Laboratory for Molecular Medicine: Hearing Loss Tests

OtoGenome™ test (110 genes)

For hearing loss and related syndromes.

Background

Hearing loss has an incidence of one in 250 births and over half of isolated childhood hearing loss has a genetic etiology, with many genes involved. Gene variants can be inherited in an autosomal recessive, autosomal dominant, X-linked, or mitochondrial pattern. The comprehensive approach of the OtoGenome™ test now makes it possible to simultaneously screen 110 genes* known to cause both nonsyndromic hearing loss and syndromes that can present as isolated hearing loss, such as Usher, Pendred, Jervell and Lange-Nielsen (JLNS), Branchio-Oto-Renal (BOR), deafness and male infertility (DIS), Perrault, Alport, and Waardenburg syndromes.

The Otogenome™ test includes genes associated with:

• Nonsyndromic hearing loss: 84 genes
• Usher syndrome (hearing loss and retinitis pigmentosa): CDH23, CLRN1, ADGRV1, MYO7A, PCDH15, USH1C, USH1G, USH2A, CIB2, HARS, WHRN
• Pendred syndrome/Hearing loss with EVA or Mondini dysplasia: SLC26A4 (PDS)
• Branchio-oto-renal syndrome: EYA1, SIX1
• Waardenburg syndrome: EDN3, EDNRB, MITF, PAX3, SNAI2, SOX10
• Auditory neuropathy/dys-synchrony: OTOF, DFNB59
• Maternally-inherited/Aminoglycoside-induced hearing loss: MTTS1 (tRNAser(UCN)), MTRNR1 (12S rRNA)
• Jervell and Lange-Nielsen syndrome: KCNQ1, KCNE1
• Perrault syndrome: CLPP, HARS2, HSD17B4, LARS2
• Alport syndrome: COL4A5, COL4A3, COL4A4
• Muckle Wells syndrome (Cryopyrin-associated periodic syndrome (CAPS)): NLRP3
• Brown-Vialetto-Van Laere syndrome: SLC52A3, SLC52A2
• CHARGE syndrome: CHD7
• Hearing loss with cone-rode dystrophy: CEP78
• Hearing loss with high myopia: SLITRK6

Determining the etiology of hearing loss is important in determining prognosis (e.g., whether the severity of hearing impairment will worsen), optimal therapeutic interventions (e.g., hearing aids, cochlear implant, sign language), and recurrence risks to future children and other family members. Furthermore, a positive result from this test may predict the onset of syndromic features (e.g., adolescent-onset vision impairment in Usher syndrome, long QT in JLNS, renal abnormalities in BOR, or thyroid abnormalities in Pendred syndrome). On the other hand, a negative result substantially reduces the likelihood that a syndrome is present, alleviating concerns about the future development of these features. Among individuals with sensorineural hearing loss up to 5% have hearing loss associated with Pendred syndrome and up to 10% have Usher syndrome.

Gene information

Testing strategy

The OtoGenome test is best suited for individuals who have a diagnosis of 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. Onset of features associated with a syndromic type of hearing loss can be delayed or variable. Given the genetic heterogeneity of hearing loss, the OtoGenome test allows for a shortened diagnostic course by analyzing 110 genes in a single test.

Testing may be considered in a reflexive manner, with the Connexin test (GJB2 sequencing and GJB6 deletion analysis) performed first, and if negative or inconclusive the OtoGenome test is performed.

