Syndromic Hearing Loss Panel
In addition, it also includes the maternally inherited mitochondrial genome.
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.
The Blueprint Genetics Syndromic Hearing Loss Panel (test code EA0401):
Read about our accreditations, certifications and CE-marked IVD medical devices here.
Refer to the most current version of ICD-10-CM manual for a complete list of ICD-10 codes.
- Blood (min. 1ml) in an EDTA tube
- Extracted DNA, min. 2 μg in TE buffer or equivalent
- Saliva (Please see Sample Requirements for accepted saliva kits)
Label the sample tube with your patient’s name, date of birth and the date of sample collection.
We do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. In addition, if the patient is affected with a hematological malignancy, DNA extracted from a non-hematological source (e.g. skin fibroblasts) is strongly recommended.
Please note that, in rare cases, mitochondrial genome (mtDNA) variants may not be detectable in blood or saliva in which case DNA extracted from post-mitotic tissue such as skeletal muscle may be a better option.
Read more about our sample requirements here.
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
To view complete table content, scroll horizontally.
|ABHD12||Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract||AR||16||20|
|ACTG1*||Deafness, Baraitser-Winter syndrome||AD||27||47|
|ADGRV1||Usher syndrome, type IIC||AR||71||236|
|ANKH||Calcium pyrophosphate deposition disease (familial chondrocalcinosis type 2), Craniometaphyseal dysplasia autosomal dominant type||AD||13||20|
|ARSG||Usher syndrome, type IV||AR||1||1|
|ATP6V1B1||Renal tubular acidosis with deafness||AR||15||56|
|ATP6V1B2||Deafness, congenital, with onychodystrophy, autosomal dominant, Zimmermann-Laband syndrome 2||AD||6||3|
|BCS1L||Bjornstad syndrome, GRACILE syndrome, Leigh syndrome, Mitochondrial complex III deficiency, nuclear type 1||AR||42||37|
|BSND||Sensorineural deafness with mild renal dysfunction, Bartter syndrome||AR||10||20|
|C10ORF2||Perrault syndrome, Mitochondrial DNA depletion syndrome, Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant, 3||AD/AR||37||80|
|CACNA1D||Primary aldosteronism, seizures, and neurologic abnormalities, Sinoatrial node dysfunction and deafness||AD/AR||7||8|
|CD151||Raph blood group, Nephropathy with pretibial epidermolysis bullosa and deafness||AR||1||3|
|CDH23||Deafness, Usher syndrome, type 1D||AR||94||358|
|CDKN1C||Beckwith-Wiedemann syndrome, IMAGE syndrome||AD||35||81|
|CEP250||Cone rod dystrophy and hearing loss||AR||5|
|CEP78||Cone rod dystrophy and hearing loss||AR||7||9|
|CHD7||Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome||AD||276||860|
|CHSY1||Temtamy preaxial brachydactyly syndrome||AR||6||16|
|CIB2||Deafness, Usher syndrome type IJ||AR||5||18|
|CLRN1||Retinitis pigmentosa, Usher sydnrome, type 3A||AR||24||39|
|COL11A1||Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2||AD/AR||34||94|
|COL11A2||Weissenbacher-Zweymuller syndrome, Deafness, Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular)||AD/AR||29||57|
|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||180||561|
|COL4A3||Alport syndrome, Hematuria, benign familial||AD/AR||123||264|
|COL4A6||Deafness, with cochlear malformation||XL||11||5|
|COL9A1||Multiple epiphyseal dysplasia type 6 (EDM6), Stickler syndrome, type IV||AD/AR||9||6|
|COL9A2||Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2)||AD/AR||7||12|
|COL9A3||Multiple epihyseal dysplasia type 3 (EDM3), Stickler syndrome recessive type||AD/AR||10||14|
|DFNB31||Usher syndrome, type 2D, Deafness, autosomal recessive 31||AR||12||31|
|DLX5||Split-hand/foot malformation with sensorineural hearing loss, Split-hand/foot malformation||AD/AR||3||9|
|DNMT1||Neuropathy, hereditary sensory, Cerebellar ataxia, deafness, and narcolepsy||AD||9||20|
