Comprehensive Hearing Loss and Deafness Panel
Test code: EA0501
The Blueprint Genetics Comprehensive Hearing Loss and Deafness Panel is a 158 gene test for genetic diagnostics of patients with clinical suspicion of Alport syndrome, branchio-oto-renal (BOR) syndrome, non-syndromic genetic deafness, Pendred syndrome, sensorineural hearing loss, unilateral and bilateral, Stickler syndrome, Usher syndrome or Waardenburg syndrome.
Hearing loss is a genetically and clinically heterogenous group of diseases and syndromes and may be classified in several different ways. This Panel includes comprehensively genes associated with both syndromic and non-syndromic hearing loss. In addition to protein coding regions, two disease causing intronic variants of HGF gene are targeted in this Panel. Inheritance of these disorders may be autosomal recessive or dominant as well as X-linked. This comprehensive Panel includes Waardenburg Syndrome Panel, Pendred Syndrome Panel, Usher Syndrome Panel, Stickler Syndrome Panel, Alport Syndrome Panel, Branchio-Oto-Renal Panel, Syndromic Hearing Loss Panel and Non-Syndromic Hearing Loss Panel.
About Hearing Loss and Deafness
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 in isolation, without other associated medical disorders. In syndromic hearing loss, symptoms affecting other parts of the body occur interlinked with hearing impairnment or deafness. Sensorineural hearing loss can be unilateral or bilateral and it can be stable or progressive. In addition, the loss may appear with various intensivity to high, middle or low tones. Some 75%-to-85% of congenital hereditary hearing impairnment have non-syndromic origin, while the remaining 15%-to-25% is syndromic in origin. The prevalence of non-syndromic hearing loss is 3-4:10000 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. Altogether syndromic hearing loss accounts for 20% to 30% of congenital hearing loss and deafness and the combined prevalence of syndromic hearing loss is approximately 1-2:10000.
Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.
|ABHD12||Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract||AR||10||15|
|ACTG1*||Deafness, Baraitser-Winter syndrome||AD||17||37|
|ANKH||Calcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant type||AD||12||21|
|ATP6V1B1||Renal tubular acidosis with deafness||AR||8||39|
|BSND||Sensorineural deafness with mild renal dysfunction, Bartter syndrome||AR||10||21|
|CACNA1D||Primary aldosteronism, seizures, and neurologic abnormalities, Sinoatrial node dysfunction and deafness||AD/AR||4||5|
|CD151||Raph blood group||BG||1||4|
|CDH23||Deafness, Usher syndrome||AR/Digenic||48||294|
|CDKN1C||Beckwith-Wiedemann syndrome, IMAGE syndrome||AD||25||79|
|CHD7||Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome||AD||128||746|
|CHSY1||Temtamy preaxial brachydactyly syndrome||AR||6||10|
|CIB2||Deafness, Usher syndrome||AR||4||15|
|CLRN1||Retinitis pigmentosa, Usher syndrome||AR||14||32|
|COL2A1||Avascular necrosis of femoral head, Rhegmatogenous retinal detachment, Epiphyseal dysplasia, with myopia and deafness, Czech dysplasia, Achondrogenesis type 2, Platyspondylic dysplasia Torrance type, Hypochondrogenesis, Spondyloepiphyseal dysplasia congenital (SEDC), Spondyloepimetaphyseal dysplasia (SEMD) Strudwick type, Kniest dysplasia, Spondyloperipheral dysplasia, Mild SED with premature onset arthrosis, SED with metatarsal shortening, Stickler syndrome type 1||AD||106||537|
|COL4A6||Deafness, with cochlear malformation||XL||12||4|
|COL9A1||Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 (EDM6)||AR||3||4|
|COL9A2||Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2)||AR||5||12|
|COL9A3||Multiple epihyseal dysplasia type 3 (EDM3)||AD||3||16|
|COL11A1||Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2||AD/AR||18||76|
|COL11A2||Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular)||AD/AR||17||51|
|DFNB31||Deafness, Usher syndrome||AR||9||28|
|DIAPH3||Non-syndromic sensorineural deafness||AD/AR||1||6|
|DLX5||Split-hand/foot malformation with sensorineural hearing loss||AR||3||8|
|DSPP||Dentin dysplasia, Dentinogenesis imperfecta, Deafness, with dentinogenesis imperfecta||AD||8||48|
|EDN3||Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndrome||AD/AR||6||21|
|EDNRB||Hirschsprung disease, ABCD syndrome, Waardenburg syndrome||AD/AR||5||62|
|EYA1||Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome||AD||33||186|
|EYA4||Dilated cardiomyopathy (DCM)||AD||8||22|
|FGF3||Deafness, congenital with inner ear agenesis, microtia, and microdontia||AR||12||20|
|FGFR3||Lacrimoauriculodentodigital syndrome, Muenke syndrome, Crouzon syndrome with acanthosis nigricans, Camptodactyly, tall stature, and hearing loss (CATSHL) syndrome, Achondroplasia, Hypochondroplasia, Thanatophoric dysplasia type 1, Thanatophoric dysplasia type 2, SADDAN||AD/AR||47||68|
|FOXI1||Pendred syndrome, Enlarged vestibular aqueduct||AR||1||8|
|GJB2||Deafness, Bart-Pumphrey syndrome, Keratoderma, palmoplantar, with deafness, Vohwinkel syndrome, Hystrix-like ichthyosis with deafness, Keratitis-icthyosis-deafness syndrome||AD/AR/Digenic||96||385|
|GPSM2||Deafness, Chudley-McCullough syndrome||AR||10||11|