Methodology

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, CLRN1 (excludes exon 1B in NM_174880.1)*, COCH, COL11A2, COL4A3 (excludes exons 36 and 51 in NM_000091.4), COL4A4 (excludes exon 31 in NM_000092.4), COL4A5, DFNA5, DFNB59, DIABLO, DIAPH1 (excludes exon 16 and intron 23 in NM_005219.4), EDN3, EDNRB, EPS8 (excludes exons 3, 10, 16, and 18in NM_004447.5), ESPN (excludes exons 1, 3, 4, 7, and 8 in NM_031475.2), ESRRB, EYA1, EYA4, GIPC3, GJB2, GJB6, GPSM2, GRHL2, GRXCR1, HARS, HARS2, HGF (excludes exon 12 in NM_000601.4), HSD17B4, ILDR1, KARS, KCNE1, KCNQ1, KCNQ4 (excludes exon 1 in NM_004700.3), KITLG, LARS2, LHFPL5, LOXHD1, LRTOMT (excludes exons 3B and 6B in NM_001145307.1* and exon 6A in NM_145309.2)*, MARVELD2, MIR96, MITF, MSRB3, MTRNR1 (excludes m.648-m.950), MTTS1,MYH14 (excludes exon 28 in NM_001145809.1), MYH9, MYO15A (excludes exon 2 in NM_016239.3), MYO3A, MYO6, MYO7A, NLRP3, OSBPL2, OTOA (excludes exons 2 and 21-27 in NM_144672.3), OTOF, OTOG (excludes exon 32 in NM_001277269.1), OTOGL, P2RX2 (excludes exon 1 in NM_174873.1), PAX3, PCDH15, PDZD7, POU3F4, POU4F3, PRPS1, RDX, RIPOR2, S1PR2, SERPINB6, SIX1, SLC26A4, SLC52A2, SLC52A3, SLITRK6, SMPX, SNAI2, SOX10, STRC (NM_153700.2), SYNE4, TBC1D24, TECTA, TIMM8A, TMC1, TMIE, TMPRSS3, TPRN, TRIOBP, USH1C, USH1G, USH2A (includes deep intronic c.7595-2144A>G variant), WFS1, WHRN.

*Exon from an alternate transcript. For additional information on reference sequences and exon coverage, please contact the laboratory

This assay is performed using Genomic DNA extracted from blood or saliva that is fragmented, adapter ligated, and barcoded. Library fragments are sequenced (2x150 base paired end) using Sequencing-By-Synthesis (SBS) chemistry and the Illumina NovaSeq sequencer with a minimum coverage of at least 20X for 90%. Sequence data are aligned to the GRCh38 assembly after discarding low quality sequences. Illumina's DRAGEN (Dynamic Read Analysis for GENomics) platform is used for demultiplexing, read mapping, genome alignment, read sorting, duplicate marking, and variant calling. Technical sensitivity of this assay is 99.10% (95% CI: 99.04-99.16%) and the positive predictive value is 99.39% (95% CI: 99.37-99.41%). Sanger sequencing is used for fill-in when bases have <12x coverage. All clinically significant variants are confirmed by Sanger sequencing or droplet digital PCR; variants classified as likely benign or benign are not confirmed.

Droplet digital PCR (ddPCR) is performed using a probe at (GRCh38chr13:20220606-20220626) to test for the presence or absence of the previously reported deletions in the DFNB1 (GJB6 gene) region, including the GJB6-D13S1854 309kb deletion, the GJB6-D13S1854 232kb deletion, and the deletions reported by Wilch 2010 (PMID: 20236118) and Feldman 2009 (PMID: 19101659). Any deletions that are identified are further clarified using the ddPCR probes at the following locations: GRCh38 chr13:20230971-20230994, chr13:20515194-20515219, chr13:20481175-20481197, chr13:20429796-20429815.

Droplet digital PCR (ddPCR) is performed to screen for common large deletions in STRC and CATSPER2 genes. It is performed using a probe at STRC intron 25 (GRCh38chr15:43600818-43600842) to test for the presence of a deletion in STRC. Any deletions that are identified are further clarified using ddPCR probes at the following locations: STRC exon 23 (GRCh38chr15: 43603322-43603344) and CATSPER2 exon 7 (GRCh38chr15:43639043-43639062). Deletions that do not affect the STRC intron 25 (GRCh38chr15: 43600818-43600842) region will not be identified. 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 changes within covered regions.

The initial sequencing component of this test was performed by the Broad Clinical Laboratory, LLC (27 Blue Sky Drive, Burlington, MA 01803; CLIA# 22D2055652), and the Sanger confirmation, Droplet digital PCR (ddPCR), interpretive algorithms and clinical reports are generated by the Laboratory for Molecular Medicine at Mass General Brigham Personalized Medicine (LMM, 65 Landsdowne St, Cambridge, MA 02139; 617-768-8500; CLIA#22D1005307). This test has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary.

Limitations

Copy number variants that do not affect the GJB6 GRCh37 chr13:21003868-21003954 or the STRC intron 25 (GRCh37chr15:43892948-43893040) probed regions will not be detected by this assay. CATSPER2 deletions will only be reported if an STRC deletion was also identified. Duplications in STRC and/or CATSPER2 will not be reported because exact breakpoints cannot be determined by this testing methodology and duplications in these genes are not known to be associated with hearing loss and/or male infertility.

