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FeedbackMassively Parallel Sequencing
- Diagnostic test or carrier screening for GJB2-related nonsyndromic hearing loss (NSHL)
- May be used as first-tier genetic test for individuals with suspected autosomal recessive NSHL
Polymerase Chain Reaction (PCR)/Capillary Electrophoresis
- Diagnostic test for individuals with NSHL and one identified GJB2 variant
- Carrier screening if family history of GJB6 deletion or for reproductive partner of individual with GJB6 or GJB2 pathogenic variants
Massively Parallel Sequencing
- Testing for a known familial sequence variant by sequencing gene of interest. A copy of the family member’s test result documenting the familial gene variant is REQUIRED.
- To determine if the variant(s) of interest are detectable by this assay, contact an ARUP genetic counselor at 800-242-2787.
Hearing loss can be syndromic or nonsyndromic and may be a result of genetic, physiologic, or disease factors. Depending on the cause, hearing loss may have a variable age of onset from birth to early childhood and range in severity from mild to profound. A genetic cause is found in 50% of individuals born with hearing loss. Genetic testing to determine the etiology of hearing loss can identify previously unrecognized syndromic forms of hearing loss and may be used for genetic counseling to assess the chance of recurrence.
Disease Overview
Symptoms
Hearing loss may be:
- Prelingual or postlingual in onset
- Syndromic (associated with other findings) or nonsyndromic
- Sensorineural, conductive, or mixed etiology
- Variable in presentation based on genetic and environmental cause(s) of the hearing loss
Prevalence and/or Incidence
- 1/500 born with hearing loss
- Up to 50% of individuals with severe-to-profound autosomal recessive hearing loss have one or two pathogenic variants in the GJB2 gene. However, the prevalence varies by ethnicity.
- Approximately 99% of these individuals are homozygous or compound heterozygous for pathogenic variants in GJB2.
- Approximately 1% of these individuals have one GJB2 pathogenic variant and a GJB6 deletion.
- Large GJB6 gene deletions involving GJB2 cis-regulatory elements result in loss of GJB2 expression.
Genotype-Phenotype Correlation
- GJB2 (connexin 26) or GJB6 (connexin 30) biallelic variants: sensorineural NSHL that is commonly stable and bilateral with prelingual onset
- Truncating GJB2 variants are associated with a higher chance for severe hearing loss than nontruncating variants
- GJB2 autosomal dominant sequence variants: causative of autosomal dominant deafness type 3A (DFNA3A) as well as syndromic forms of hearing loss including keratosis and ichthyosis
Test Interpretation
Connexin 26 (GJB2) Sequencing and Deletion/Duplication
Gene(s) Tested
GJB2 (NM_004004)
Testing Procedure
This test is performed using the following sequence of steps:
- Selected genomic regions, primarily coding exons and exon-intron boundaries, from the targeted genes are isolated from extracted genomic DNA using a probe-based hybrid capture enrichment workflow.
- Enriched DNA is sequenced by massively parallel sequencing (MPS; also known as next generation sequencing [NGS]) followed by paired-end read alignment and variant calling using a custom bioinformatics pipeline. The pipeline includes an algorithm for detection of large (single exon-level or larger) deletions and duplications.
- Sanger sequencing is performed as necessary to fill in regions of low coverage and in certain situations, to confirm variant calls.
- Large deletion/duplication calls made using MPS are confirmed by an orthogonal exon-level microarray when sample quality and technical conditions allow.
Clinical Sensitivity
Greater than 99% for GJB2-associated hearing loss (DFNB1A)
Analytic Sensitivity/Specificity
| Variant Class | Analytic Sensitivity (PPA) Estimatea (%) and 95% Credibility Region (%) |
Analytic Specificity (NPA) (%) |
|---|---|---|
|
SNVs |
>99 (96.9-99.4) |
>99.9 |
|
Deletions 1-10 bpb |
93.8 (84.3-98.2) |
>99.9 |
|
Insertions 1-10 bpb |
94.8 (86.8-98.5) |
>99.9 |
|
Exon-levelc Deletions |
97.8 (90.3-99.8) (single coding GJB2 exon) |
>99.9 |
| Exon-levelc Duplications |
83.3 (56.4-96.4) (single coding GJB2 exon) |
>99.9 |
|
aGenes included on this test are a subset of a larger methods-based validation from which the PPA values are derived. These values do not apply to testing performed by multiplex ligation-dependent probe amplification (MLPA). bVariants greater than 10 bp may be detected, but the analytic sensitivity may be reduced. cIn most cases, a single exon deletion or duplication is less than 450 bp and 3 exons span a genomic region larger than 700 bp. bp, base pairs; NPA, negative percent agreement; PPA, positive percent agreement; SNVs, single nucleotide variants |
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Limitations
- A negative result does not exclude a heritable form of hearing loss.
- Diagnostic errors can occur due to rare sequence variations.
- Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplant.
- The following will not be evaluated:
- Variants outside the coding regions, intron-exon boundaries and selected noncoding variants of GJB2
- Regulatory region variants and deep intronic variants
- Breakpoints of large deletions/duplications
- Noncoding transcripts
- The following may not be detected:
- Deletions/duplications/insertions of any size by massively parallel sequencing
- Some variants due to technical limitations in the presence of pseudogenes, repetitive, or homologous regions
- Low-level somatic variants
Hearing Loss, Nonsyndromic, Connexin 30 (GJB6) 2 Deletions
Gene(s) Tested
GJB6
Clinical Sensitivity
Analytical Sensitivity
99%
Limitations
- Diagnostic errors can occur due to rare sequence variations.
- GJB6 variants other than 309kb del(GJB6-D13S1830) and 232kb del(GJB6-D13S1854) will not be identified.
- Interpretation of this test result may be impacted if the individual has had an allogeneic stem cell transplant.
References
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24651602
Alford RL, Arnos KS, Fox M, et al. American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis of hearing loss. Genet Med. 2014;16(4):347-355.
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GeneReviews - Hereditary Hearing Loss and Deafness Overview
Shearer AE, Hildebrand MS, Smith RJH. Hereditary hearing loss and deafness overview. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Jul 2017; accessed Dec 2021.
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GeneReviews - Nonsyndromic Hearing Loss and Deafness, DFNB1
Smith RJH, Jones MKN. Nonsyndromic hearing loss and deafness, DFNB1. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Aug 2016; accessed Dec 2021.
GeneReviews - Nonsyndromic Hearing Loss and Deafness, Mitochondrial
Usami S, Nishio S. Nonsyndromic hearing loss and deafness, mitochondrial. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last update Jun 2018; accessed Dec 2021.