Liquid Biopsy Circulating Tumour DNA Sequencing (Research/Investigational Purposes Only)

Alternate test name

Liquid Biopsy Circulating Tumour DNA Low-Pass Whole Genome Sequencing (LP-WGS) 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

Cerebrospinal fluid (CSF), blood, other fluids (please specify source)

Specimen requirements

Minimum 1 mL fluid is preferred. Collect in STRECK Cell-Free DNA BCT CE tube(s). This is a specialized tube type containing a preservative reagent that allows for isolation of high-quality cell-free DNA. Please refer to the associated Lab Information Sheet: STRECK Tube Information.

Storage and transportation

FLUID SPECIMENS

Specimens must be stored and transported at room temperature (6^oC to 37^oC)
Do not refrigerate or freeze.
Specimens must be received within 7 days of collection.

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

Liquid Biopsy Circulating Tumour DNA Sequencing (Research/Investigational Purposes Only) - requisition

Background and clinical significance

Liquid biopsy is a minimally invasive alternative to surgical biopsies with multiple potential applications, including 1) diagnostic molecular characterization for patients with hard to biopsy tumours, 2) ongoing monitoring for response to treatment (minimal residual disease; MRD), 3) early detection of disease progression, and 4) development of therapy resistance through acquisition of new mutations.

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 case information, including any histological findings (if available). The Targeted Hybrid Capture Panel and Low-Pass Whole Genome 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.

This assay is optimized to work well with very low input material (such as that obtained from a liquid biopsy) of potentially low quality, but will additionally work with standard pathology specimens including formalin-fixed paraffin embedded (FFPE) or fresh frozen (FF) tissue. Refer to the related test, Tumour Genomic DNA Sequencing, for information on FFPE and FF tissue testing.

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