GTR Test Accession:
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GTR000247961.4
CAP
Last updated in GTR:
2024-02-07
View version history
GTR000247961.4,
last updated:
2024-02-07
GTR000247961.3,
last updated:
2023-02-08
GTR000247961.2,
last updated:
2016-02-17
GTR000247961.1,
registered in GTR:
2015-03-03
Last annual review date for the lab: 2024-02-07
LinkOut
At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation
Conditions (1):
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Autosomal recessive nonsyndromic hearing loss 1A
Genes (2):
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GJB2 (13q12.11);
GJB6 (13q12.11)
Methods (3):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); PCR; ...
Target population: Help
Diagnosis of DFNB1 depends on molecular genetic testing to identify …
Clinical validity:
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Diagnosis of DFNB1 depends on molecular genetic testing to identify …
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Test short name:
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CX30
Specimen Source:
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- Cell culture
- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Licensed Physician
Test Order Code:
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Non-syndromic Recessive Deafness
Lab contact:
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Contact Policy:
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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:
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Please complete the requisition found on the websiter and ensure that it is signed by the referring physician
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Confirmation of research findings
Custom Deletion/Duplication Testing
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Decline to answer
Test strategy:
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All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that …
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View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Conditions
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Total conditions: 1
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 2
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 3
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Deletion/duplication analysis
PCR
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Applied Biosystems 3730 capillary sequencing instrument
Illumina MiSeq/NextSeq
Illumina MiSeq/NextSeq
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation
Clinical validity:
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Diagnosis of DFNB1 depends on molecular genetic testing to identify deafness-causing mutations in GJB2 and/or GJB6 that alter the gap junction beta-2 protein (connexin 26) and the gap junction beta-6 protein (connexin 30), respectively. Clinically available molecular genetic testing of GJB2 and GJB6 detects more than 99% of deafness-causing mutations …
View more
View citations (2)
- Smith RJH, Azaiez H, Booth K. -Related Autosomal Recessive Nonsyndromic Hearing Loss. 1998 Sep 28 [updated 2023 Jul 20]. 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: 20301449.
- https://www.ncbi.nlm.nih.gov/books/NBK1272
Clinical utility:
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Target population:
Help
Diagnosis of DFNB1 depends on molecular genetic testing to identify deafness-causing mutations in GJB2 and/or GJB6 that alter the gap junction beta-2 protein (connexin 26) and the gap junction beta-6 protein (connexin 30), respectively. Clinically available molecular genetic testing of GJB2 and GJB6 detects more than 99% of deafness-causing mutations …
View more
View citations (1)
- Smith RJH, Azaiez H, Booth K. -Related Autosomal Recessive Nonsyndromic Hearing Loss. 1998 Sep 28 [updated 2023 Jul 20]. 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: 20301449.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Novel variations are interrogated using a series of tools. Literature reviews and a search of relevant databases and dbSNP is pursued. This is followed by evaluation using web based insilco analysis including, but not restricted to SIFT, Polyphen2, AlignGVGD, SNPs&GO and ASSEDA(splice). If the pathogenicity is still indeterminate (ACMG group … View more
Novel variations are interrogated using a series of tools. Literature reviews and a search of relevant databases and dbSNP is pursued. This is followed by evaluation using web based insilco analysis including, but not restricted to SIFT, Polyphen2, AlignGVGD, SNPs&GO and ASSEDA(splice). If the pathogenicity is still indeterminate (ACMG group … View more
Will the lab re-contact the ordering physician if variant interpretation changes?
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Not provided.
Not provided.
Recommended fields not provided:
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
Help
All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that …
View more
View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Test Confirmation:
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Mutations identified are repeated in an independent asssay
Test Comments:
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Detection of recurrent 309 kb deletion (GJB6-D13S1830) by PAGE analysis
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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This methodology is predicted to have >99% sensitivity for the reginos screened
View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
VUS:
Software used to interpret novel variations
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May include, but not restricted to SNP&Go, SIFT, Polyphen2, dbSNP, ASSEDA
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
May include, but not restricted to SNP&Go, SIFT, Polyphen2, dbSNP, ASSEDA
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
Recommended fields not provided:
Assay limitations,
Description of internal test validation method,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Clinical resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.