|EDN3||Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndrome||AD/AR||7||21|
|EDNRB||Hirschsprung disease, ABCD syndrome, Waardenburg syndrome||AD/AR||12||66|
|EIF3F||Intellectual disability, autosomal recessive||AR|
|ESPN*||Deafness, Deafness, autosomal recessive 36||AD/AR||12||15|
|EYA1||Otofaciocervical syndrome, Branchiootic syndrome, Branchiootorenal syndrome||AD||56||218|
|FDXR||Auditory neuropathy and optic atrophy||AR||5||19|
|FGF3||Deafness, congenital with inner ear agenesis, microtia, and microdontia||AR||13||20|
|FOXI1||Pendred syndrome, Enlarged vestibular aqueduct||AR||1||11|
|GATA3||Hypomagnesemia, renal, Hypoparathyroidism, sensorineural deafness, and renal dysplasia||AD||22||86|
|GJA1*||Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia severe type, Syndactyly type 3||AD/AR||31||107|
|HARS||Charcot-Marie-Tooth disease, axonal, type 2W, Usher syndrome, type 3B||AD/AR||6||12|
|HOXB1||Facial paresis, hereditary congenital||AR||3||6|
|KCNE1||Long QT syndrome, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||11||46|
|KCNJ10||Seizures, sensorineural deafness, ataxia, mental retardation, and electrolyte imbalance (SESAME syndrome), Pendred syndrome, Enlarged vestibular aqueduct||AR/Digenic||13||29|
|KCNQ1||Short QT syndrome, Long QT syndrome, Atrial fibrillation, Jervell and Lange-Nielsen syndrome||AD/AR/Digenic||298||631|
|KIT||Gastrointestinal stromal tumor, Piebaldism||AD||79||116|
|LARS2||Perrault syndrome, Hydrops, lactic acidosis, and sideroblastic anemia (HLASA)||AR||14||14|
|LRP2||Donnai-Barrow syndrome, Faciooculoacousticorenal syndrome||AR||24||38|
|MAN2B1||Mannosidosis, alpha B, lysosomal||AR||63||149|
|MITF||Tietz albinism-deafness syndrome, Waardenburg syndrome, Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD)||AD/AR||32||58|
|MT-ATP6||Neuropathy, ataxia, and retinitis pigmentosa, Leber hereditary optic neuropathy, Ataxia and polyneuropathy, adult-onset, Cardiomyopathy, infantile hypertrophic, Leigh syndrome, Striatonigral degeneration, infantile, mitochondrial||Mitochondrial||19|
|MT-ATP8||Cardiomyopathy, apical hypertrophic, and neuropathy, Cardiomyopathy, infantile hypertrophic||Mitochondrial||4|
|MT-CO1||Myoglobinuria, recurrent, Leber hereditary optic neuropathy, Sideroblastic anemia, Cytochrome C oxidase deficiency, Deafness, mitochondrial||Mitochondrial||17|
|MT-CO2||Cytochrome c oxidase deficiency||Mitochondrial||8|
|MT-CO3||Cytochrome c oxidase deficiency, Leber hereditary optic neuropathy||Mitochondrial||9|
|MT-ND1||Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Leber hereditary optic neuropathy, Leber optic atrophy and dystonia||Mitochondrial||21|
|MT-ND2||Leber hereditary optic neuropathy, Mitochondrial complex I deficiency||Mitochondrial||6|
|MT-ND3||Leber optic atrophy and dystonia, Mitochondrial complex I deficiency||Mitochondrial||7|
|MT-ND4||Leber hereditary optic neuropathy, Leber optic atrophy and dystonia, Mitochondrial complex I deficiency||Mitochondrial||11|
|MT-ND4L||Leber hereditary optic neuropathy||Mitochondrial||2|
|MT-ND5||Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Leber hereditary optic neuropathy, Mitochondrial complex I deficiency||Mitochondrial||19|
|MT-ND6||Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Oncocytoma, Leber hereditary optic neuropathy, Leber optic atrophy and dystonia, Mitochondrial complex I deficiency||Mitochondrial||16|
|MT-TC||Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes||Mitochondrial||3|
|MT-TE||Diabetes-deafness syndrome, Mitochondrial myopathy, infantile, transient, Mitochondrial myopathy with diabetes||Mitochondrial||5|
|MT-TF||Myoclonic epilepsy with ragged red fibers, Nephropathy, tubulointerstitial, Encephalopathy, mitochondrial, Epilepsy, mitochondrial, Myopathy, mitochondrial, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes||Mitochondrial||7|
|MT-TK||Myoclonic epilepsy with ragged red fibers, Leigh syndrome||Mitochondrial||5|
