This test will be available only for the following cancer types during its initial phase:
- Cholangiocarcinoma: Only cases for which a prior tumor analysis of the FGFR gene has not been performed are eligible for comprehensive genomic profiling (CGP)
- High-grade serous ovarian cancer: Only cases for which the presence or absence of a BRCA gene alteration is not already available are eligible for CGP
- Metastatic castration-resistant prostate cancer: CGP is available only for cases in which prior tumor- or blood-based BRCA testing was uninformative for actionable BRCA alterations. For CGP to be performed, the results of any prior BRCA testing must be indicated on the requisition.
No other cancer types will be accepted at this time.
This test is a capture-based targeted next-generation sequencing (NGS) assay designed for comprehensive genomic profiling (CGP) to detect somatic DNA and RNA alterations across a selected set of genes relevant to solid tumors. Although the assay includes 523 genes, analysis is restricted to a predefined subset (virtual panel) based on the availability of approved therapies in Quebec. The test detects sequence variants (SNVs and indels) and copy number variants (CNVs) in DNA, as well as gene fusions in RNA for a selected group of genes. In addition, it evaluates tumor mutation burden (TMB), microsatellite instability (MSI), and homologous recombination deficiency (HRD).
This test is performed in parallel on DNA and RNA extracted from the same fresh, frozen or formalin-fixed paraffin-embedded (FFPE) tumour specimen using the TruSight™ Oncology 500 v2 (TSO500 v2) assay (Illumina). Secondary analysis is performed using DRAGEN (Illumina), with DNA and RNA sequences aligned to reference genome GRCh37 (hg19). The DRAGEN pipeline is used to perform read mapping, sequence alignment, and identification of genomic alterations including single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants according to the manufacturer’s validated workflow. Tertiary analysis is conducted in-house, where variants are annotated using SnpEff and multiple publicly available databases to assess clinical relevance, population frequency, and known pathogenicity. Quality control metrics are assessed at both the sequencing and variant calling stages to ensure data integrity and assay performance meet predefined acceptance criteria.
This assay does not detect all possible genomic alterations, including low allelic fraction variants below the limit of detection, complex structural variants, large/complex indels or variants within regions of high complexity. Negative results do not exclude the presence of undetected alterations.
Test performance depends on tumour cell content (TCC), tumour heterogeneity and nucleic acid quality. A minimum TCC of 20% is required; samples below this threshold may yield false-negative results and are reported as unsatisfactory.
The assay cannot reliably distinguish between somatic and germline variants.
Detection thresholds and coverage requirements apply: SNVs/indels require ≥5 supporting reads at ≥250 depth (~5% allele frequency). CNV detection is limited to full gene events, with exon-level resolution detected for BRCA1 and BRCA2 and variably for other genes, depending on coverage and quality. Amplifications are reported at ≥5 copies. Valid DNA analysis requires ≥95% of targeted bases covered at ≥250. RNA-based fusion detection requires the following sequencing quality metrics: at least 9,000,000 total mapped reads; a minimum coverage of ≥500X for each gene; an acceptable coefficient of variation <93; and a median insert size ≥80 bp, with ≥5 supporting reads.
Results are generated using a capture-based method and must be interpreted in the context of clinical and other diagnostic findings. Accuracy also depends on correct sample identification and clinical information. Analytical sensitivity (FFPE samples with ≥20% tumour content) is estimated as follows: 95.06% for SNVs/indels (CI: 92.10–97.15), 96.3% for CNVs (CI: 81.03-99.91), 100% for MSI (CI: 71.51–100.00), 95% for TMB (CI: 75.13–99.87), 93% for HRD (CI: 66.13–99.82) and 100% for gene fusions (CI: 96.11–100.00).
Assay sensitivity may be reduced by poor DNA/RNA quality or low tumour content, increasing the risk of false negatives. TMB estimates may be inflated in samples with elevated chimeric alignments (>5%) and/or high tumour purity (>85%).
Variants are interpreted and categorized based on their clinical impact, as per standards and guidelines in the field (PMID: 27993330): Tier I, variants with strong clinical significance (level A and B evidence); Tier II, variants with potential clinical significance (level C and D evidence); Tier III, variants with unknown clinical significance; and Tier IV, benign or likely benign variants. Only Tier I and Tier II variants are reported. Classifications are limited by the information available for any given phenotype, gene, locus, or variant.
Structural variants classified as benign or likely benign, observed at a significant frequency among all tested samples, or in population databases with no existing published evidence of cancer association, are not reported.
Turnaround time: 15 working days
Specimens accepted:
- 10 x 10 μm scrolls in 1.5 mL tube
- 10 x 10 μm unstained slides
A tumour cell content (TCC) of 20% or more is required. This information is mandatory to assess the validity of the test.
Please see our Test information sheet for additional details.
Submit your test request using our Comprehensive genomic profiling requisition.