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Driving research forward with state-of-the-art clinical laboratories.

The Advanced Molecular Diagnostics Laboratory

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Welcome to AMDL

AMDL is a clinical CAP/CLIA accredited molecular diagnostics laboratory at the Princess Margaret Cancer Centre, located on the 7th floor. The primary mission of AMDL is to support clinical trials and translational research projects requiring clinical-grade (CAP/CLIA) molecular testing at Princess Margaret Cancer Centre. AMDL works closely with our partner Molecular Diagnostics lab in Toronto General Hospital to transition protocols into clinical tests.

CLINICAL-GRADE (CAP/CLIA) MOLECULAR TESTING PROVIDED AT THE PRINCESS MARGARET

Since 2011, over

20,000

samples have been processed

Trusted by over

100

researchers

Over

9

years of experience since 2011

How Can We Help?

In collaboration with the physicians at Princess Margaret Cancer Centre and the Cancer Genomics Program, the AMDL develops, evaluates, and implements high complexity genomic tests to meet the needs of clinical programs.

Don't see what you need? Please contact us.

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Sample Prep

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NGS (Next Gen Sequencing)

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NanoString

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ddPCR (Droplet Digital PCR)

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Design and Analysis

Our Services

AMDL helps support our clients by providing tailored services and study-specific requisitions. We offer a variety of services to support research activities, including nucleic acid extraction and banking, next-generation sequencing (Illumina and Ion Torrent platforms), NanoString, ddPCR, MLPA, and Sanger sequencing. Please see below for our current testing menu or contact us for more information.


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Sample Prep

Processing and extraction along with CAP/CLIA sample banking.

FFPE Tissues

Extracted/Accepted Nucleic Acids:
  • DNA
  • RNA
Sample Requirements:
FFPE Tumour tissue with 25mm2 tumour tissue surface area (minimum 10mm2) and with minimum 30% nucleated tumour cells
  • FFPE block – 2 x1mm punch biopsies
  • FFPE slides – 15 unstained sections at 7 microns thickness on uncoated slides, air dried, stored at room temperature, and sent to lab within 5-7 days of cutting

For mdall samples (<25mm2), additional unstained slides may be needed to extract sufficient material for testing

Fresh Frozen Tissue (Laser-Capture Micro-dissected)

Extracted/Accepted Nucleic Acids:
  • DNA
Sample Requirements:
>1M cells (total)

Sample(s) must arrive in fresh cell lysis solution prepared by the lab. Please contact us.

Blood/Bone Marrow

Extracted/Accepted Nucleic Acids:
  • DNA
  • RNA
Sample Requirements:
1 ml

Blood/Plasma (Streck)

Extracted/Accepted Nucleic Acids:
  • DNA
  • cfDNA
Sample Requirements:
1 full streck tube (8-10ml)

Blood (PAXgene)

  • RNA
Sample Requirements:
1ml (8ml total once mixed with the buffer in the tube)

Nucleic Acids

Extracted/Accepted Nucleic Acids:
  • DNA
  • RNA
  • cfDNA
Sample Requirements:

Assay dependent - Please contact the laboratory to inquire

Cell suspensions/pellets, lines (or fixed cells/cell lines)

Extracted/Accepted Nucleic Acids:
  • DNA
Sample Requirements:

Assay dependent - Please contact the laboratory to inquire

Saliva

Extracted/Accepted Nucleic Acids:
  • DNA
Sample Requirements:
Full Oragene collection tube (saliva to "Fill line" on OG-600 tube, mixed with stabilizers included in integrated lid)
Sample Type Extracted/Accepted
Nucleic Acids
Sample Requirements
FFPE Tissue DNA
RNA
FFPE Tumour tissue with 25mm2 tumour tissue surface area (minimum 10mm2) and with minimum 30% nucleated tumour cells
  • FFPE block – 2 x1mm punch biopsies
  • FFPE slides – 15 unstained sections at 7 microns thickness on uncoated slides, air dried, stored at room temperature, and sent to lab within 5-7 days of cutting
For small samples (<25mm2), additional unstained slides may be needed to extract sufficient material for testing
Fresh Frozen Tissue (Laser-Capture Micro-dissected) DNA >1M cells (total)

Sample(s) must arrive in fresh cell lysis solution prepared by the lab. Please contact us.

Blood/Bone Marrow DNA
RNA
1 ml
Blood/Plasma (Streck) DNA
cfDNA
1 full streck tube (8-10ml)
Blood (PAXgene) RNA 1ml (8ml total once mixed with the buffer in the tube)
Nucleic Acids DNA
RNA
cfDNA

Assay dependent - Please contact the laboratory to inquire

Cell suspensions/pellets, lines (or fixed cells/cell lines) DNA

Assay dependent - Please contact the laboratory to inquire

Saliva DNA Full Oragene collection tube (saliva to "Fill line" on OG-600 tube, mixed with stabilizers included in integrated lid)
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Next Gen Sequencing

A comprehensive investigation of cancer genes and selected non-cancer genes within patient blood and tumour samples can provide information about diagnosis, patient risk stratification and response to therapy, as well as help determine potential application of targeted therapies for different malignancies.

