This test may be ordered for patients with the following tumour types:
- Breast (Triple-negative, HER2-negative, high-risk ER+, gBRCA-positive*)
- Ovarian (High-grade non-mucinous)
- Prostate (Castration-resistant)
- Pancreas (All)
* Patients with a germline BRCA1/2 pathogenic variant
This test detects sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of BRCA1 (NM_007294.4) and BRCA2 (NM_000059.4). Selected known pathogenic non-coding variants are also covered by this assay.
Panel content
| Gene | Transcript |
|---|---|
| BRCA1 | NM_007294.4 |
| BRCA2 | NM_000059.4 |
Targeted regions are enriched using hybridization probes (IDT) and sequencing libraries are prepared using the Illumina DNA Prep with Enrichment kit. Paired-end massively parallel sequencing of 150-bp fragments is performed with an Illumina instrument. Sequences are aligned and compared to reference genome GRCh37. Variants are interpreted as per standards and guidelines in the field (PMID: 25741868). Only clinically relevant variants are reported. Benign/likely benign variants, variants of uncertain significance with limited evidence for pathogenicity, and non-actionable low-risk alleles are not reported. Clinically relevant variants are confirmed by an orthogonal method (amplicon-based sequencing, gap-PCR, TaqMan, or MLPA). CNV results are confirmed by MLPA.
A negative result does not rule out the presence of an alteration that is present below the limits of detection of this assay. The minimum percentage of tumour nuclei required in the submitted sample is 10%; lower percentages may result in false negatives. All samples with less than 10% tumour nuclei will be reported as unsatisfactory. The minimum percentage of tumour nuclei required for CNV detection is 40%; lower percentages may result in false negatives. This test does not allow definitive differentiation between germline and somatic variants. Test sensitivity can vary depending on DNA quality, tumour cell percentage, and tumour heterogeneity.
For SNVs and indels, the threshold for variant calling is set at five or more reads, at a minimal sequencing depth of 250 reads, which are the recommended criteria to confidently call variants at an allele frequency of 5% (PMID: 28341590). For DNA sequences, at least 95% of targeted bases must be covered by 250 reads or more to qualify a sample as valid for analysis. The ability to detect CNVs is highly dependent on the quality of the DNA, and therefore poor quality DNA may result in an inability to detect CNVs and an unsatisfactory result.
Only clinically relevant variants (i.e. Pathogenic/Likely pathogenic) are reported.
Turnaround time: 4-6 weeks
Specimens accepted:
- 10 x 10 μm scrolls in 1.5 mL tube
- 10 x 10 μm unstained slides
- A tumour cell content (TCC) of 10% or more is required. This information is mandatory to assess the validity of the test.
Please see our Preparation and Shipping Guidelines for additional details.
Submit your test request using our solid tumour requisition.