OtoGenome Test for Hearing Loss (110 Genes)
GTR Test Accession: Help GTR000509148.13
INHERITED DISEASESYNDROMIC DISEASEDYSMORPHOLOGY ... View more
Last updated in GTR: 2023-12-01
Last annual review date for the lab: 2023-12-01 LinkOut
At a Glance
Diagnosis
Hereditary hearing loss and deafness; Alport syndrome; Alstrom syndrome more...
ACTG1 (17q25.3); ADCY1 (7p12.3); ADGRV1 (5q14.3); ALMS1 (2p13.1); ATP6V1B1 (2p13.3) more...
Molecular Genetics - Deletion/duplication analysis: VisCap analysis; ...
Individuals with apparently nonsyndromic hearing loss
Not provided
Not provided
Ordering Information
Offered by: Help
Laboratory for Molecular Medicine
View lab's website
View lab's test page
Test short name: Help
OtoGenome
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
  • Registered Nurse
Test Order Code: Help
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
Physician must complete test requisition and submit a blood sample (see sample requirements)
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Test development: Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required: Help
Yes
Test strategy: Help
The OtoGenome™ Test is best suited for individuals who have a diagnosed hearing loss for which an underlying etiology has not yet been identified. For an individual with apparently non-syndromic hearing loss, this panel covers both non-syndromic causes of hearing loss as well as those which can present as non-syndromic. … View more
View citations (3)
  • Shearer AE, Hildebrand MS, Schaefer AM, Smith RJH. Genetic Hearing Loss Overview. 1999 Feb 14 [updated 2023 Sep 28]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301607.
  • Molecular diagnosis of hearing loss. Brown KK, et al. Curr Protoc Hum Genet. 2012;Chapter 9:Unit 9.16. doi:10.1002/0471142905.hg0916s72. PMID: 22241658.
  • https://www.ncbi.nlm.nih.gov/books/NBK1434
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Recommended fields not provided:
Conditions Help
Total conditions: 23
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 109
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 3
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
VisCap analysis
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NextSeq 550
Targeted variant analysis
PCR
Clinical Information
Test purpose: Help
Diagnosis
Target population: Help
Individuals with apparently nonsyndromic hearing loss
View citations (2)
  • Shearer AE, Hildebrand MS, Schaefer AM, Smith RJH. Genetic Hearing Loss Overview. 1999 Feb 14 [updated 2023 Sep 28]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301607.
  • Molecular diagnosis of hearing loss. Brown KK, et al. Curr Protoc Hum Genet. 2012;Chapter 9:Unit 9.16. doi:10.1002/0471142905.hg0916s72. PMID: 22241658.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
All VUS's are reported

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Yes. *Please call. Offered on a case-by-case basis.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
No. Ordering provider is encouraged to periodically contact the lab to see if there is any new information available. However, if the ordering physician has GeneInsight Clinic, they may receive automatic updates on classification through that program.
Research:
Is research allowed on the sample after clinical testing is complete? Help
No
Recommended fields not provided:
Technical Information
Test Procedure: Help
This OtoGenome Panel includes 110 genes: ACTG1, ADCY1 (excludes exon 1 in NM_021116.2), ADGRV1, ALMS1 (excludes exon 1 in NM_015120.4), ATP6V1B1, BCS1L, BSND, CABP2, CACNA1D, CATSPER2 (deletion analysis only), CCDC50, CD164 (excludes exon 7 in NM_001142403.1), CDC14A, CDH23, CEACAM16, CEP78 (excludes exon 12 in NM_001098802.1), CHD7, CIB2, CLDN14, CLIC5, CLPP, … View more
Test Confirmation: Help
All clinically significant variants are confirmed by Sanger sequencing or an alternate assay.
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This test is 99.93% sensitive (95% CI =99.92-99.94%) to detect variants changing a single base and 96.75% sensitive to detect insertion/deletions (95% CI =96.28-97.22%) within covered regions. Technical positive predictive value for single nucleotide variant changes is 99.42% (95% CI = 99.37-99.48%) and 94.16% (95% CI = 93.34-94.97%) for insertion/deletion … View more
Assay limitations: Help
This test does not detect variants in non-coding regions, aside from the splice junctions, that could affect gene expression and a few exons have been excluded due to technical difficulties. CNV analysis is only performed when data meets necessary quality standards and may not be available for all cases.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations Help
Alamut, UCSC Genome Browser, gnomAd, ExAC, ESP, 1000 Genomes, PolyPhen, SIFT, AlignGVGD, and more.

Laboratory's policy on reporting novel variations Help
All novel VUS's are reported
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.