- Congenital or early-onset sensorineural/mixed hearing loss
- Sensorineural/mixed hearing loss AND family history of hearing loss (provide detailed pedigree on requisition)
- Progressive or late-onset sensorineural/mixed 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.
How to submit your request
Access to this test is restricted to physicians practicing in the following specialties:
- Medical Genetics
- Pediatrics
- Otolaryngology
If you belong to one of those specialties AND your patient meets at least one of the below indications, you are eligible to order this test.
We strongly encourage all test to be requested in Trio (preferably) or in Duo.
A Trio analysis involves providing a sample for both biological parents of your patient, in addition to their sample.
A Duo analysis involves providing a sample for one biological parent of your patient, in addition to their sample.
In order to request this test, you will need to:
- Print and fill a molecular genetics requisition for your patient AND for the parents of your patient if the test is requested in Trio or Duo.
- Print and fill an eligibility criteria form for your patient.
- Forward the samples, the filled molecular genetics requisitions and the filled eligibility criteria form to the core molecular diagnostic laboratory (CMDL) of the MUHC (address at the top of the requisition).
Please use this tutorial for how to order the non-syndromic hearing loss panel to facilitate the submission process.
The CMDL reserves the right to suspend or cancel any incomplete request OR request for which the clinical information provided suggests a syndromic etiology of hearing loss rather than a non-syndromic etiology.
If you have any question, please contact us.
Turnaround time: 6-8 weeks
Specimen accepted:
- 2 x 4 mL blood in EDTA tubes (purple top tube)
- 1 x buccal swab collected using the Oragene OCR-100 saliva kit