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Nonsyndromic Hearing Loss and Deafness Sequencing Panel

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

NGS Sequencing

Test Code Test Copy GenesCPT Code Copy CPT Codes
1363 CCDC50 81479 Add to Order
CEACAM16 81479
CIB2 81479
CLDN14 81479
COCH 81479
CRYM 81479
DFNB59 81405
DIABLO 81479
DIAPH1 81479
ESRRB 81479
EYA4 81479
FGF3 81479
GIPC3 81479
GJB2 81252
GJB3 81479
GJB6 81479
GPSM2 81479
GRHL2 81479
GRXCR1 81479
HGF 81479
ILDR1 81479
KCNQ4 81479
LHFPL5 81479
LOXHD1 81479
LRTOMT 81479
MARVELD2 81479
MSRB3 81479
MYH14 81479
MYH9 81479
MYO15A 81479
MYO3A 81479
MYO6 81479
OTOA 81479
OTOF 81479
POU4F3 81479
PRPS1 81479
RDX 81479
SERPINB6 81479
SLC17A8 81479
SLC26A5 81479
SMPX 81479
TECTA 81479
TJP2 81479
TMC1 81479
TMIE 81479
TMPRSS3 81479
TPRN 81479
TRIOBP 81479
Full Panel Price* $1100.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
1363 Genes x (48) $1100.00 81252, 81405, 81479(x46) Add to Order
Pricing Comment

We are happy to accommodate requests for single genes or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered on our PGxome Custom Panel.

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 26 days.

Clinical Sensitivity

Although this panel contains genes with mutations that exhibit autosomal dominant, autosomal recessive and X-linked inheritance, autosomal recessive genes predominate. Approximately 50% of autosomal recessive nonsyndromic hearing loss can be attributed to mutations in GJB2 and GJB6. The other 50% of cases are attributed to mutations in numerous other genes, many of which have been found to cause deafness in only one or two families (Hilgert et al. 2009).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 CCDC50$690.00 81479 Add to Order
CEACAM16$690.00 81479
CIB2$690.00 81479
CLDN14$690.00 81479
COCH$690.00 81479
CRYM$690.00 81479
DFNB59$690.00 81479
DIABLO$690.00 81479
DIAPH1$690.00 81479
ESRRB$690.00 81479
EYA4$690.00 81479
FGF3$690.00 81479
GIPC3$690.00 81479
GJB2$690.00 81479
GJB3$690.00 81479
GJB6$690.00 81479
GRHL2$690.00 81479
GRXCR1$690.00 81479
HGF$690.00 81479
ILDR1$690.00 81479
KCNQ4$690.00 81479
LHFPL5$690.00 81479
LOXHD1$690.00 81479
LRTOMT$690.00 81479
MARVELD2$690.00 81479
MSRB3$690.00 81479
MYH14$690.00 81479
MYH9$690.00 81479
MYO15A$690.00 81479
MYO3A$690.00 81479
MYO6$690.00 81479
OTOA$690.00 81479
OTOF$690.00 81479
POU4F3$690.00 81479
PRPS1$690.00 81479
RDX$690.00 81479
SERPINB6$690.00 81479
SLC17A8$690.00 81479
SLC26A5$690.00 81479
SMPX$690.00 81479
TECTA$690.00 81479
TJP2$690.00 81479
TMC1$690.00 81479
TMIE$690.00 81479
TMPRSS3$690.00 81479
TPRN$690.00 81479
TRIOBP$690.00 81479
Full Panel Price* $1670.00
Test Code Test Copy Genes Total Price CPT Codes Copy CPT Codes
600 Genes x (47) $1670.00 81479(x47) 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 Sensitivity

Copy number variants have been shown to be involved in up to 20% of nonsyndromic hearing loss diagnoses (Shearer et al. 2014; Sloan-Heggen et al. 2016). However, the clinical sensitivity of this panel of nonsyndromic hearing loss genes is currently unknown. Please note that OTOA is analyzed only for exons 1-20 due to homology.