This test does not include sequencing of the GJB6 or CATSPER2 genes. It will not detect variants in non-coding regions, aside the canonical splice sites STRC. There is reduced sensitivity for larger indels and variants in low complexity regions. It will not detect triplet repeat expansions, translocations, inversions, gene-pseudogene conversions, or other complex rearrangements. Low level mosaic variants may not be identified. Certain exons are excluded due to homology or other technical limitations (see above for excluded regions).

Variant classifications are based on ACMG/AMP criteria (Richards et al. 2015) with ClinGen rule specifications. Variants are reported according to HGVS nomenclature. Likely benign and benign variants are not included in this report but are available upon request. This test does not routinely detect variants in non-coding regions (aside from the canonical splice sites), triplet repeat expansions, translocations, inversions, and copy number variants encompassing less than two consecutive exons. There is reduced detection for larger indels, variants in low complexity regions, and variants in regions with high homology.

Analytical and clinical sensitivity

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 changes within covered regions.

How to order

Requisition form

All samples must be accompanied with a completed requisition form. Please make sure any identifiers used on the specimens are provided on the paperwork. Consent page should be signed by a health care provider. Any incomplete or missing paperwork may delay the start of testing.

Ordering

• Test Description: OtoGenome (110 Genes)
• Turnaround time: 8 - 12 weeks

Specimen required:

• 4-8ml of whole blood (3-5ml for an infant) in a lavender top tube (K2EDTA or K3EDTA) or
• 10 ug of DNA at a minimum concentration of 25 ng/ul (please provide DNA concentration)

If providing DNA, please provide name and CLIA # of lab performing blood extraction

Billing information

The Laboratory for Molecular Medicine offers several billing options for our clients and their patients; however, we do not bill insurance companies and are unable to begin testing without accurate billing information.

• CPT code: 81430 (1), 81431 (1)
• Price: $2,500

Connexin test: GJB2 sequencing and DFNB1 (GJB6) deletion

Common autosomal recessive hearing loss tests.

Background

Over half of isolated childhood hearing loss has a genetic etiology, with many genes involved. The most common genetic causes of autosomal recessive, non-syndromic hearing loss are pathogenic changes in theDFNB1 locus, which includes the GJB2 and GJB6 genes.

The mutation spectrum in connexin-related hearing loss includes sequence variants in the GJB2 gene or large deletions in the DFNB1 locus which may include all or part of the GJB6 gene. Previously reported deletions included the GJB6-D13S1830 deletion, the GJB6-D13S1854 deletion, and a 131-kb deletion reported by Wilch (2010; PMID: 20236118). These deletions are thought to result in the loss of a cis-regulatory element of GJB2, thereby resulting in a lack of expression of the GJB2 allele (PMID: 19723508). Therefore, connexin-related hearing loss is caused by either a homozygous or compound heterozygous pathogenic variants in the GJB2 gene, a homozygous or compound heterozygous DFNB1 deletion or compound heterozygous variants including one deletion of and one pathogenic variant in the GJB2 gene. The hearing loss is nonsyndromic, sensorineural, and typically congenital but can present in early childhood. The severity can range from mild to profound and over time about 50% of those with a connexin related hearing loss will progress in severity. This hearing loss is most commonly inherited in an autosomal recessive pattern meaning that each parent is unaffected but is a carrier of a single variant in the GJB2 gene. Two carriers have a 25% (or one in four) risk for having an affected child.

Gene Information

• Gene: GJB2

  • Protein: Gap Junction protein, beta 2 (Connexin 26)
  • OMIM#: 121011
  • Locus: 13q12

• Gene: GJB6

  • Protein: Gap Junction protein, beta 6 (Connexin 30)
  • OMIM#: 604418
  • Locus: 13q12

Testing strategy

Given the large contribution of the GJB2 and GJB6 genes to genetic causes of hearing loss, the testing of these two genes is often the first line strategy in a diagnostic work up.  Genetic testing for these two genes would be recommended in a child born with hearing loss of any severity. This is true even if there is no family history of hearing loss, as this is the most common presentation. The Connexin test alone gives parents the highest likelihood of obtaining a cause for their child's hearing loss. Furthermore, a positive test result can alleviate concerns that other medical problems may arise in their child due to the association of hearing loss with many other syndromes (e.g., Usher syndrome in which blindness can develop at a later age). If the results are negative then additional tests, including more comprehensive panels, such as the OtoGenome™ can be pursued.

