- Is a 89 gene panel that includes assessment of non-coding variants
Is ideal for patients suspected to have a syndromic form of hearing loss. The genes on this panel are included on the Comprehensive Hearing Loss and Deafness Panel.
Is not ideal for patients suspected to have non-syndromic hearing loss. Please refer to our Non-Syndromic Hearing Loss Panel or our Comprehensive Hearing Loss and Deafness Panel.
Number of genes89
CPT codesSEQ 81404
The Blueprint Genetics Syndromic Hearing Loss Panel (test code EA0401):
- Is a 89 gene panel that includes assessment of selected non-coding disease-causing variants
- Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only
Commonly used ICD-10 code(s) when ordering the Syndromic Hearing Loss Panel
|Q87.89||Branchio-oto-renal (BOR) syndrome|
- EDTA blood, min. 1 ml
- Purified DNA, min. 3μg
- 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.
Hearing loss is a genetically heterogenous group of phenotypes varying in severity and causes. In syndromic hearing loss, one or more organ systems are also affected in addition to the hearing impairment or deafness. 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 1-2:10,000. The most common syndromic causes of hearing loss include Alport syndrome, branchio-oto-renal (BOR) syndrome, Pendred syndrome, Stickler syndrome, Usher syndrome and Waardenburg syndrome.
Genes in the Syndromic Hearing Loss Panel and their clinical significance
|ABHD12||Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract||AR||12||18|
|ACTG1*||Deafness, Baraitser-Winter syndrome||AD||21||43|
|ADGRV1||Usher syndrome, Febrile seizures, familial, 4||AR/Digenic||58||164|
|ANKH||Calcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant type||AD||12||20|
|ATP6V1B1||Renal tubular acidosis with deafness||AR||9||54|
|ATP6V1B2||Deafness, congenital, with onychodystrophy, autosomal dominant, Zimmermann-Laband syndrome 2||AD||5||2|
|BSND||Sensorineural deafness with mild renal dysfunction, Bartter syndrome||AR||10||19|
|C10ORF2||Perrault syndrome, Mitochondrial DNA depletion syndrome||AR||37|
|CACNA1D||Primary aldosteronism, seizures, and neurologic abnormalities, Sinoatrial node dysfunction and deafness||AD/AR||6||5|
|CD151||Raph blood group||BG||1|
|CDH23||Deafness, Usher syndrome||AR/Digenic||69||332|
|CDKN1C||Beckwith-Wiedemann syndrome, IMAGE syndrome||AD||24||81|
|CEP78||Cone rod dystrophy and hearing loss||7||8|
|CHD7||Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome||AD||192||784|
|CHSY1||Temtamy preaxial brachydactyly syndrome||AR||6||11|
|CIB2||Deafness, Usher syndrome||AR||4||15|
|CLRN1||Retinitis pigmentosa, Usher syndrome||AR||17||34|
|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||138||541|
|COL4A3||Alport syndrome, Hematuria, benign familial||AD/AR||34||229|
|COL4A6||Deafness, with cochlear malformation||XL||11||4|
|COL9A1||Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 (EDM6)||AR||7||5|
|COL9A2||Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2)||AD/AR||7||12|
|COL9A3||Multiple epihyseal dysplasia type 3 (EDM3)||AD/AR||6||15|
|COL11A1||Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2||AD/AR||22||81|
|COL11A2||Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular)||AD/AR||23||54|
|DFNB31||Deafness, Usher syndrome||AR||11||30|
|DLX5||Split-hand/foot malformation with sensorineural hearing loss||AR||3||8|
|DNMT1||Neuropathy, hereditary sensory, Cerebellar ataxia, deafness, and narcolepsy||AD||10||19|
|EDN3||Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndrome||AD/AR||6||21|
|EDNRB||Hirschsprung disease, ABCD syndrome, Waardenburg syndrome||AD/AR||7||66|
|EYA1||Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome||AD||39||197|
|FDXR||Auditory neuropathy and optic atrophy||AR||4|
|FGF3||Deafness, congenital with inner ear agenesis, microtia, and microdontia||AR||13||20|
|FOXI1||Pendred syndrome, Enlarged vestibular aqueduct||AR||1||9|
|GJA1*||Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3||AD/AR||28||105|
|HARS*||Usher syndrome, Charcot-Marie-Tooth disease, axonal, type 2W||AR||5||9|
|HOXB1||Facial paresis, hereditary congenital||AR||1||5|
|KCNE1||Long QT syndrome, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||8||45|
|KCNJ10||Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SESAME syndrome), Pendred syndrome, Enlarged vestibular aqueduct||AR/Digenic||14||24|
|KCNQ1||Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||258||599|