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Clinical Features

Sensorineural hearing loss (SNHL) is one of the most common human disabilities that can be caused by heritable genetic changes (mono- or polygenic). SNHL may also be acquired (non-genetic) due to environmental effects or mechanical stress. Hereditary hearing loss can be classified according to age at onset (prelingual or post-lingual), audiological characters, vestibular phenotype, inheritance type (autosomal dominant, recessive or X-linked), and responsible genetic locus (Smith et al. 2013). Causes of hereditary hearing loss can be syndromic (with specific clinical manifestations associated with malformations of the external ear or other organs or with medical problems involving other organ systems) or nonsyndromic (no associated visible abnormalities of the external ear or any related medical problems). Nonsyndromic hearing loss and deafness is characterized by childhood-onset, progressive, moderate-to-severe high-frequency sensorineural hearing impairment. The audioprofile may vary significantly, even among family members (Smith et al. 2013). Molecular genetic testing is possible for many types of syndromic and nonsyndromic deafness and plays a prominent role in diagnosis and genetic counseling of deafness (Shearer and Smith 2012).

Genetics

Congenital or prelingual nonsyndromic hearing loss (NSHL) hearing loss occurs in approximately 1 in 500 infants and is caused by genetic factors in at least 50-70% of cases (Smith, Bale, and White 2005). NSHL exhibits multiple modes of inheritance. The different gene loci for nonsyndromic hearing loss are designated DFN (for DeaFNess) and named based on the mode of inheritance: DFNA for autosomal dominant, DFNB for autosomal recessive and DFNX for X-linked inheritance, respectively. Within the prelingual nonsyndromic hearing loss group, inheritance is 75%-90% autosomal recessive, 10%-20% autosomal dominant, and 1%-1.5% X-linked (Smith et al. 2013). Approximately 50% of autosomal recessive nonsyndromic hearing loss can be attributed to mutations in GJB2 (which encodes the protein connexin 26) and GJB6 (which encodes the protein connexin 30). The other 50% of cases are attributed to mutations in numerous other genes, many of which have been found to cause deafness in only one or two families (Hilgert et al. 2009) including but not limited to CCDC50, CEACAM16, CIB2, CLDN14, COCH, CRYM, DIABLO, DIAPH1, ESRRB, EYA4, FGF3, FGFR3, GIPC3, GJB2, GJB3, GJB6, GPSM2, GRHL2, GRXCR1, HGF, ILDR1, KCNQ4, LHFPL5, LOXHD1, LRTOMT, MARVELD2, MSRB3, MYH14, MHY9, MYO15A, MYO3A, MYO6, OTOA, OTOF, PJVK, POU4F3, PRPS1, RDX, SERPINB6, SLC17A8, SLC26A5, SMPX, TECTA, TJP2, TMC1, TMIE, TMPRSS3 (Smith et al. 2013). See individual gene test descriptions for information on molecular biology of gene products.

Testing Strategy

For this NGS panel, the full coding regions, plus ~10 bp of non-coding DNA flanking each exon, are sequenced for each of the genes listed below. Sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization method, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for any regions not captured or with insufficient number of sequence reads. All pathogenic, undocumented and questionable variant calls are confirmed by Sanger sequencing.

In addition to the above, for GJB2 we also sequence the minimal promoter region (position -3489 to -3362 relative to the start codon) together with the first exon consisting entirely of UTR and the second exon consisting of UTR and coding sequence. For HGF we also sequence one intronic region containing known regulatory variants. Please note that OTOA is sequenced only for exons 1-20, TRIOBP is sequenced minus exon 7 and TPRN is sequenced minus exon 1. These will be updated in the near future.

Indications for Test

Nonsyndromic hearing loss and deafness is suspected in individuals with the following: Pre- or postlingual, mild to profound, progressive sensorineural hearing impairment, no syndrome related clinical manifestations or systemic findings identified by medical history and physical examination and /or a family history of nonsyndromic hearing loss (Smith et al. 2013).