In addition, this test can be offered to someone whose partner is a known carrier of a pathogenic variant in the GJB2 gene or a known GJB6 genes deletion. In this situation, the test can identify or rule out carrier status in a hearing individual and determine the risk for connexin-related hearing loss in future children.

Methodology

• Sanger sequencing of exon 1 and exon 2 of the GJB2 (connexin 26 gene (NM_004004)
• DFNB1 (GJB6) Deletions: Droplet digital PCR (ddPCR) is performed using a probe at (GRCh38chr13:20220606-20220626) to test for the presence or absence of the previously reported deletions in the DFNB1 (GJB6 gene) region, including the GJB6-D13S1854 309kb deletion, the GJB6-D13S1854 232kb deletion, and the deletions reported by Wilch 2010 (PMID: 20236118) and Feldman 2009 (PMID: 19101659). Any deletions that are identified are further clarified using the ddPCR probes at the following locations: GRCh38 chr13:20230971-20230994, chr13:20515194-20515219, chr13:20481175-20481197, chr13:20429796-20429815.

Analytical and clinical sensitivity

This assay is more than 99.9% accurate in detecting variants in the GJB2 sequence analyzed. Two GJB2 variants are detected in approximately 20% of individuals with nonsyndromic sensorineural hearing loss. However, a negative result does not rule out a diagnosis of GJB2-related hearing loss because there may be other variants within the GJB2 gene (for example, within the promoter or other non-coding or regulatory regions) that are not detected by this test. The GJB6-D13S1830 deletion may be present in 2-67% of persons with a single GJB2 variant, the exact percentage depending on ethnicity. The presence of two copies of the deletion is rare.

How to order

Requisition form

All samples must be accompanied with a completed requisition form. Please make sure any identifiers used on the specimens are provided on the paperwork. Consent page should be signed by a health care provider. Any incomplete or missing paperwork may delay the start of testing.

Ordering

• Test Codes:

  • GJB2 (Connexin 26) Gene Sequencing - lmCX26-a_L
  • GJB6 (Connexin 30) Deletion - lmCX30-a_L

• Turnaround time: 3 weeks

• Specimen required:

  • 4-8ml of whole blood (3-5ml for an infant) in a lavender top tube (K2EDTA or K3EDTA) or
  • 10 ug of DNA at a minimum concentration of 25 ng/ul (please provide DNA concentration)

If providing DNA, please provide name and CLIA # of lab performing blood extraction

Billing information

The Laboratory for Molecular Medicine offers several billing options for our clients and their patients; however, we do not bill insurance companies and are unable to begin testing without accurate billing information.

• CPT code: GJB2- 81252, GJB6 - 81254
• Price: $600

SLC26A4 (PDS) gene test

Pendred syndrome or hearing loss with EVA test.

Background

SLC26A4-related hearing loss is unique among inherited hearing impairments in that all individuals with two variants in this gene have a particular abnormality of the inner ear that can be observed by MRI or CT scan of the temporal bone. This abnormality, known as enlarged vestibular aqueducts (EVA), may be seen alone or in combination with Mondini dysplasia (a common cavity malformation of the inner ear). Although variants in this gene are not the only cause of hearing loss with EVA, SLC26A4 contributes significantly to this etiology. As a result, it is recommended that the SLC26A4 gene test be ordered for all individuals with nonsyndromic hearing loss and EVA. This is true even if there is no family history of hearing loss, which is a common presentation in autosomal recessive conditions.

Some individuals with pathogenic SLC26A4 variants also develop goiter (enlargement of the thyroid), though most usually retain normal thyroid function. It has been suggested that the likelihood of having or developing thyroid disease may be correlated with the number of variants (one versus two) identified in the gene (Pryor et al, 2005). Goiter (thyroid enlargement) is seen in about 20% of cases and hypothyroidism can occasionally occur. The combined occurrence of hearing loss, temporal bone abnormalities, and thyroid dysfunction define the SLC26A4-related disorder, Pendred syndrome, which represents the most common syndromic form of deafness.

