Non-Syndromic Hearing Loss Panel

Updated
Summary
  • Is a 101 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of unilateral or bilateral non-syndromic hearing loss.

    Is not ideal for individuals suspected to have syndromic hearing loss. Please refer to our Syndromic Hearing Loss Panel.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

101

Test code

EA0201

Panel size

Large

CPT codes
81430

Summary

The Blueprint Genetics Non-Syndromic Hearing Loss Panel (test code EA0201):

ICD codes

Commonly used ICD-10 code(s) when ordering the Non-Syndromic Hearing Loss Panel

ICD-10 Disease
H90.5 Sensorineural hearing loss, unilateral and bilateral
H35.50 Usher syndrome, type IV
Q87.89 Branchio-oto-renal (BOR) syndrome

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

Label the sample tube with your patient's name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.

Sensorineural hearing loss is a genetically very heterogenous group of phenotypes varying in severity and causes. Non-syndromic sensorineural hearing loss is a partial or total loss of hearing that occurs without other associated clinical findings. Hearing loss can be unilateral or bilateral and it can be stable or progressive. In addition, specific types of non-syndromic hearing loss may show distinctive pattern of hearing loss for high, middle or low tones. Some 60-70% of congenital hereditary hearing impairment have non-syndromic origin, and the prevalence is estimated to be 3-4:10,000 neonates and increases with age. In many populations, mutations in GJB2 are the most prevalent explaining up to 50% of all non-syndromic hearing losses. Non-syndromic hearing loss is genetically heterogenous, as more than >60 autosomal dominant loci and >90 autosomal recessive loci have been identified (http://www.hereditaryhearingloss.org).