|MT-TL1||Cytochrome c oxidase deficiency, Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, Diabetes-deafness syndrome, Cyclic vomiting syndrome, SIDS, susceptibility to||Mitochondrial||14|
|MT-TL2||Mitochondrial multisystemic disorder, Progressive external ophthalmoplegia, Mitochondrial Myopathy, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes||Mitochondrial||5|
|MT-TM||Leigh syndrome, Mitochondrial multisystemic disorder||Mitochondrial||1|
|MT-TN||Progressive external ophthalmoplegia, Mitochondrial multisystemic disorder||Mitochondrial||3|
|MT-TQ||Mitochondrial multisystemic disorder||Mitochondrial||2|
|MT-TS1||Myoclonic epilepsy with ragged red fibers, Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes||Mitochondrial||10|
|MT-TS2||Mitochondrial multisystemic disorder||Mitochondrial||2|
|MT-TV||Hypertrophic cardiomyopathy (HCM), Leigh syndrome, Mitochondrial multisystemic disorder, Mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes||Mitochondrial||3|
|MT-TW||Leigh syndrome, Myopathy, mitochondrial||Mitochondrial||8|
|MT-TY||Mitochondrial multisystemic disorder||Mitochondrial||4|
|MYH9||Sebastian syndrome, May-Hegglin anomaly, Epstein syndrome, Fechtner syndrome, Macrothrombocytopenia and progressive sensorineural deafness, Deafness, autosomal dominant 17||AD||25||117|
|MYO7A||Deafness, autosomal dominant 11, Usher syndrome, type I, Deafness, autosomal recessive 2||AD/AR||239||515|
|NDP||Exudative vitreoretinopathy, Norrie disease||XL||31||167|
|NLRP3||Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndrome, Familial cold-induced autoinflammatory syndrome 1, Deafness||AD||20||136|
|PAX3||Craniofacial-deafness-hand syndrome, Waardenburg syndrome||AD/AR||54||149|
|PCDH15||Deafness, Usher syndrome, type 1D||AR/Digenic||113||118|
|PDZD7#||Deafness, autosomal recessive||AR||11||19|
|PEX1||Heimler syndrome, Peroxisome biogenesis factor disorder 1A, Peroxisome biogenesis factor disorder 1B||AR||112||134|
|PEX26||Adrenoleukodystrophy, neonatal, Zellweger syndrome, Peroxisome biogenesis disorder||AR||13||27|
|PEX6||Heimler syndrome, Peroxisome biogenesis disorder 4A, Peroxisome biogenesis disorder 4B||AR||58||107|
|POLR1C#||Treacher Collins syndrome||AR||17||21|
|POLR1D||Treacher Collins syndrome||AD/AR||9||26|
|PRPS1*||Phosphoribosylpyrophosphate synthetase I superactivity, Arts syndrome, Charcot-Marie-Tooth disease, X-linked recessive, 5, Deafness, X-linked 1||XL||27||32|
|SALL1*||Townes-Brocks syndrome 1||AD||31||87|
|SIX1||Deafness, Branchiootic syndrome, Branchiootorenal syndrome||AD||11||19|
|SLC19A2||Thiamine-responsive megaloblastic anemia syndrome||AR||14||51|
|SLC26A4||Deafness, Pendred syndrome, Enlarged vestibular aqueduct||AR||181||548|
|SLC52A2||Brown-Vialetto-Van Laere syndrome||AR||27||25|
|SLC52A3||Fazio-Londe disease, Brown-Vialetto-Van Laere syndrome||AR||30||42|
|SLITRK6||Deafness and myopia||AR||3||5|
|SMAD4||Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Polyposis, juvenile intestinal, Myhre dysplasia, Hereditary hemorrhagic telangiectasia||AD||179||143|
|SNAI2||Waardenburg syndrome, Piebaldism||AR||2||4|
|SOX10||Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Kallmann syndrome||AD||56||148|
|TBL1X||Congenital hypothyroidism, Hearing loss||2||8|
|TCOF1||Treacher Collins syndrome||AD||50||330|
|TIMM8A*||Mohr-Tranebjaerg syndrome, Jensen syndrome, Opticoacoustic nerve atrophy with dementia||XL||11||21|
|TSHZ1||Aural atresia, congenital||AD||2||4|
|TUBB4B||Leber congenital amaurosis, Hearing loss||AD||2||3|
|USH1C||Deafness, Usher syndrome, type IC||AR||45||51|
|USH1G||Usher syndrome, type 1G||AR||13||32|
|USH2A||Retinitis pigmentosa 39, Usher syndrome, type 2A||AR||401||1169|
|WFS1||Wolfram syndrome, Wolfram-like syndrome, autosomal dominant, Deafness, autosomal dominant 6/14/38, Cataract 41||AD/AR||69||362|
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.