|GRHL2||Ectodermal dysplasia/short stature syndrome||AD/AR||6||6|
|HOXB1||Facial paresis, hereditary congenital||AR||1||5|
|KCNE1||Long QT syndrome, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||6||46|
|KCNJ10||Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SESAME syndrome), Pendred syndrome, Enlarged vestibular aqueduct||AR/Digenic||14||26|
|KCNQ1||Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||237||590|
|LRP2||Donnai-Barrow syndrome, Faciooculoacousticorenal syndrome||AR||15||28|
|MET||Deafness, Renal cell carcinoma, papillary||AD/AR||13||23|
|MITF||Renal cell carcinoma with or without malignant melanoma, Tietz albinism-deafness syndrome, Waardenburg syndrome, Melanoma, cutaneous malignant||AD||15||50|
|MYH9||Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness||AD||19||113|
|MYH14||Deafness, Peripheral neuropathy, myopathy, hoarseness, and hearing loss||AD||6||26|
|MYO7A||Deafness, Usher syndrome||AR||125||402|
|NARS2||Combined oxidative phosphorylation deficiency||AR||3||6|
|NDP||Exudative vitreoretinopathy, Norrie disease||XL||25||155|
|NLRP3||Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndrome||AD||15||125|
|PAX3||Craniofacial-deafness-hand syndrome, Waardenburg syndrome||AD/AR||20||135|
|PCDH15||Deafness, Usher syndrome||AR/Digenic||28||97|
|POLR1C||Treacher Collins syndrome||AR||13||18|
|POLR1D||Treacher Collins syndrome||AD/AR||7||25|
|PRPS1*||Deafness, Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome||XL||22||26|
|RMND1*||Combined oxidative phosphorylation deficiency||AR||13||13|
|RPS6KA3||Coffin-Lowry syndrome, Mental retardation||XL||35||161|
|SALL4||Acro-renal-ocular syndrome, Duane-radial ray/Okohiro syndrome||AD||15||48|
|SIX1||Deafness, Branchiootic syndrome, Branchiootorenal syndrome||AD||9||15|
|SLC19A2||Thiamine-responsive megaloblastic anemia syndrome||AR||10||47|
|SLC26A4||Deafness, Pendred syndrome, Enlarged vestibular aqueduct||AR||98||521|
|SLC29A3||Histiocytosis-lymphadenopathy plus syndrome, Dysosteosclerosis||AR||17||22|
|SLC33A1*||Congenital cataracts, hearing loss, and neurodegeneration||AR||6||7|
|SLITRK6||Deafness and myopia||AR||3||3|
|SMAD4||Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasia||AD||119||128|
|SOX10||Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease||AD||31||119|
|SUCLA2||Mitochondrial DNA depletion syndrome||AR||8||26|
|SUCLG1||Mitochondrial DNA depletion syndrome||AR||12||28|
|TBC1D24||Deafness, Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndrome||AD/AR||27||41|
|TCOF1||Treacher Collins syndrome||AD||17||303|
|TIMM8A*||Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia||XL||11||21|
|TJP2||Cholestasis, progressive familial intrahepatic, Hypercholanemia, familial||AR||15||15|
|TRMU||Liver failure, infantile, Reversible infantile respiratory chain deficiency||AR||12||16|
|USH1C||Deafness, Usher syndrome||AR||13||45|
|USH2A||Usher syndrome, Retinitis pigmentosa||AR||147||924|
- * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.
Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/); HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/ac/). The list of associated (gene specific) phenotypes are generated from CDG (http://research.nhgri.nih.gov/CGD/) or Orphanet (http://www.orpha.net/) databases.
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number||Comment||Reference|
Blueprint Genetics offers a Comprehensive Hearing Loss and Deafness Panel that covers classical genes associated with Alport syndrome, branchio-oto-renal (BOR) syndrome, CHARGE syndrome, Jervell and Lange-Nielsen syndrome, Mohr-Tranebjaerg syndrome, non-syndromic genetic deafness, Norrie disease, Pendred syndrome, sensorineural hearing loss, unilateral and bilateral, Stickler syndrome, treacher Collins syndrome, Usher syndrome and Waardenburg syndrome. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.
Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.
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. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (http://www.1000genomes.org), the NHLBI GO Exome Sequencing Project (ESP; http://evs.gs.washington.edu/EVS), the Exome Aggregation Consortium (ExAC; http://exac.broadinstitute.org), ClinVar database of genotype-phenotype associations (http://www.ncbi.nlm.nih.gov/clinvar) and the Human Gene Mutation Database (http://www.hgmd.cf.ac.uk). The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (http://sift.jcvi.org), Polyphen (http://genetics.bwh.harvard.edu/pph2/), and Mutation Taster (http://www.mutationtaster.org).
Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.
In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.
Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.
A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.
We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.
Full service only
Choose an analysis method
ICD & CPT codes
Commonly used ICD-10 codes when ordering the Comprehensive Hearing Loss and Deafness Panel
|H90.5||Sensorineural hearing loss, unilateral and bilateral|
|Q87.8||Branchio-oto-renal (BOR) syndrome|
Accepted sample types
- EDTA blood, min. 1 ml
- Purified DNA, min. 5μg
- Saliva (Oragene DNA OG-500 kit)
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.