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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.


Since 2011, over


samples have been processed

Trusted by over




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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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.

** Scroll to the right to see the whole table.

Sample Type Product Extraction Method Kit Quantification Method Available Testing
Blood/Plasma cfDNA (cell-free DNA) Automated (King Fisher Apex) MagMAX™ Cell-Free DNA Isolation Kit 4200 TapeStation NGS
cfTNA (cell-free DNA and RNA) Automated (King Fisher Apex) MagMAX™ Cell-Free Total Nucleic Acid Isolation Kit 4200 TapeStation
Blood Plasma Manual N/A N/A N/A
Blood, bone marrow, tissue (FFPE, fresh frozen), saliva, cell lines/pellets DNA Manual QIAGEN:
  • QIAamp DNA Mini Kit
  • QIAamp DNA Micro Kit
Qubit 2.0 ddPCR (various assays)
Automated (Maxwell® RSC, QIAsymphony) Maxwell® RSC:
  • DNA/RNA FFPE Kit (co-isolation)
  • simplyRNA Tissue Kit
  • Whole Blood DNA Kit
  • QIAsymphony DSP DNA Midi Kit
Blood, bone marrow, tissue (FFPE), cell lines/pellets RNA Manual QIAGEN RNeasy Mini Kit Qubit 2.0
4200 TapeStation
ddPCR (various assays)
NGS NanoString - LSC17
Automated (Maxwell® RSC) Maxwell® RSC:
  • DNA/RNA FFPE kit (co-isolation)
  • simplyRNA Tissue Kit
Tissue miRNA Automated (Maxwell® RSC) miRNA Tissue Kit (miRNA + total RNA) TruSight Oncology 500 (Illumina)

Sample Requirements

** Scroll to the right to see the whole table.

Accepted Sample Type Extracted/Accepted
Nucleic Acids
Sample Requirements
Blood/Plasma (Streck) DNA
ddPCR: 1 full streck tube (8-10ml)
NGS: 2 full streck tubes (8-10ml each)
Blood/Bone Marrow DNA
1 ml
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.

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

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

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Next Gen Sequencing

A comprehensive investigation of cancer genes and selected non-cancer genes within patient blood/plasma 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.

** Expand the panels below or click the name of NGS Panels on the last column for more detailed information.

Sample Type Sample Source NGS Panels
cfDNA (cell-free DNA) Plasma
DNA Blood, bone marrow, tissue (FFPE, fresh frozen), saliva, cell lines/pellets (fixed or suspensions)
RNA Blood, bone marrow, tissue (FFPE), cell lines/pellets (fixed or suspensions)
▸ TSO 500 (Illumina)
  • Gene List
  • Sample type: DNA from tissue
  • Pan-cancer panel with the ability to test both DNA and RNA extracted from the same patient sample in one workflow
  • Covers coding regions of 523 cancer relevant genes from DNA and 55 genes from RNA
  • 57 regions analyzed for CNV
  • Asses SNVs, InDels, CNVs, splice variants, fusions, MSI, and TMB
Platform: Illumina NextSeq 500
Input: 40-80ng DNA; 85ng RNA
▸ DDRplus Panel
  • Gene List
  • Sample Type: cfDNA from plasma and genomic DNA from blood
  • Custom-designed panel using the Agilent Technologies SureSelect XT HS2 Target Enrichment system
  • Assesses variants in the exons and flanking introns (+/-20bp) of 201 genes involved in various DNA repair pathways, as well as those known to have predictive/prognostic and/or diagnostic utility in the clinical management of various cancers
  • Uses the incorporation of unique molecular barcodes into each library fragment at the ligation step to enable more sensitive detection of low variant allele fractions
Platform: Illumina NextSeq 500
Input: 25-50ng cfDNA; 150ng DNA
▸ 37-Gene Panel (custom)
  • Gene List
  • Sample type: cfDNA extracted from plasma and genomic DNA from bone marrow
  • Custom panel examining the exons and intron flanking regions of 37 genes involved in Multiple Myeloma
  • All coding regions of KRAS, NRAS, BRAF, PIK3CA
Platform: Illumina NextSeq 500
Input: 20ng cfDNA; 100ng DNA
▸ Other NGS Panels in development
  • Lymphoma LySeq v2 (custom)
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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

Available for Research use:

  1. nCounter XT Elements gene expression assay, LExA assay
  2. nCounter, 3 target assay (genes: CD3E, IRF4, ZAP70)
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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.

DNA and Circulating Tumor DNA (ctDNA)

  • 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 standard laboratory assays
  • Commercially available and custom designed probe sets
  • Validated genes for DNA: EGFR, KRAS, NRAS, PIK3CA, BRAF, IDH1, IDH2, JAK2, DNMT3A (others can be made on demand)
  • Validated genes for cfDNA: BRAF (others can be made on demand)

Viral DNA

  • Enables the detection of viral DNA targets down to 0.3%
  • Custom designed probe set
  • Validated targets: HPV-16 (exons 6 and 7)
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


a list of select projects we participated in

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

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

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Validating novel liquid biopsy platforms for ctDNA NGS in routine clinical use for patients with advanced lung cancer, ensuring complete genotyping and evaluating molecular resistance to targeted therapy.


Evaluating genomic markers of response, in tissue and plasma, to combination therapy of binimetinib (MEK) plus pembrolizumab (PD-L1) in patients with treatment-naïve advanced stage non-small cell lung cancer (NSCLC).


Assessment of genomic markers for response and resistance to MET inhibitors in a platform study, enabling treatment access for patients with advanced NSCLC and alterations in MET/ROS1.

Our Team

Lab Staff
  • icon of personTong Zhang (Charge Technologist)
  • icon of personJonette Martin (Senior Technologist)
  • icon of personPablo Jaramillo
  • icon of personNatalie Boruvka
  • icon of personSean Kim
  • icon of personHinal Surti
Bioinformatics Staff
  • icon of personNatalie Stickle
  • icon of personZhibin Lu
  • icon of personIrene Chae
  • icon of personRoozbeh Dolatshahi
  • icon of personGregory Downs
  • icon of personMatthew Stoodley
Annotation Specialists
  • icon of personClare Sheen
  • icon of personAyesha Kidwai
  • icon of personAndrew Seto
  • icon of personHarpreet Kaur
  • icon of personEmily Chen
  • icon of personMailoan Panchalingam


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 leverages an in-house variant knowledgebase and custom pipeline for managing reporting of variants from NGS testing. The team gathers and reviews 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 for somatic variants (Li et al., J Mol Diagn. 2017) or pathogenicity for 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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