Some, or all, of the gene is duplicated in the genome. Read more.
The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#). Due to possible limitations these genes may not be available as single gene tests.
Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), 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 Mitomap databases.
Non-coding variants covered by Syndromic Hearing Loss Panel
To view complete table content, scroll horizontally.
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number|
The strengths of this test include:
- CAP accredited laboratory
- 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
- Some of the panels include the whole mitochondrial genome (please see the Panel Content section)
- Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
- ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
- Our rigorous variant classification scheme
- Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
- Our comprehensive clinical statements
Variants in the *KCNE1* gene should not be used for risk assessment at the moment. Specifically, *KCNE1* c.253G>A, p.(Asp85Asn) variant has been considered to be a mild risk factor for acquired long QT syndrome. However, in the newest version of the reference genome GRCh38, a gene KCNE1B, nearly identical to *KCNE1* has appeared. By using standard NGS technologies, as well as Sanger sequencing, it is not possible to get reliable region-specific sequences for these genes. It is likely that reads that have been earlier mapped to *KCNE1* actually belong to *KCNE1B*. Moreover, it is currently unclear whether *KCNE1B* produces a protein product, and if a protein is produced, whether the gene is expressed in heart. More independent data characterizing *KCNE1B* and its function are needed. Currently, all *KCNE1* sequence data and the literature related to *KCNE1* variants should be interpreted with caution. The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: *PDZD7* (NM_024895:10), *POLR1C* (NM_001318876:9). 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
- Some of the panels include the whole mitochondrial genome but not all (please see the Panel Content section)
- 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 in nuclear genes (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- Stretches of mononucleotide repeats
- Low level heteroplasmy in mtDNA (>90% are detected at 5% level)
- Indels larger than 50bp
- Single exon deletions or duplications
- Variants within pseudogene regions/duplicated segments
- Some disease causing variants present in mtDNA are not detectable from blood, thus post-mitotic tissue such as skeletal muscle may be required for establishing molecular diagnosis.
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.
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.
The performance metrics listed below are from an initial validation performed at our main laboratory in Finland. The performance metrics of our laboratory in Marlborough, MA, are equivalent.
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%|
|Microdeletion/-duplication sdrs (large CNVs, n=37))|
|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%|
Performance of Blueprint Genetics Mitochondrial Sequencing Assay.
