- Congenital or early-onset sensorineural hearing loss
- Sensorineural hearing loss AND family history of hearing loss (provide detailed pedigree on requisition)
- Progressive or late-onset sensorineural hearing loss AND acquired causes excluded
This test is a capture-based targeted sequencing assay designed to detect sequence alterations (SNVs, indels) and copy number variants (CNVs) in the coding exons and flanking intronic regions (+/- 10 bp) of 169 genes.
Sample DNA is extracted at the CMDL and sent to the Centre Québécois de Génomique Clinique (CQGC) for exome and mitochondrial DNA sequencing using KAPA HyperExome v2 capture (Roche Diagnostics™) on a NovaSeq X Plus (Illumina™). Sequences are aligned and compared to reference genome GRCh38 for the 169 genes included in the panel and variants are detected using the DRAGEN (Illumina™) bioinformatics pipeline. This analysis reaches an average coverage of 100X. A multiplex ligation-dependent probe amplification (MLPA) is performed in parallel for confirmation of copy number variants (CNVs) in STRC, CATSPER2 and OTOA. Any reportable variants that do not reach minimum quality standards are confirmed by an orthogonal method (Sanger, qPCR). Reportable single nucleotide variants (SNVs) and insertions/deletions identified in STRC and OTOA are confirmed by long range PCR to exclude pseudogene variants. Sample identity is verified by comparing the genotype of 16 single nucleotide polymorphisms (SNPs) obtained from sequence alignment with the results of an independent genotyping method (SNaPshot™, Applied Biosystems™).
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, and postzygotic variants, may not be detected (PMID: 34007000). This assay also may not identify low mosaicism variants or exclude parental germline mosaicism for *de novo* variants. In addition, some variants in the following genes may not be reliably detected due to pseudogene regions/duplicated segments: ACTG1, ALMS1, CISD2, ESPN, PNPT1, PRPS1, RDX, and TIMM8A. If you suspect a variant in one of those genes, please contact the laboratory. Base on validation studies, the threshold for detection of mitochondrial heteroplasmy is estimated at 5-10%. 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). For some genes, interpretation is done using the guidelines of a ClinGen variant curation expert panel (VCEP). Only clinically relevant variants are reported. (Likely) benign variants, variants of uncertain significance (VUS) with limited evidence for pathogenicity, non-actionable low-risk alleles and carrier statuses for disorders with low clinical correlation are not reported, as per guidelines in the field (acgs.uk.com/quality/best-practice-guidelines). 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)
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 the completed eligibility criteria form.