The incidence of SLC26A4 related hearing loss is approximately one in 7500 and variants in this gene may cause up to 5-10% of congenital hearing loss. The hearing loss is typically bilateral severe or profound sensorineural hearing loss, which can be progressive or fluctuating. Variability in the severity of hearing loss is seen, with some individuals exhibiting a milder hearing loss. Autosomal recessive inheritance has been observed, however a large number of individuals with hearing loss and EVA have been found to carry single pathogenic variants in SLC26A4, indicating a more complex genetic etiology.

Gene Information

• Gene: SLC26A4

  • Protein: Solute Carrier Family 26, Member 4
  • OMIM#: 605646
  • Locus: 7q31

Testing strategy

Testing for the SLC26A4 gene is recommended for individuals with sensorineural hearing loss with temporal bone abnormalities (observed on a CT scan or MRI of the inner ear) including enlarged (dilated) vestibular aqueduct and/or Mondini malformation. This test is also recommended for individuals with hearing loss and goiter or a positive perchlorate discharge test. The presence of one or two pathogenic variants is considered a positive result. Two variants may indicate a higher likelihood of developing thyroid disease.

Methodology

This test is performed by Sanger sequencing of the coding regions and splice sites of the SLC26A4 gene. This test does not detect large deletions or variants in non-coding regions that could affect gene expression.

Analytical and clinical sensitivity

This test is greater than 99.9% accurate in detecting variants in the sequence analyzed. Approximately 50% of individuals with DFNB4 or Pendred syndrome have pathogenic variants in SLC26A4 (Alasti 2014 PMID:20301640).

How to order

Requisition form

All samples must be accompanied with a completed requisition form. Please make sure any identifiers used on the specimens are provided on the paperwork. Consent page should be signed by a health care provider. Any incomplete or missing paperwork may delay the start of testing.

Ordering

• Test code: lmSLC26A4-a_L

• Turnaround time: 4 weeks

• Specimen required:

  • 4-8ml of whole blood (3-5ml for an infant) in a lavender top tube (K2EDTA or K3EDTA) or
  • 10 ug of DNA at a minimum concentration of 25 ng/ul (please provide DNA concentration)

If providing DNA, please provide name and CLIA # of lab performing blood extraction

Billing information

The Laboratory for Molecular Medicine offers several billing options for our clients and their patients; however, we do not bill insurance companies and are unable to begin testing without accurate billing information.

• CPT code: 81406
• Price: $1,100

WFS1 gene sequencing test

Low-frequency non-syndromic hearing loss.

Background

Pathogenic variants in the WFS1 gene can cause a range of conditions collectively known as the WFS1-related disorders. These disorders include isolated autosomal dominant low frequency hearing loss (DFNA6/14/38), Wolfram-like disease, and Wolfram syndrome.

DFNA6/14/38 is inherited in an autosomal dominant pattern and is characterized by sensorineural hearing loss that is typically congenital, progressive, and affects the lower frequencies (greater than or equal to 2,000 Hz).

Wolfram syndrome is a rare autosomal recessive condition characterized by juvenile onset diabetes mellitus and progressive optic atrophy (Wolfram and Wagner 1938). It is also known by the acronym DIDMOAD which describes the main features identified in individuals including diabetes insipidus, diabetes mellitus, optic atrophy, and deafness. Additional symptoms include progressive neurologic abnormalities and endocrine abnormalities.

Wolfram-like disease is a rare autosomal dominant condition characterized by low frequency sensorineural hearing loss and variable features of Wolfram syndrome.

These features may include diabetes mellitus, psychiatric illness, and optic atrophy.

Gene Information

• Gene: WFS1

  • Protein: WFS1 Protein
  • OMIM#: 605201
  • Locus: 4p16.1

Testing strategy

WFS1 gene sequencing is appropriate for individuals with isolated low frequency hearing loss and a dominant family history, features of Wolfram syndrome or features of Wolfram-like disease. Testing affected individuals is the most informative strategy in identifying a genetic cause of these conditions.

Methodology

This test is performed by Sanger sequencing of the coding regions and splice sites of the WFS1 gene. This test does not detect large deletions or variants in non-coding regions that could affect gene expression.

Analytical and clinical sensitivity

This test is greater than 99.9% accurate in detecting variants in the sequence analyzed.