|Sensitivity %||Specificity %|
|ANALYTIC VALIDATION (NA samples; n=4)|
|Single nucleotide variants|
|Heteroplasmic (45-100%)||100.0% (50/50)||100.0%|
|Heteroplasmic (35-45%)||100.0% (87/87)||100.0%|
|Heteroplasmic (25-35%)||100.0% (73/73)||100.0%|
|Heteroplasmic (15-25%)||100.0% (77/77)||100.0%|
|Heteroplasmic (10-15%)||100.0% (74/74)||100.0%|
|Heteroplasmic (5-10%)||100.0% (3/3)||100.0%|
|Heteroplasmic (<5%)||50.0% (2/4)||100.0%|
|CLINICAL VALIDATION (n=76 samples)|
|Single nucleotide variants n=2026 SNVs|
|Heteroplasmic (45-100%)||100.0% (1940/1940)||100.0%|
|Heteroplasmic (35-45%)||100.0% (4/4)||100.0%|
|Heteroplasmic (25-35%)||100.0% (3/3)||100.0%|
|Heteroplasmic (15-25%)||100.0% (3/3)||100.0%|
|Heteroplasmic (10-15%)||100.0% (9/9)||100.0%|
|Heteroplasmic (5-10%)||92.3% (12/13)||99.98%|
|Heteroplasmic (<5%)||88.9% (48/54)||99.93%|
|Insertions and deletions by sequence analysis n=40 indels|
|Heteroplasmic (45-100%) 1-10bp||100.0% (32/32)||100.0%|
|Heteroplasmic (5-45%) 1-10bp||100.0% (3/3)||100.0%|
|Heteroplasmic (<5%) 1-10bp||100.0% (5/5)||99,997%|
|SIMULATION DATA /(mitomap mutations)|
|Insertions, and deletions 1-24 bps by sequence analysis; n=17|
|Homoplasmic (100%) 1-24bp||100.0% (17/17)||99.98%|
|Heteroplasmic (50%)||100.0% (17/17)||99.99%|
|Heteroplasmic (25%)||100.0% (17/17)||100.0%|
|Heteroplasmic (20%)||100.0% (17/17)||100.0%|
|Heteroplasmic (15%)||100.0% (17/17)||100.0%|
|Heteroplasmic (10%)||94.1% (16/17)||100.0%|
|Heteroplasmic (5%)||94.1% (16/17)||100.0%|
|Copy number variants (separate artifical mutations; n=1500)|
|Homoplasmic (100%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (50%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (30%) 500 bp, 1kb, 5 kb||100.0%||100.0%|
|Heteroplasmic (20%) 500 bp, 1kb, 5 kb||99.7%||100.0%|
|Heteroplasmic (10%) 500 bp, 1kb, 5 kb||99.0%||100.0%|
|The performance presented above reached by following coverage metrics at assay level (n=66)|
|Mean of medians||Median of medians|
|Mean sequencing depth MQ0 (clinical)||18224X||17366X|
|Nucleotides with >1000x MQ0 sequencing coverage (%) (clinical)||100%|
|rho zero cell line (=no mtDNA), mean sequencing depth||12X|
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. If the test includes the mitochondrial genome the target region gene list contains the mitochondrial genes. 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 suboptimal coverage (<20X for nuclear genes and <1000X for mtDNA) 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 cornerstone of clinical interpretation and resulting patient management decisions. Our classifications follow the ACMG guideline 2015.
The final step in the analysis is orthogonal confirmation. Sequence and copy number variants classified as pathogenic, likely pathogenic, and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing or by orthogonal methods such as qPCR/ddPCR when they do not meet our stringent NGS quality metrics for a true positive call.
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 healthcare provider at no additional cost, according to our latest follow-up reporting policy.
- Alford RL et al. American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis ofhearingloss. Genet Med. 2014 Apr;16(4):347-55.
- Alport Syndrome Foundation
- CHARGE Syndrome Foundation
- Casazza G et al. Evaluation and management of syndromic congenital hearing loss. Curr Opin Otolaryngol Head Neck Surg. 2017 Oct;25(5):378-384.
- GeneReviews - Alport Syndrome
- GeneReviews - BOR Syndrome
- GeneReviews - Hereditary Hearing Loss and Deafness Overview
- GeneReviews - Jervell and Lange-Nielsen syndrome
- GeneReviews - Pendred Syndrome
- GeneReviews - Stickler Syndrome
- GeneReviews - Treacher Collins syndrome
- GeneReviews - Usher Syndrome, type I
- GeneReviews - Usher Syndrome, type II
- GeneReviews - Waardenburg Syndrome
- NORD - Alport Syndrome
- NORD - BOR Syndrome
- NORD - CHARGE Syndrome
- NORD - Jervell and Lange-Nielsen Syndrome
- NORD - Norrie Disease
- NORD - Stickler Syndrome
- NORD - Treacher Collins syndrome
- NORD - Usher Syndrome
- NORD - Waardenburg Syndrome
- Norrie Disease Association
- Stickler Syndrome Support Group UK
- Stickler Syndrome Support Group US
- The Cain Foundation for BOR syndrome
- Usher Syndrome Coalition