Background
Hearing loss is the most common sensory impairment with an incidence of 1 in 250 births. Over half of these children have a genetic cause for their hearing loss with approximately 100 genes implicated in isolated hearing loss and several hundred in syndromic hearing loss. Of the many genes associated with hearing loss, clinical testing has only been available for a subset. The comprehensive approach of the OtoChip now makes it possible to sequence ~70,000 bases of DNA across 19 genes in parallel, which tests for the following clinical presentations (see table for gene specific clinical information).

• Nonsyndromic autosomal recessive/sporadic hearing loss: CDH23, DFNB31 (WHRN), GJB6, MYO6, MYO7A, OTOF, PCDH15, SLC26A4 (PDS), TMC1, TMIE, TMPRSS3, USH1C
• Nonsyndromic autosomal dominant hearing loss: GJB6, MYO6, MYO7A, TMC1
• Maternally-inherited/Aminoglycoside-induced: MTTS (tRNAser(UCN)) and 6 mutations in MTRNR1 (12S rRNA)
• Auditory neuropathy/dys-synchrony: OTOF
• Pendred syndrome/Hearing loss with EVA or Mondini dysplasia: SLC26A4 (PDS)
• Usher syndrome (Hearing loss and retinitis pigmentosa): CDH23, CLRN1, DFNB31, GPR98 (exons 8, 20, 31-41 & 89), MYO7A, PCDH15, USH1C, USH1G, USH2A

Determining the etiology of hearing loss is important for management. Such a discovery aids in determining prognosis (i.e. whether the loss will worsen), the best intervention (e.g. hearing aids, cochlear implant, sign language) and recurrence risks to future children and other family members. Furthermore, it can either eliminate the possibility that a syndrome might be present, with other clinical problems that have not yet manifested (e.g. adolescent-onset retinitis pigmentosa in Usher syndrome), or predict the onset of such features if a test for a syndromic cause is positive. Of individuals with sensorineural hearing loss up to 5% have hearing loss associated with Pendred syndrome and up to 10% have Usher syndrome.

Testing Strategy
The approach to genetic testing for individuals with hearing loss or Usher syndrome is outlined in the following flow chart. Pathogenic variants in the GJB2 (Connexin 26) gene and the ΔGJB6-D13S1830 (Connexin 30) deletion are the most common cause of nonsyndromic hearing loss and testing is positive in 15-20% of children with hearing loss. The OtoChip does not detect the common 35delG & 167delT variants in GJB2 or the ΔGJB6-D13S1830 deletion. Therefore, individuals with nonsyndromic hearing loss should have GJB2ΔGJB6-D13S1830 testing before the OtoChip. In addition, if an individual has hearing loss with EVA or Mondini dysplasia we recommend SLC26A4 gene sequencing before the OtoChip. If an individual has auditory neuropathy/dys-synchrony, we recommend OTOF gene sequencing before the OtoChip. This is because these tests have a higher analytical sensitivity than chip-based sequencing. Individuals with hearing loss and retinitis pigmentosa should go directly to the OtoChip.

The OtoChip is a sequencing based array that has a similar detection rate for substitution mutations as compared to traditional dideoxy sequencing. However, the OtoChip has a lower detection rate for small deletions/insertions. If an individual is found to have one pathogenic mutation in a particular gene on the OtoChip it is recommended that they have follow-up testing of that gene by dideoxy sequencing to determine if there is a second mutation in the gene that was not detected by the OtoChip.

GENETIC TESTING STRATEGY

Turn-Around-Times
Approximately 8 weeks

Methodology
This test is performed by oligonucleotide hybridization-based DNA sequencing of ~70,000 bases of DNA covering the coding regions and splice sites (-3/+5) of the CDH23, CLRN1, GJB2 (excludes 35delG), GJB6, GPR98 (exons 8, 20, 31-41 and 89), MYO6, MYO7A, OTOF, PCDH15, SLC26A4 (PDS), TMC1, TMIE, TMPRSS3, MTTS (tRNAser(UCN)), USH1C, USH1G, USH2A, DFNB31 genes and genotyping of mutations 961delT, 961T>C, 961T>G, 1095T>C, 1494T>C, 1555A>G in MTRNR1 (12S rRNA), using a custom design on the Affymetrix GeneChip platform.

Analytical Sensitivity
This assay is greater than 97% sensitive for detecting substitution variants in the sequence analyzed. This test does not examine most non-coding regions that could affect gene expression. Compared to dideoxy sequencing this test has significantly reduced sensitivity (37%) for detecting small insertions and deletions (indels), except for 280 previously identified indels for which genotyping probes have been included. These indels can be detected at 95% sensitivity. Like traditional sequencing tests, the OtoChip has very little sensitivity for detecting large deletions, insertions and other copy number changes.

Clinical Sensitivity
Very limited data exists to predict the clinical sensitivity of this test. We assume that the test will have a reasonable sensitivity in patients with bilateral SNHL and high sensitivity in those with diagnosed Usher syndrome. We are currently collecting data to provide more accurate figures.

Cost and CPT codes:
CPT codes: 83898(4), 83900(1), 83901(422), 83892(1), 88386(1)
Price: $3800

If you have any questions, please call the Laboratory for Molecular Medicine at 617-768-8500 or email us at LMM@partners.org

Printable version (pdf 140 KB)