Diseases

Name Inheritance OMIM ID
Chudley-McCullough syndrome 604213
Deafness With Labyrinthine Aplasia Microtia And Microdontia (Lamm) 610706
Deafness, Autosomal Dominant 1 124900
Deafness, Autosomal Dominant 10 601316
Deafness, Autosomal Dominant 12 601543
Deafness, Autosomal Dominant 15 602459
Deafness, Autosomal Dominant 17 603622
Deafness, Autosomal Dominant 22 606346
Deafness, Autosomal Dominant 25 605583
Deafness, Autosomal Dominant 28 608641
Deafness, Autosomal Dominant 2A 600101
Deafness, Autosomal Dominant 2B 612644
Deafness, Autosomal Dominant 36 606705
Deafness, Autosomal Dominant 3A 601544
Deafness, Autosomal Dominant 3B 612643
Deafness, Autosomal Dominant 4 600652
Deafness, Autosomal Dominant 40 616357
Deafness, Autosomal Dominant 44 607453
Deafness, Autosomal Dominant 48 607841
Deafness, Autosomal Dominant 4B 614614
Deafness, Autosomal Dominant 64 614152
Deafness, Autosomal Dominant 9 601369
Deafness, Autosomal Recessive 10 605316
Deafness, Autosomal Recessive 15 601869
Deafness, Autosomal Recessive 1A 220290
Deafness, Autosomal Recessive 1B 612645
Deafness, Autosomal Recessive 21 603629
Deafness, Autosomal Recessive 22 607039
Deafness, Autosomal Recessive 24 611022
Deafness, Autosomal Recessive 25 613285
Deafness, Autosomal Recessive 28 609823
Deafness, Autosomal Recessive 29 614035
Deafness, Autosomal Recessive 3 600316
Deafness, Autosomal Recessive 30 607101
Deafness, Autosomal Recessive 35 608565
Deafness, Autosomal Recessive 37 607821
Deafness, Autosomal Recessive 39 608265
Deafness, Autosomal Recessive 42 609646
Deafness, Autosomal Recessive 48 609439
Deafness, Autosomal Recessive 49 610153
Deafness, Autosomal Recessive 59 610220
Deafness, Autosomal Recessive 6 600971
Deafness, Autosomal Recessive 61 613865
Deafness, Autosomal Recessive 63 611451
Deafness, Autosomal Recessive 67 610265
Deafness, Autosomal Recessive 7 600974
Deafness, Autosomal Recessive 74 613718
Deafness, Autosomal Recessive 77 613079
Deafness, Autosomal Recessive 79 613307
Deafness, Autosomal Recessive 8/10 601072
Deafness, Autosomal Recessive 9 601071
Deafness, Autosomal Recessive 91 613453
Deafness, X-Linked 1 304500
Deafness, X-Linked 4 300066

