Sample Submission & Costs
How to Submit Samples to Us
TGL supports clinical research studies by through collaborative research networks within Canada, including the Princess Margaret Cancer Genomics Program (CGP), Tumor Immunotherapy Program (TIP) , and the Terry Fox Marathon of Hope Initiative.
TGL specializes in library synthesis, sequencing, analysis, and accredited clinical reporting for cfDNA, and Formalin Fixed Paraffin Embedded (FFPE) and/or fresh frozen tissue based genomic assays. Our oncology expertise focuses on IQMH/CAP accredited assays including total RNA, whole genome, and targeted ctDNA assays.
If your study requires accredited assays with clinical report please contact Dax Torti firstname.lastname@example.org for further details. If your existing Research Only (RUO) project is ongoing, please see below for general submission guidelines.
Manual 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 the following:
Required Ethics Approvals
Various ethics boards 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 board depending on the study sponsor.
Please ensure that you have submitted an amendment to your respective REB, including TGL and OICR Genomics as part of your workflow and how our lab will assist in your research. TGL requires a copy of the study protocol, consent forms, REB approval notice/letter, and other relevant study documentation.
Review our Manual for Grant Applications, Proposals and Clinical Research Protocols (V1.10, updated 200727) and speak to your clinical research program manager, or call for further information.
All projects must receive ethics approval before initiating.
Personal Health Information (PHI) is restricted. For CAP/IQMH accredited assays, limited PHI may be submitted through our secure requisition portal including patient name, date of birth, referring physician and hospital, tissue collection date and referring lab. Only study clinical coordinators affiliated with the clinical research study and submitting healthcare provider, or CCMG/ACMG certified medical geneticists may review/access this information. We will also collect the following non-PHI: patient study ID, patient sample study ID, site of biopsy/surgery, primary cancer diagnosis, tumor type, oncotree code, % tumor cellularity and % tumor necrosis.
All accredited assay submissions must use our secure requisition portal. Request an account upon study approval. Tissues submitted for accredited assays must include a shipment manifest generated by our requisition portal. Samples may only be identified with patient study ID, patient sample study ID, and requisition ID. Accredited assay submissions must never contain labels with PHI, PHI may only be submitted through our secure requisition portal.
Material, Intellectual Property And 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 TGL’s UHN-OICR master agreement (MCA 2016-0694) and study specific Statement of Work form template. Three party agreements and/or alternate agreement structures may be required, particularly studies with clinical reporting requirements. Please contact Dax Torti (email@example.com).
Collaborative 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 (V1.10, updated 200727) 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 appreciate publication acknowledgements that recognize contributions of the PM-OICR Translational Genomics Laboratory.
Tumour Tissue Recommendations
FFPE tissues: 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.
Fresh frozen tissues: when/if cutting OCT mounted tissue for H&E or other purposes, always seal the cut surface with additional OCT and freeze. We recommend wrapping the tissue in parafilm, then aluminum foil, to prevent ice crystal formation/tissue structural damage.
A total tumor surface area of >150 mm2 (15mm2 tumor surface area X 10 slides) will yield sufficient DNA and RNA for whole genome and transcriptome sequencing libraries; macrodissection of multiple slides may be required. A maximum of 600mm2 of tumor tissue (100mm2 tumor surface area X 6 slides) may be extracted. In general, a “pinky sized” tumor will require 10 sections, while a thumbnail size tumor will require 5 sections.
250 ul of Buffy Coat is required for whole genome assays. Alternatively, 1X10ml EDTA or STRECK tube may be submitted.
ctDNA assays require 3*10ml STRECK tubes for each blood draw.
LCM tissues: LCM tissues must be shipped in extraction buffer. Contact firstname.lastname@example.org.
A pathologist must mark the tumor area on H&E with permanent black marker. We request the pathologist estimate the % total tumor area relative to normal tissue within the tumor area, the % viable tumor and % necrotic tumor for the circled region. Circled tumor regions should have a minimum cellularity of 40%. CAP-IQMH submissions require entry of this information into our digital requisition form.
Please provide a de-identified pathology report for research use only studies (RUO). 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).
All Research Use Only (RUO) assays require a sample submission sheet. Access to OICR is restricted. A receptionist at OICR will notify TGL of your arrival. Samples may be dropped off in person at TGL labs between 10-4 p.m. on normal business days. OICR is located on the fifth floor at 661 University Avenue. Take the elevator bank perpendicular to the MaRS west tower reception desk. For shipping instructions, see below.
Accredited (IQMH/CAP) assay submissions must be submitted and approved through our online study specific requisition portal. Program Managers may request accounts for their assigned clinical coordinators. All accredited assay sample submissions must route to OICR Genomics’ Tissue Portal.
TGL currently supports existing research only project streams. All new projects are restricted to those studies requiring accredited assays and clinical reports. Legacy Research Use Only (RUO) assay input guidance is provided below. If your RUO project will be hosted on cBioPortal, please complete a cBioPortal Access Request Form.
|Research Use Only Assay Options|
|Whole Genome (FFPE or fresh frozen-LCM)||100 ng minimum (FFPE); 25 ng minimum (fresh frozen, LCM)|
|Illumina TruSeq Total RNA Ribozero Gold (FFPE or fresh frozen-LCM)||200 ng minimum (FFPE); 50ng minimum (fresh frozen, LCM)|
|cfMeDIP Methylation Assay||10ng minimum|
|cfMeDIP Methylation Assay + Targeted Sequencing (Dual Assay)||50ng minimum|
|ctDNA Targeted Sequencing Assays||10ng minimum; preferable 40ng|
|IQMH/CAP Assay Options|
|Whole Genome (FFPE or fresh frozen-LCM)||Minimum 80X Tumor, 30X normal|
|Illumina TruSeq Total RNA Ribozero Gold (FFPE or fresh frozen-LCM)||80 million clusters|
|ctDNA Targeted Sequencing Panels (Bespoke)||10,000-20,000X|
Recommended inputs 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.
Research Use Only (RUO) Costs
|Research Use Only Assay Options|
|Buffy Coat Extraction (Normal)||$13.94|
|Tumor Tissue (FFPE/fresh frozen) Extraction from Slides (DNA/RNA co-isolation)||$19.67|
|cfDNA Extraction from Plasma (10mls)||$45.28|
|Shallow Whole Genome (sWGS) (FFPE/fresh frozen, Tumour)||$81.99|
|Illumina TruSeq Total RNA & Sequencing (FFPE/fresh frozen, Tumor)||$984.31|
|cfMeDIP cfDNA Methylation Assay & Sequencing (including plasma ctDNA extraction)||$884.76|
|ctDNA Targeted Sequencing Assays, 10,000X or 20,000X||Variable on design|
*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.
Request a quote for the cost of your sequencing project.
All sequencing 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 email@example.com.
International shipments must include three copies of a commercial invoice form.
If shipping from North America, ship no later than Wednesday to ensure 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.
IQMH/CAP accredited submissions must utilize our online requisition submission portal. Contact firstname.lastname@example.org.
Dr. Dax Torti
PM-OICR Translational Genomics Lab
661 University Avenue
Toronto, Ontario M5G 0A3