TGL including tissue site and diagnosis. If H&E images are scanned at your institute, we request a minimum of 20X resolution (TGL scans at 40X) including pathology markup. Please forward image files as “.SVS” format (Aperio Image File Format, type code 3 recommended) via secure file transfer; images will be incorporated into cbioportal (Aperio eSlide manager interface). TGL prefers to receive marked H&E, but will accept digital scans with tumor markup to guide tissue extraction. If the entire tissue section is tumor, the entire tissue may be circled and scored. Ideally a total surface area of >150 mm2 (15mm2 tumor surface area X 10 slides) will yield sufficient DNA and RNA for exome and RNA sequencing libraries; macro dissection of multiple slides may be required. A maximum of 600mm2 of tumor tissue (100mm2 tumor surface area X 6 slides) may be extracted over 1 purification column set. This information may be detailed in PM-OICR TGL submission sheets. De-identified study codes must be used on all documentation. PM-OICR TGL requests de-identified pathology reports be forwarded through secure file transfer.

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 (850K) (Fresh frozen or FFPE) 250ng minimum- 1ug recommended*

Sequencing
Illumina TruSeq Total RNA Ribozero Gold (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*
cfMeDIP cfDNA Methylation Assay 10ng minimum*
ctDNA Targeted Sequencing Assays 10ng minimum*

Recommended Read Depths
Exome 250X Tumor 50X Normal mean target coverage 125bpX125bp
RNA-seq (Total RNA) 80 million clusters, 75bpX75bp
cfMeDIP (Methylated cfDNA Assay) 60 million clusters, minimum 75bpX75bp
ctDNA Targeted Sequencing Assays 10,000-20,000X

*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) $16.83
Tumor Tissue (FFPE) Extraction from Slides (DNA/RNA co-isolation) $19.67
cfDNA Extraction from Plasma (10mls) $43.20
Illumina TruSeq Total RNA & Sequencing (FFPE, Tumor) $926.82
Agilent SureSelect XT Exome V6 +COSMIC & Sequencing Normal (Buffy coat) $476.35
Agilent SureSelect XT Exome V6 + COSMIC & Sequencing Tumor (FFPE) $1,211.68
Illumina TruSeq Methylation EPIC Exome & Sequencing Tumor (FFPE) $1,487.56
Illumina Infinium Methylation EPIC Array Tumor (Fresh frozen) $474.26
Illumina TruSeq Methylation EPIC Array Tumor (FFPE) $568.74
cfMeDIP cfDNA Methylation Assay & Sequencing (including plasma ctDNA extraction $534.58
ctDNA Targeted Sequencing Assays, 10,000X (10-29 gene, $268.79; 30-49 gene, $361.30; 50-99 gene panel, $490.91) (updated 181130)

*Pricing reflects reagent costs, including pre-analytic MiSeq library validation (where applicable) and may be used to estimate a project budget prior to requesting an official quote. PM-OICR TGL subsidizes labor costs for academic collaborations. Official quotes include "In-Kind" contributions from UHN and OICR core funding. NovaSeq pricing may reduce your project's costs further, ask for a quote if you are considering switching from HiSeq2500 to NovaSeq. 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