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Deafness, Autosomal Dominant 10 (DFNA10) via the EYA4 Gene
Deafness, Autosomal Dominant 12 (DFNA12) and Deafness, Autosomal Recessive 21 (DFNB21) via the TECTA Gene
Deafness, Autosomal Dominant 15 (DFNA15) via POU4F3 Gene Sequencing with CNV Detection
Deafness, Autosomal Dominant 22 (DFNA22) and Deafness, Autosomal Recessive 37 (DFNB37) via the MYO6 Gene
Deafness, Autosomal Dominant 25 (DFNA25) via SLC17A8 Gene Sequencing with CNV Detection
Deafness, Autosomal Dominant 2A (DFNA2A) via the KCNQ4 Gene
Deafness, Autosomal Dominant 2B (DFNA2B) via the GJB3 Gene
Deafness, Autosomal Dominant 36 (DFNA36) and Deafness, Autosomal Recessive 7 (DFNB7) via the TMC1 Gene
Deafness, Autosomal Dominant 3A (DFNA3A) and Deafness, Autosomal Recessive 1A (DFNB1A) via the GJB2 Gene
Deafness, Autosomal Dominant 3B (DFNA3B) and Deafness, Autosomal Recessive 1B (DFNB1B) via the GJB6 Gene
Deafness, Autosomal Dominant 40 (DFNA40) via CRYM Gene Sequencing with CNV Detection
Deafness, Autosomal Dominant 44 (DFNA44) via the CCDC50 Gene
Deafness, Autosomal Dominant 4A (DFNA4A) via the MYH14 Gene
Deafness, Autosomal Dominant 4B (DFNA4B) via CEACAM16 Gene Sequencing with CNV Detection
Deafness, Autosomal Dominant 51 (DFNA51) via the TJP2 Gene
Deafness, Autosomal Dominant 64 (DFNA64) via the DIABLO Gene
Deafness, Autosomal Recessive 15 (DFNB15) via GIPC3 Gene Sequencing with CNV Detection
Deafness, Autosomal Recessive 22 (DFNB22) via the OTOA Gene
Deafness, Autosomal Recessive 24 (DFNB24) via RDX Gene Sequencing with CNV Detection
Deafness, Autosomal Recessive 25 (DFNB25) via GRXCR1 Gene Sequencing with CNV Detection
Deafness, Autosomal Recessive 28 (DFNB28) via the TRIOBP Gene
Deafness, Autosomal Recessive 29 (DFNB29) via the CLDN14 Gene
Deafness, Autosomal Recessive 3 (DFNB3) via the MYO15A Gene
Deafness, Autosomal Recessive 30 (DFNB30) via the MYO3A Gene
Deafness, Autosomal Recessive 35 (DFNB35) via the ESRRB Gene
Deafness, Autosomal Recessive 39 (DFNB39) via the HGF Gene
Deafness, Autosomal Recessive 42 (DFNB42) via the ILDR1 Gene
Deafness, Autosomal Recessive 49 (DFNB49) via MARVELD2 Gene Sequencing with CNV Detection
Deafness, Autosomal Recessive 59 (DFNB59) via the DFNB59 Gene
Deafness, Autosomal Recessive 6 (DFNB6) via TMIE Gene Sequencing with CNV Detection
Deafness, Autosomal Recessive 61 (DFNB61) via the SLC26A5 Gene
Deafness, Autosomal Recessive 63 (DFNB63) via the LRTOMT Gene
Deafness, Autosomal Recessive 67 (DFNB67) via the LHFPL5 Gene
Deafness, Autosomal Recessive 74 (DFNB74) via MSRB3 Gene Sequencing with CNV Detection
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CONTACTS

Genetic Counselors
Geneticist
Citations
  • Hilgert N. et al. 2009. Mutation Research. 681: 189-96. PubMed ID: 18804553
  • Shearer A.E. et al. 2014. Genome Medicine. 6: 37. PubMed ID: 24963352
  • Shearer A.E., Smith RJ. 2012. Current Opinion in Pediatrics. 24: 679-86. PubMed ID: 23042251
  • Sloan-Heggen C.M. et al. 2016. Human Genetics. 135: 441-50. PubMed ID: 26969326
  • Smith R.J.H. et al. 2013. Deafness and Hereditary Hearing Loss Overview. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, Smith RJ, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301607
  • Smith RJ et al. 2005 Sensorineural Hearing Loss in Children. Lancet 365: 879–90. PubMed ID: 15752533
Order Kits
TEST METHODS

NextGen Sequencing using PG-Select Capture Probes

Test Procedure

We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon.  As required, genomic DNA is extracted from the patient specimen.  For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes.  Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA).  Regions with insufficient coverage by NGS are covered by Sanger sequencing.  All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.

For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions.  After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.

Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).

(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants

Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org).  Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.

Analytical Validity

As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.

In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.   

Analytical Limitations

Interpretation of the test results is limited by the information that is currently available.  Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.

When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles.  Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion.   In these cases, the report will contain no information about the second allele.  Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).

We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon.  Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.

In most 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 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.

Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood).   Test reports contain no information about the DNA sequence in other cell-types.

We cannot be certain that the reference sequences are correct.

Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.

We have confidence in our ability to track a specimen once it has been received by PreventionGenetics.  However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.

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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