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Deafness, Autosomal Recessive 6 (DFNB6) via the TMIE Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1479 TMIE$540.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

The clinical sensitivity of this test has been reported to range up to 8%. In India, 0.09% (1/1,120) of nonsdynromic hearing loss cases harbored disease-causing variants in the TMIE gene (Nishio and Usami 2015). In another study from India, 0.8% (3/374) of families with autosomal recessive, nonsyndromic hearing loss tested positive for disease-causing TMIE variants (Ganapathy et al. 2014). In Iran, 0.7% (1/144) of families with autosomal recessive nonsyndromic hearing loss presented with pathogenic sequence variants in the TMIE gene (Babanejad et al. 2012). In two independent studies conducted in Turkey, 3.4% (1/29; Atik et al. 2015) of families with autosomal recessive nonsyndromic hearing loss and 8.2% (4/49; Duman et al. 2011) of families with nonsyndromic deafness and consanguineous parents were determined to have causative TMIE sequence variants. Approximately 4.1% (7/172) of Jordanian and Pakistani families with autosomal recessive nonsyndromic hearing loss who tested negative for pathogenic sequence variants in the GJB2 gene harbored disease-causing variants in the TMIE gene (Santos et al. 2006).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 TMIE$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

Autosomal recessive deafness 6 (DFNB6) is a prelingual, severe to profound, stable nonsyndromic hearing loss disorder (Santos et al. 2006). The audioprofile of most nonsyndromic hearing loss cases can be distinct, thus assisting in the development of an evaluation strategy for molecular genetic testing and in generating a prognosis on the rate of hearing loss per year (Hildebrand et al. 2008). Pure-tone audiometry of DFNB6 individuals generally shows downsloping to flat audiograms, indicating all-frequency hearing loss, with more severe impairment at high frequencies (Chaïb et al. 1996). Affected individuals also do not generate an auditory brainstem response up to 100 decibels. DFNB6 individuals do not have balance problems, nor severe motor dysfunction. Parents of DFNB6 patients are obligate carriers, often showing normal audiometric tests (Chaïb et al. 1996).

Genetics

DFNB6 is an autosomal recessive hearing disorder that is caused by pathogenic sequence variants in the transmembrane inner ear-expressed gene (TMIE) gene, which is located on chromosome 3p21.31 (Fukushima et al. 1995). The TMIE gene consists of four coding exons that encode a 154-amino acid peptide that consists of at least one transmembrane domain (Mitchem et al. 2002). The mature TMIE protein has been localized to the plasma membrane of cochlear cells and serves as a site of interaction for other molecules via its highly charged C-terminal domain (Shin et al. 2010). Previous investigations have also suggested that the TMIE protein plays an important role in signal trafficking between cells, as well as in signal tranduction in the auditory system (Karuppasamy et al. 2011). Functional studies using animal models have shown that pathogenic changes in the TMIE protein result in alterations in sensory hair cells in the cochlea, including defects in stereocilia, which are the apical projections that are involved in mechanoelectrical transduction of sound, thereby resulting in hearing loss (Mitchem et al., 2002; Shen et al. 2008; Gleason et al. 2009; Zhao et al. 2014). To date, a total of about 10 pathogenic TMIE variants have been reported. These variants include both missense and chain termination (nonsense, frameshift and splicing) (Naz et al. 2002; Human Gene Mutation Database).

Testing Strategy

This test involves bidirectional Sanger DNA sequencing of the four coding exons of the TMIE gene. The entire coding region and ~20 bp of flanking non-coding DNA on either side of each splice site are sequenced. We will also sequence any portion (Test #100) or portions of the exon (Test #200) in family members of patients with known mutations or to confirm research results.

Indications for Test

The ideal TMIE test candidates are individuals who present prelingual, severe to profound, stable, autosomal recessive nonsyndromic hearing loss that does not involve abnormalities of the external or inner ear.

Gene

Official Gene Symbol OMIM ID
TMIE 607237
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Deafness, Autosomal Recessive 6 600971

Related Test

Name
Nonsyndromic Hearing Loss and Deafness Sequencing Panel

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Atik T. et al. 2015. Plos One. 10: e0142154. PubMed ID: 26561413
  • Babanejad M. et al. 2012. American Journal of Medical Genetics. Part A. 158A: 2485-92. PubMed ID: 22903915
  • Chaïb H. et al. 1996. Human Molecular Genetics. 5: 155-8. PubMed ID: 8789454
  • Duman D. et al. 2011. Genetic Testing and Molecular Biomarkers. 15: 29-33. PubMed ID: 21117948
  • Fukushima K. et al. 1995. Genome Research. 5: 305-8. PubMed ID: 8593615
  • Ganapathy A. et al. 2014. Plos One. 9: e84773. PubMed ID: 24416283
  • Gleason M.R. et al. 2009. Proceedings of the National Academy of Sciences of the United States of America. 106: 21347-52. PubMed ID: 19934034
  • Hildebrand M.S. et al. 2008. Genetics in Medicine. 10: 797-804. PubMed ID: 18941426
  • Human Gene Mutation Database (Bio-base).
  • Karuppasamy S. et al. 2011. Laboratory Animal Research. 27: 339-42. PubMed ID: 22232643
  • Mitchem K.L. et al. 2002. Human Molecular Genetics. 11: 1887-98. PubMed ID: 12140191
  • Naz S. et al. 2002. American Journal of Human Genetics. 71: 632-6. PubMed ID: 12145746
  • Nishio S.Y., Usami S. 2015. The Annals of Otology, Rhinology, and Laryngology. 124 Suppl 1: 49S-60S. PubMed ID: 25788563
  • Santos R.L. et al. 2006. Journal of Molecular Medicine (berlin, Germany). 84: 226-31. PubMed ID: 16389551
  • Shen Y.C. et al. 2008. Developmental Dynamics : an Official Publication of the American Association of Anatomists. 237: 941-52. PubMed ID: 18330929
  • Shin M.J. et al. 2010. Comparative Medicine. 60: 288-94. PubMed ID: 20819378
  • Zhao B. et al. 2014. Neuron. 84: 954-67. PubMed ID: 25467981
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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