Genes in the Non-Syndromic Hearing Loss Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ACTG1* Deafness, Baraitser-Winter syndrome AD 27 47
ADCY1 Deafness AR 1 1
ATP2B2 Sensorineural hearing loss AD 3 7
BDP1* Hearing loss AD/AR 1 1
BSND Sensorineural deafness with mild renal dysfunction, Bartter syndrome AR 10 20
CABP2 Deafness AR 1 6
CCDC50 Deafness AD 1 4
CD164 Deafness, autosomal dominant 66 AD 1 1
CDC14A Deafness, autosomal recessive 105 AR 7 9
CDH23 Deafness, Usher syndrome, type IV AR/Digenic 94 358
CEACAM16 Deafness AD/AR 4 4
CIB2 Deafness, Usher syndrome, type IV AR 5 18
CLDN14 Deafness AR 11 12
CLIC5 Deafness AR 1 2
COCH Deafness AD 14 29
COL11A2 Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular) AD/AR 29 57
COL4A6 Deafness, with cochlear malformation XL 11 5
CRYM Deafness AD 2 4
DCDC2 Deafness, Nephronophthisis, Sclerosing cholangitis, neonatal AR 13 9
DFNA5 Deafness AD 7 13
DFNB31 Deafness, Usher syndrome, type IV AR 12 31
DFNB59 Deafness AR 12 20
DIABLO Deafness AD 1 2
DIAPH1 Deafness, Seizures, cortical blindness, and microcephaly syndrome (SCBMS) AD/AR 10 15
DIAPH3 Non-syndromic sensorineural deafness AD 1 9
DMXL2 Deafness, autosomal dominant, 71 AR 2 6
DSPP Dentin dysplasia, Dentinogenesis imperfecta, Deafness, with dentinogenesis imperfecta AD 11 53
ELMOD3 Deafness AR 1 2
EPS8 Deafness AR 2 2
EPS8L2 Deafness, autosomal recessive 106 AR 2 2
ESPN* Deafness, Usher syndrome, type IV AD/AR 12 15
ESRRB Deafness AR 12 19
EYA4 Dilated cardiomyopathy (DCM), Deafness, autosomal dominant 10 AD 15 28
FAM65B Deafness AR 1 2
GIPC3 Deafness AR 9 20
GJB2 Deafness, Bart-Pumphrey syndrome, Keratoderma, palmoplantar, with deafness, Vohwinkel syndrome, Hystrix-like ichthyosis with deafness, Keratitis-icthyosis-deafness syndrome AD/AR/Digenic 133 405
GJB3 Deafness, Erythrokeratodermia variabilis et progressiva 1, Deafness, autosomal dominant 2B AD/AR 11 40
GJB6 Deafness, Deafness, autosomal dominant 3B, Ectodermal dysplasia, hidrotic (Clouston syndrome) AD/AR 10 33
GPSM2 Deafness, Chudley-McCullough syndrome AR 18 11
GRHL2 Ectodermal dysplasia/short stature syndrome, Deafness, autosomal dominant 28, Corneal dystrophy, posterior polymorphous AD/AR 12 12
GRXCR1 Deafness AR 8 9
GRXCR2 Deafness AR 1 2
HGF Deafness AR 4 10
HOMER2 Deafness AD 2 1
ILDR1 Deafness AR 8 27
KARS Charcot-Marie-Tooth disease AR 9 23
KCNQ4 Deafness AD 28 37
LHFPL5 Deafness AR 7 10
LMX1A Hearing loss AD/AR 1 4
LOXHD1 Deafness AD/AR 26 60
LRTOMT Deafness AR 7 17
MARVELD2 Deafness AR 9 17
MET Deafness, Renal cell carcinoma, papillary, Osteofibrous dysplasia, susceptibility to AD/AR 20 34
MIR96 Deafness AD 2 4
MPZL2 Sensorineural hearing loss AR 4
MSRB3 Deafness AR 5 2
MYH14 Deafness, Peripheral neuropathy, myopathy, hoarseness, and hearing loss AD 7 44
MYH9 Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness, Deafness, autosomal dominant 17 AD 25 117
MYO15A Deafness AR 97 235
MYO3A Deafness AR 9 22
MYO6 Deafness, Deafness, autosomal dominant, 22 AD/AR 24 68
MYO7A Deafness, Usher syndrome, type IV, Deafness, autosomal dominant 11 AD/AR 239 515
NARS2 Combined oxidative phosphorylation deficiency AR 12 12
OSBPL2 Deafness AD 2 3
OTOA#* Deafness AR 19 28
OTOF Neuropathy, Deafness AR 107 163
OTOG Deafness AR 18 3
OTOGL Deafness AR 26 23
P2RX2 Deafness AD 2 4
PCDH15 Deafness, Usher syndrome, type IV AR/Digenic 113 118
PDE1C Hearing loss AD 2 2
PNPT1* Deafness, Combined oxidative phosphorylation deficiency, 13 AR 11 13
POU3F4 Deafness XL 25 80
POU4F3 Deafness AD 9 33
PRPS1* Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Deafness, X-linked 1 XL 27 32
RDX* Deafness AR 6 10
S1PR2 Deafness, autosomal recessive 68 AR 2 3
SERPINB6 Deafness AR 2 3
SIX1 Deafness, Branchiootic syndrome, Branchiootorenal syndrome AD 11 19
SLC17A8 Deafness AD 1 8
SLC22A4 Hearing loss AR 2
SLC26A4 Deafness, Pendred syndrome, Enlarged vestibular aqueduct AR 181 548
SLC26A5 Deafness AR 2 7
SLITRK6 Deafness and myopia AR 3 5
SMPX Deafness XL 8 14
STRC#* Deafness AR 31 85
SYNE4 Deafness AR 6 2
TBC1D24 Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome, Deafness, autosomal dominant, 65, Myoclonic epilepsy, infantile, familial, Epileptic encephalopathy, early infantile, 16, Deafness, autosomal recessive 86 AD/AR 43 55
TECTA Deafness AD/AR 36 120
TJP2 Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial, Deafness, autosomal dominant 51 AD/AR 25 27
TMC1 Deafness, Deafness, autosomal dominant 36 AD/AR 33 91
TMEM132E Hearing loss AR 1
TMIE Deafness AR 9 10
TMPRSS3 Deafness AR 25 82
TNC Deafness AD 3 6
TPRN# Deafness AR 6 12
TRIOBP Deafness AR 22 40
TSPEAR Deafness AR 2 7
USH1C Deafness, Usher syndrome, type IV AR 45 51
WBP2 Deafness, autosomal recessive 107 AR 3 3
WFS1 Wolfram syndrome, Deafness, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41 AD/AR 69 362

