This test is a capture-based targeted resequencing assay designed to detect sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of 113 genes.
Sample DNA is extracted at the CMDL. Extracted DNA is sent to the Centre Québécois de Génomique Clinique (CQGC) for exome sequencing on a NovaSeq X Plus (Illumina™). The average coverage of this assay is 100X. Sequences are aligned and compared to reference genome GRCh38 and variants are detected using the DRAGEN (Illumina™) bioinformatics pipeline.
A negative result does not rule out the possibility that a variant not detected by this assay is present in this individual. Unless explicitly specified, only coding exons and flanking intronic regions are covered by this assay. This test does not detect all possible variants in the genes tested. 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). Additionally, copy number variants in PMS2 exons 11-15 may not be detected due to a highly homologous pseudogene. If there is a suspicion for a PMS2 variant, please contact the laboratory. Interpretation of results is highly dependent on the clinical and demographic information provided.
Variants are interpreted as per standards and guidelines in the field (PMID: 25741868) by CCMG-accredited molecular geneticists of the MUHC. Only clinically relevant variants are reported. Any reportable variants are confirmed by an orthogonal method. Classification of variants may change over time in 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)
Submit your test request using our molecular genetics requisition and attach the clinical information sheet.