How to order

Requisition form

All samples must be accompanied with a completed requisition form. Please make sure any identifiers used on the specimens are provided on the paperwork. Consent page should be signed by a health care provider. Any incomplete or missing paperwork may delay the start of testing.

Ordering

• Test code: lmWFS1-a_L

• Turnaround time: 3 weeks

• Specimen required:

  • 4-8ml of whole blood (3-5ml for an infant) in a lavender top tube (K2EDTA or K3EDTA) or
  • 10 ug of DNA at a minimum concentration of 25 ng/ul (please provide DNA concentration)

If providing DNA, please provide name and CLIA # of lab performing blood extraction

Billing information

The Laboratory for Molecular Medicine offers several billing options for our clients and their patients; however, we do not bill insurance companies and are unable to begin testing without accurate billing information.

• CPT code: 81479
• Price: $750

POU3F4 gene test

X-linked hearing loss with stapes fixation or Perilymphatic Gusher.

Background

Hearing loss caused by pathogenic variants in the POU3F4 gene accounts for approximately 40% of X-linked nonsyndromic hearing loss. Individuals, usually males, with variants in this gene have characteristic clinical and radiological features, a perilymphatic flow (or "gusher") that can occur during stapes surgery. The hearing loss in these individuals can be mixed with the sensorineural component usually presenting in infancy and showing progression with age. The conductive hearing loss component, which may or may not be present, is due to fixation of the stapes. Importantly, if POU3F4 testing is positive, a stapes surgery is contraindicated due to the occurrence of a perilymphatic gusher, which can worsen the severity of the hearing loss. Vestibular problems and temporal bone abnormalities such as dilatation of the lateral end of the internal auditory meatus (IAM) and/or deficiency of bone between the basal turn of the cochlea and the IAM are also common. Female carriers of a POU3F4 variant may show a slight hearing loss with or without the perilymphatic gusher, most likely due to skewed X-inactivation. Children of a female with an identified pathogenic variant in POU3F4 will have a 50% risk of inheriting the same variant. Male offspring carrying the pathogenic variant will be affected. Females will be carriers or mildly affected. An affected male will pass along a pathogenic variant to all of his daughters, but none of his sons. De novo variants and somatic mosaicism have been reported (de Kok 1997 PMID: 9298820).

Gene Information

• Gene: POU3F4

  • Protein: Pou Domain, Class 3, Transcription Factor 4
  • OMIM#: 300039
  • Locus: Xq21.1

Testing strategy

Sequencing of the POU3F4 gene is recommended for males with hearing loss and identification of stapes fixation and perilymphatic gusher. Testing for POU3F4 may be indicated in a family with an X-linked pattern of nonsyndromic hearing loss, a history of vestibular problems, or temporal bone abnormalities associated with POU3F4-related hearing loss; however, additional genes associated with X-linked hearing loss have been identified, and are present on the OtoGenome™ test. The detection of a pathogenic variant in POU3F4 will allow one to determine whether a stapedectomy is contraindicated.

Females with mild features or those with affected male relatives should also consider testing to determine carrier status.

Methodology

This test is performed by Sanger sequencing of the coding regions and splice sites of the POU3F4 gene. This test does not detect large deletions or variants in non-coding regions that could affect gene expression cases.

Analytical and clinical sensitivity

This test is greater than 99.9% accurate in detecting variants in the sequence analyzed. Pathogenic variants in the POU3F4 gene may account for approximately 40% of X-linked nonsyndromic hearing loss.

How to order

Requisition form

All samples must be accompanied with a completed requisition form. Please make sure any identifiers used on the specimens are provided on the paperwork. Consent page should be signed by a health care provider. Any incomplete or missing paperwork may delay the start of testing.

Ordering

• Test code: lmPOU3F4-a_L

• Turnaround time: 3 weeks

• Specimen required:

  • 4-8ml of whole blood (3-5ml for an infant) in a lavender top tube (K2EDTA or K3EDTA) or
  • 10 ug of DNA at a minimum concentration of 25 ng/ul (please provide DNA concentration)

If providing DNA, please provide name and CLIA # of lab performing blood extraction

Billing information

The Laboratory for Molecular Medicine offers several billing options for our clients and their patients; however, we do not bill insurance companies and are unable to begin testing without accurate billing information.

• CPT code: 81479
• Price: $500