▸ Hi5
  • Gene List
  • Full exons and flanking regions for 562 genes known to be involved in cancer and its clinical management
  • full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1, and an upstream promoter region of TERT, in order to aid in the detection of large deletions or duplications in these genes which are known to cause inherited cancers
  • 9 genes causing the inherited disorders Malignant Hyperthermia or Amyloidosis are also included for purposes of laboratory throughput and batching
  • 124 regions tested for microsatellite instability (MSI)
  • 44 highly polymorphic SNPs for sample identification purposes
  • Custom designed Agilent hybrid capture panel
  • DNA from solid tumour to asses SNV, InDel and CNV
Platform: Illumina NextSeq 500
Input: 250ng DNA; KAPA Input: 100ng DNA
▸ Ion TorrentTM OncomineTM Comprehensive Assay v3
  • Gene List
  • High sensitivity assay that provides insight into relevant actionable variants in tumour samples
  • 161 genes curated for high impact genomic analysis
  • Commercially available amplicon panel (ThermoFisher)
  • DNA/RNA from tumour tissue to asses SNV, InDel, Fusion and CNV
Platform: Ion Torrent, Ion S5XL
Input: 20ng DNA, 40ng RNA
  • TSO 500 (Illumina)
  • 37-gene Myeloma panel (custom)
▸ Other NGS Panels in development
  • Hematological Malignancy panel (custom)
  • FusionPlex Lung (Archer Dx)
  • Lymphoma LySeq v2 66 (custom)
  • smMIP (collaborated with OICR Dr. Sagi Abelson)
  • DDRplus panel
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NanoString

NanoString technology enables the direct detection of RNA, DNA or protein in a sample using patented molecular barcodes and a unique hybridization and detection platform.

Panels currently validated and available:

LSC17 assay: Custom 17 gene panel for stratifying acute myeloid leukemia (AML) patients for their level of relapse risk. Read more about it here.
Platform: NanoString nCounter

Technology:

  1. nCounter XT Elements gene expression assay, LSC17 assay
  2. nCounter Standard Chemistry assay, RHL30 assay (Reference)
  3. nCounter XT Elements gene expression assay, LExA assay
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Droplet Digital PCR

ddPCR enables the quantitation of nucleic acids in a sample using a miniaturized PCR procedure that is executed in a high-throughput manner.

  • Enables the detection of potentially relevant variants at frequencies as low as 0.5%
  • Somatically acquired variants that affect patient management can sometimes occur at frequencies less than ten percent (10%), which are difficult to detect by Sanger sequencing or other standard laboratory assays
  • Commercially available and custom designed probe sets
  • Validated genes include: EGFR, KRAS, NRAS, PIK3CA, BRAF, IDH1, IDH2, JAK2, DNMT3A (others can be made on demand)
Platform: BioRad QX200
Under investigation: Methylation as an indicator of tissue of origin
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Design and Analysis

Design advice for your clinical research assay and validation and testing according to CAP/CLIA guidelines

Contact us for more details

Projects

a list of select projects we participated in

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OCTANE

Ontario-wide Cancer Targeted Nucleic Acid Evaluation (OCTANE) tumour profiling initiative led by Dr. Phil Bedard.

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BioDIVA/VENUS

Gynecologic cancers molecular profiling initiatives led by Drs. Amit Oza and Stéphanie Lheureux.

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LUNGS-2

Study for NSCLC expanded molecular profiling, and detection of resistance mutations in ctDNA, led by Dr. Natasha Leighl.

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SMART-AML

Study using the Leukemia Stem Cell 17-gene signature (LSC17) assay developed by Dr. John Dick and Jean Wang, with study led by Drs. Steven Chan and Jean Wang.

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MCRN

Myeloma study examining circulating tumour DNA, led by Dr. Suzanne Trudel.

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PERSPECTIVE

Saliva DNA profiling using a custom NGS panel of 295 genetic variants relevant to breast cancer risk.

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LIBERATE

The Liquid Biopsy Evaluation and Repository Development AT Princess Margaret (LIBERATE) program facilitates biobanking liquid biopsies for future research studies from PM patients across the institute. From liquid biopsies, scientists are able to run tests to look for cancer cells or their DNA in patients without using a needle or a knife to obtain a sample from the tumor itself. Research into the use of liquid biopsies include identifying those patients with minimal residual disease (or “MRD”) where conventional scans cannot detect microscopic recurrence; tracking patients during their treatment for advanced cancer to change course early if there are signs of microscopic progression, and understanding molecular mechanisms that cause treatment resistance.

Our Team

Lab Staff
  • Tong Zhang (Charge Technologist)
  • Jonette Martin (Senior Technologist)
  • Nadia Al-Youssef
  • Pablo Jaramillo
  • Ada Wong
  • Natalie Boruvka
  • Christine Ishu
  • Adriana Verdecia
  • Hinal Surti
Bioinformatics Staff
  • Natalie Stickle
  • Zhibin Lu
  • Irene Chae
  • Gregory Downs
  • Roozbeh Dolatshahi
Annotation Specialists
  • Nicole Park
  • Andrew Seto
  • Rong Zeng
  • Clare Sheen

Questions?

Please contact the lab director to discuss your clinical research project and how we can help.

  • Advanced Molecular Diagnostics Laboratory
  • Princess Margaret Cancer Centre
  • Rm 7-606, 610 University Ave, Toronto, ON, M5G 2M9
  • Phone: 416-946-4501 x5036


AMDL offers several different advanced technologies to provide interpretable results. Details about these technologies and custom panels can be found in the ‘Our Services’ section. Information about commercially available panels can also be found on vendors’ websites. Please contact us so we can discuss and assist you with meeting your research objectives.

Contact us for more details.

The annotation team uses the variant assessment software Alissa Interpret (Agilent Technologies) to manage reporting variants from NGS testing, while gathering and reviewing evidence from curated variant and gene databases, human disease knowledge resources and clinical and scientific literature. Variants are classified based on the available evidence of the variant’s degree of clinical actionability of the somatic variants (Sukhai et al., Genet Med. 2016) or pathogenicity of the germline variants (Richards et al., Genet Med. 2015).

Please contact us for more details.

Yes, we are open to arranging visits, please contact us.

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