Tumour Genomic DNA Sequencing (Research/Investigational Purposes Only)

Alternate test name

Tumour Genomic DNA Low-Pass Whole Genome Sequencing and Targeted Hybrid Capture Panel Sequencing

Gene name / Alternate gene name

Please refer to the associated Lab Information Sheet: Tumour and Liquid Biopsy NGS Gene Information.

Lab area

Pathology - Molecular

Method and equipment

This is a DNA-based next generation sequencing (NGS) test. Low-pass whole genome sequencing determines genome-wide copy number profiles and mismatch repair deficiency (MMRD) signatures. Targeted hybrid capture panel sequencing profiles specific fusions, SNV/indels, and gene-level CNVs in 128 cancer-related genes. Sequencing is performed via two-channel sequencing-by-synthesis (SBS) chemistry on an Illumina NovaSeq 6000 instrument.

Expected turn-around time

Fifteen (15) business days

Specimen type

Tumour

Specimen requirements

Frozen tissue (40 mg) or 10 x 10 micron FFPE sections or FFPE Block or DNA extracted from tumour (200 ng). The tissue provided must be representative of the tumour. One H&E stained slide representative of the tested tissue should be provided.

Storage and transportation

SNAP FROZEN TISSUES
• All frozen tissues must be shipped on dry ice.
• Specimen must be sent Monday through Wednesday only.
• Never place samples directly on the dry ice.
• We recommend a minimum of 4 kg (approx. 10 lbs.) of dry ice for international shipments.
• Do not over-pack. Over-packed Styrofoam will crack and dry ice will be consumed faster.
• Regulations require that the diamond shaped dry ice sticker be placed on the outside of the shipping box.

PARAFFIN SCROLLS
• Scrolls from FFPE tissues can be shipped at room temperature.
• Scrolls must be shipped immediately after shaving.

PARAFFIN BLOCKS
• Block(s) from FFPE tissues can be shipped at room temperature.

DNA
• Ship at room temperature.

To avoid compromising specimen integrity, ship Monday through Wednesday only.
Do not ship specimen on the day of or the day before a Canadian statutory holiday.
Canadian Holidays to consider:
• New Year’s Day – January 1
• Good Friday – the Friday before Easter
• Victoria Day – Monday on or before May 24
• Canada Day – July 1
• Civic Holiday – First Monday in August
• Labour Day – First Monday in September
• Thanksgiving – Second Monday in October
• Christmas Day – December 25
• Boxing Day – December 26

To avoid shipping problems:
• To schedule a shipment, contact a freight forwarder who knows how to export medical specimens from your country.
• Ask the forwarder to help you with local regulations, completing the necessary documentation and arranging to clear the shipment through Canada Customs.
• Transit times may be more than one day. Please take this into account when packaging your samples.

Shipping information

The Hospital for Sick Children

Division of Pathology

3rd Floor, Burton Wing, 555 University Avenue, Room 3110

Toronto, ON

Canada

M5G 1X8

Phone: 416-813-5967

Hours: Monday to Friday, 8 a.m. to 5 p.m.

Off hours: Please send to Rapid Response Laboratory, 555 University Avenue, Room 3642

Requisition

Tumour Genomic DNA Sequencing (Research/Investigational Purposes Only) - requisition

Background and clinical significance

DNA sequencing of tumour surgical biopsy specimens is a powerful tool for the molecular characterization of cancers.

The test has two components: Targeted Hybrid Capture Panel Sequencing and Low-Pass Whole Genome Sequencing. A custom DNA probe-based panel interrogates 128 cancer-pertinent genes to detect specific gene fusions, single nucleotide variants (SNVs) and small indels with diagnostic, prognostic and/or therapeutic relevance. Low-pass whole genome sequencing provides genome-wide copy number profiles, including whole chromosome, arm-level and segmental gains and losses, focal amplifications and deletions, and microsatellite instability (MSI)-based analysis of mismatch repair deficiency (MMRD) signatures.

Testing will be conducted based on the recommendations of our staff pathologists after they have reviewed the histological findings of the case. One H&E stained slide representative of the tested tissue should be provided for this purpose. The Low-Pass Whole Genome Sequencing and Targeted Hybrid Capture Panel Sequencing portions of the test may be ordered separately or simultaneously at the discretion of our pathologists. Sample rejection or discontinuation of testing may occur at the discretion of staff pathologists.

A liquid biopsy version of this test is available for fluid specimens in cases where surgical biopsy specimens are unavailable. Refer to the related test, Liquid Biopsy Circulating Tumour DNA Sequencing, for more information.

Please note: this test is currently for research/investigational purposes only, pending licensing by the Laboratories and Diagnostics Branch of Ontario’s Ministry of Health.

Disease condition

Cancer, central nervous system (CNS) tumours, extra-CNS solid tumours, lymphoma, leukemia