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

The Advanced Molecular Diagnostics Laboratory

Get Started

Welcome to AMDL

AMDL is a clinical CAP/CLIA accredited molecular diagnostics laboratory at the Princess Margaret Cancer Center (PMCC), 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 PMCC. 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 PMCC 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.

Icon image of two test tubes

Sample Prep

Icon image of dna

NGS (Next Gen Sequencing)

Icon image of nanostring

NanoString

Icon image of several droplet

ddPCR (Droplet Digital PCR)

Icon image of magnifying glass

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.


Icon image of two test tubes

Sample Prep

Processing and extraction along with CAP/CLIA sample banking.

FFPE Tissues 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

Blood/Bone Marrow Requirements:

1 ml

Plasma (Streck) Requirements:

1 full streck tube (8-10ml)

RNA (PAXgene) Requirements:

1ml (8ml total once mixed with the 6.9ml of additives in the tube)

Nucleic Acids Requirements:

Assay dependent - Please contact the laboratory to inquire

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

Assay dependent - Please contact the laboratory to inquire
Sample Type Requirements
FFPE Tissue 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
Blood/Bone Marrow 1 ml
Plasma (Streck) 1 full streck tube (8-10ml)
RNA (PAXgene) 1ml (8ml total once mixed with the buffer in the tube)
Nucleic Acids Assay dependent - Please contact the laboratory to inquire
Cell suspensions/pellets, lines (or fixed cells/cell lines) Assay dependent - Please contact the laboratory to inquire
Saliva Full Oragene collection tube (saliva to "Fill line" on OG-500 tube, mixed with stabilizers included in integrated lid)
Icon image of dna

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
▸ Hereditary Cancer Panel and MLPA (BRCA1, BRCA2)
  • Gene List
  • Full exons and flanking regions for 52 hereditary cancer genes and 9 non-cancer genes
  • Full length (exons and introns) of 3 genes, BRCA1, BRCA2 and MLH1
  • 44 highly polymorphic SNPs for sample identification purposes
  • Custom designed hybrid capture panel
  • DNA from blood to asses SNV, InDel and CNV
Platform: Illumina NextSeq 500 or MiSeq
Input: 250ng DNA
▸ Ion TorrentTM OncomineTM Lung cfDNA Assay
  • Gene List
  • Cell free DNA (cfDNA) isolated from plasma enables a non-invasive and cost-effective alternative to traditional biopsy samples
  • Low input, tumour-type specific, multi-biomarker assay covering 11 genes (ALK, BRAF, EGFR, ERBB2, KRAS, MAP2K1, MET, NRAS, PIK3CA, ROSI, and TP53) and 169 hotspots
  • Targets mutations in non-small cell lung cancer (NSCLC) cells
  • Derived from circulating cfDNA
  • Detection of low frequency variants (0.1%)
cfDNA input: 20ng
Platform: Ion Torrent, Ion S5XL
Panel: commercially available (ThermoFisher)
▸ Other NGS Panels in development
  • 37-gene Myeloma panel (custom)
  • Hematological Malignancy panel (custom)
  • TSO 500 (Illumina)
  • FusionPlex Lung (Archer Dx)
  • Lymphoma LySeq66 (custom)
  • smMIP (collaborated with OICR Dr. Sagi Abelson)
Icon image of nanostring

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)
Under Assessment: nCounter Cancer CN assay
Icon image of several droplet

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
Icon image of magnifying glass

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

picture of Dr. Brenard

OCTANE

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

picture of Dr.  Marcus

POCP

Prevent Ovarian Cancer Project (POCP) study for early detection of ovarian cancer, led by Dr. Marcus Bernardini.

picture of bio diva

BioDIVA/VENUS

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

picture of lungs

LUNGS-2

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

picture of smart aml

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.

picture of mcrn

MCRN

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

picture of perspective

PERSPECTIVE

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

Our Team

Lab Staff
  • Tong Zhang (Charge Technologist)
  • Jonette Martin (Senior Technologist)
Research Technologists
  • Nadia Al-Youssef
  • Alex Anabusi
  • Yao Chen
  • Pablo Jaramillo
  • James Thurber
  • Ada Wong
Bioinformatics Staff
  • Natalie Stickle
  • Zhibin Lu
  • Irene Chae
  • Gregory Downs
  • Roozbeh Dolatshahi
Annotation Specialists
  • Nicole Park
  • Andrew Seto
  • Rong Zeng

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 cases and variants for reporting, 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.

Inquiry Form

We will get in touch with you shortly.

Icons made by Freepik from www.flaticon.com is licensed by CC 3.0 BY