|KIT||Gastrointestinal stromal tumor||AD||73||109|
|LRP2||Donnai-Barrow syndrome, Faciooculoacousticorenal syndrome||AR||22||27|
|MAN2B1||Mannosidosis, alpha B, lysosomal||AR||34||142|
|MITF||Renal cell carcinoma with or without malignant melanoma, Tietz albinism-deafness syndrome, Waardenburg syndrome, Melanoma, cutaneous malignant||AD||24||55|
|MYH9||Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness||AD||21||113|
|MYO7A||Deafness, Usher syndrome||AD/AR||155||426|
|NDP||Exudative vitreoretinopathy, Norrie disease||XL||29||159|
|NLRP3||Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndrome||AD||19||127|
|PAX3||Craniofacial-deafness-hand syndrome, Waardenburg syndrome||AD/AR||22||135|
|PCDH15||Deafness, Usher syndrome||AR/Digenic||71||107|
|PEX26||Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder||AR||11||24|
|POLR1C||Treacher Collins syndrome||AR||16||20|
|POLR1D||Treacher Collins syndrome||AD/AR||7||26|
|SALL1*||Townes-Brocks syndrome 1||AD||24||83|
|SIX1||Deafness, Branchiootic syndrome, Branchiootorenal syndrome||AD||11||16|
|SLC19A2||Thiamine-responsive megaloblastic anemia syndrome||AR||11||49|
|SLC26A4||Deafness, Pendred syndrome, Enlarged vestibular aqueduct||AR||137||535|
|SLC52A2||Brown-Vialetto-Van Laere syndrome||AR||22||19|
|SLC52A3||Fazio-Londe disease, Brown-Vialetto-Van Laere syndrome||AR||33||30|
|SLITRK6||Deafness and myopia||AR||3||3|
|SMAD4||Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasia||AD||139||132|
|SOX10||Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease||AD||34||133|
|TCOF1||Treacher Collins syndrome||AD||31||320|
|TIMM8A*||Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia||XL||10||21|
|USH1C||Deafness, Usher syndrome||AR||18||48|
|USH2A||Usher syndrome, Retinitis pigmentosa, Retinitis pigmentosa 39||AR||225||1001|
|WFS1||Wolfram syndrome, Deafness||AD/AR||65||343|
* 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 the panel
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number|
Added and removed genes from the panel
|Genes added||Genes removed|
|ATP6V1B2 C10ORF2 CEP78 CLPP DCAF17 DNMT1 FDXR GJA1 HARS2 KIT LARS2 MAN2B1 MGP PEX1 PEX26 PEX6 SALL1 SLC52A2 SLC52A3|
Test strengthThe 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
- 1479 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
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. 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 syndromic hearing loss panel covers classical genes associated with Waardenburg syndrome, Alport syndrome, Pendred syndrome, Usher syndrome, Stickler syndrome, Jervell and Lange-Nielsen syndrome, Mohr-Tranebjaerg syndrome, Norrie disease, Treacher Collins syndrome, CHARGE 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 Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.
|Sensitivity % (TP/(TP+FN)||Specificity %|
|Single nucleotide variants||99.65% (412,456/413,893)||>99.99%|
|Insertions, deletions and indels by sequence analysis|
|1-10 bps||96.94% (17,070/17,608)||>99.99%|
|11-50 bps||99.07% (957/966)||>99.99%|
|Copy number variants (exon level dels/dups)|
|Clinical samples (small CNVs, n=52)|
|1 exon level deletion||92.3% (24/26)||NA|
|2 exons level deletion/duplication||100.0% (11/11)||NA|
|3-7 exons level deletion/duplication||93.3% (14/15)||NA|
|Microdeletion/-duplication sdrs (large CNVs, n=37))|
|Size range (0.1-47 Mb)||100% (37/37)|
|Simulated CNV detection|
|2 exons level deletion/duplication||90.98% (7,357/8,086)||99.96%|
|5 exons level deletion/duplication||98.63% (7,975/8,086)||99.98%|
|The performance presented above reached by WES with the following coverage metrics|
|Mean sequencing depth at exome level||174x|
|Nucleotides with >20x sequencing coverage (%)||99.4%|
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 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 such as, 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, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.
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 of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen 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 used, congress abstracts and mutation databases to help our customers 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 within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).
Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. 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.