- 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.
The Blueprint Genetics Non-Syndromic Hearing Loss Panel (test code EA0201):
Commonly used ICD-10 code(s) when ordering the Non-Syndromic Hearing Loss Panel
|H90.5||Sensorineural hearing loss, unilateral and bilateral|
|H35.50||Usher syndrome, type IV|
|Q87.89||Branchio-oto-renal (BOR) syndrome|
- 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
|ACTG1*||Deafness, Baraitser-Winter syndrome||AD||27||47|
|ATP2B2||Sensorineural hearing loss||AD||3||7|
|BSND||Sensorineural deafness with mild renal dysfunction, Bartter syndrome||AR||10||20|
|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|
|CIB2||Deafness, Usher syndrome, type IV||AR||5||18|
|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|
|DCDC2||Deafness, Nephronophthisis, Sclerosing cholangitis, neonatal||AR||13||9|
|DFNB31||Deafness, Usher syndrome, type IV||AR||12||31|
|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|
|EPS8L2||Deafness, autosomal recessive 106||AR||2||2|
|ESPN*||Deafness, Usher syndrome, type IV||AD/AR||12||15|
|EYA4||Dilated cardiomyopathy (DCM), Deafness, autosomal dominant 10||AD||15||28|
|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|
|MET||Deafness, Renal cell carcinoma, papillary, Osteofibrous dysplasia, susceptibility to||AD/AR||20||34|
|MPZL2||Sensorineural hearing loss||AR||4|
|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|
|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|
|PCDH15||Deafness, Usher syndrome, type IV||AR/Digenic||113||118|
|PNPT1*||Deafness, Combined oxidative phosphorylation deficiency, 13||AR||11||13|
|PRPS1*||Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Deafness, X-linked 1||XL||27||32|
|S1PR2||Deafness, autosomal recessive 68||AR||2||3|
|SIX1||Deafness, Branchiootic syndrome, Branchiootorenal syndrome||AD||11||19|
|SLC26A4||Deafness, Pendred syndrome, Enlarged vestibular aqueduct||AR||181||548|
|SLITRK6||Deafness and myopia||AR||3||5|
|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|
|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|
|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), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence 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|
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 genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.
Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).
Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.
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||99.2% (7,745/7,806)||>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%|
|Size range (0.1-47 Mb)||100% (25/25)|
|The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics|
|Mean sequencing depth||143X|
|Nucleotides with >20x sequencing coverage (%)||99.86%|
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.
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.