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by Non-Syndromic Hearing Loss Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
DFNA5 Chr7:24746007 c.991-15_991-13delTTC NM_004403.2 rs727505273
DIAPH3 Chr13:60738072 c.-172G>A NM_001042517.1
DIAPH3 Chr13:60738073 c.-173C>T NM_001042517.1
EYA4 Chr6:133833847 c.1282-12T>A NM_004100.4
EYA4 Chr6:133833997 c.1341-19T>A NM_004100.4
GJB2 Chr13:20763744 c.-22-2A>C NM_004004.5 rs201895089
GJB2 Chr13:20766920 c.-23+2T>A NM_004004.5
GJB2 Chr13:20766921 c.-23+1G>A NM_004004.5 rs80338940
GJB2 Chr13:20766922 c.-23G>T NM_004004.5 rs786204734
GJB2 Chr13:20767158 c.-259C>T NM_004004.5
GJB2 Chr13:20767159 c.-260C>T NM_004004.5
GRHL2 Chr8:102505149 c.20+133delA NM_024915.3
GRHL2 Chr8:102505272 c.20+257delT NM_024915.3
GRHL2 Chr8:102505561 c.20+544G>T NM_024915.3
GRXCR1 Chr4:42965170 c.627+19A>T NM_001080476.2 rs201824235
HGF Chr7:81384504 c.482+1991_482+2000delGATGATGAAA NM_000601.4 rs900334407
HGF Chr7:81384516 c.482+1986_482+1988delTGA NM_000601.4
MYO3A Chr10:26409593 c.1777-12G>A NM_017433.4
MYO6 Chr6:76593963 c.2417-1758T>G NM_004999.3
MYO7A Chr11:76839534 c.-48A>G NM_000260.3
MYO7A Chr11:76893448 c.3109-21G>A NM_000260.3
MYO7A Chr11:76915107 c.5327-14T>G NM_000260.3
MYO7A Chr11:76915110 c.5327-11A>G NM_000260.3 rs397516316
MYO7A Chr11:76919448 c.5857-27_5857-26insTTGAG NM_000260.3
PCDH15 Chr10:56560684 c.-29+1G>C NM_001142763.1
SLC26A4 Chr7:107301201 c.-103T>C NM_000441.1 rs60284988
SLC26A4 Chr7:107301244 c.-60A>G NM_000441.1 rs545973091
SLC26A4 Chr7:107301301 c.-4+1G>C NM_000441.1
SLC26A4 Chr7:107301305 c.-4+5G>A NM_000441.1 rs727503425
SLC26A4 Chr7:107323842 c.918+45_918+47delCAA NM_000441.1
SLC26A4 Chr7:107330533 c.1150-35_1150-28delTTTGTAGG NM_000441.1
SLC26A4 Chr7:107334836 c.1264-12T>A NM_000441.1
SLC26A4 Chr7:107336364 c.1438-7dupT NM_000441.1 rs754734032
SLC26A4 Chr7:107341513 c.1708-27_1708-11delTAAGTAACTTGACATTT NM_000441.1
SLC26A4 Chr7:107350439 c.2090-52_2090-49delCAAA NM_000441.1
TMC1 Chr9:75315577 c.362+18A>G NM_138691.2
WFS1 Chr4:6271704 c.-43G>T NM_006005.3

Added and removed genes from the panel

Genes added Genes removed
ATP2B2
DMXL2
LMX1A
MPZL2
PDE1C
SLC22A4

The strengths of this test include:

  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: OTOA (22-27), OTOGL (21), STRC (1-18). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene’s target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics non-Syndromic hearing loss panel covers classical genes associated with sensorineural hearing loss, unilateral and bilateral, non-syndromic genetic deafness, Usher syndrome, Baraitser-Winter syndrome and Branchio-oto-renal (BOR) syndrome. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient’s phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999
11-50 bps 99.13% (2,524/2,546) >99.9999
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as  SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.

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