This test detects sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of 31 genes. Selected known pathogenic non-coding variants are also covered by this assay.
Panel content
| Gene | Transcript |
|---|---|
| APC | NM_000038.6 |
| ATM | NM_000051.4 |
| BARD1 | NM_000465.4 |
| BMPR1A | NM_004329.3 |
| BRCA1 | NM_007294.4 |
| BRCA2 | NM_000059.4 |
| BRIP1 | NM_032043.3 |
| CDH1 | NM_004360.5 |
| CDKN2A | NM_000077.5, NM_058195.4 |
| CHEK2 | NM_007194.4 |
| CTNNA1 | NM_001903.5 |
| EPCAM | NM_002354.3 |
| GREM1 | NM_013372.7 |
| HOXB13 | NM_006361.6 |
| MLH1 | NM_000249.4 |
| MSH2 | NM_000251.3 |
| MSH3 | NM_002439.5 |
| MSH6 | NM_000179.3 |
| MUTYH | NM_001048174.2 |
| NF1 | NM_001042492.3 |
| NTHL1 | NM_002528.7 |
| PALB2 | NM_024675.4 |
| PMS2 | NM_000535.7 |
| POLD1 | NM_002691.4 |
| POLE | NM_006231.4 |
| PTEN | NM_000314.8 |
| RAD51C | NM_058216.3 |
| RAD51D | NM_002878.4 |
| SMAD4 | NM_005359.6 |
| STK11 | NM_000455.5 |
| TP53 | NM_000546.6 |
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. Sample identity is confirmed in parallel using Applied Biosystems™ SNaPshot™ Multiplex Kit. Sequence variants are called using VarDict (PMID: 27060149) and annotated using SnpEff (http://pcingola.github.io/SnpEff/). Copy number variants (CNVs) are detected using a depth of coverage analysis converted to a log2 scale. CNVs are called if at least 3 consecutive probes have less than 1.5 copies (deletion) or more than 2.4 copies (duplication). Variants are interpreted as per standards and guidelines in the field (PMID: 25741868).
Clinically relevant copy number variants are confirmed by an orthogonal method (gap-PCR, TaqMan or microarray), and only whole exon deletions/insertions for BRCA1 and BRCA2 are confirmed by MLPA (BRCA1 probe mix P002, lot number D1-0823, and BRCA2 probe mix P090 lot number C1-0622).
Based on validation study results, this test achieves >99% analytical sensitivity and specificity for SNVs, indels and CNVs. A negative result does not rule out the possibility that a rare variant not detected by this assay is present in the individual. This test does not detect all possible variants in the genes tested. Unless explicitly specified, only coding exons and flanking intronic regions are covered by this assay. Furthermore, technically challenging variant types, such as large indels, small CNVs, complex rearrangements, low-complexity repeat associated, segmental duplication associated, and postzygotic variants, may not be detected (PMID: 34007000). Interpretation of results is highly dependent on the clinical and demographic information provided.
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. Classification of variants may change over time in the light of new knowledge. Please contact the laboratory if variant reinterpretation is needed.
Turnaround time: 4-6 weeks
Specimen accepted:
- 2 x 4 mL blood in EDTA tubes (purple top tube)
Please review the eligibility criteria form to determine if the patient is eligible for testing.
Submit your test request using our molecular genetics requisition and attach the completed eligibility criteria form.