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Blueprint Genetics Vitreoretinopathy Panel

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Blueprint Genetics Vitreoretinopathy Panel Vitreoretinopathy Panel Test code: OP0701 Is a 24 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion / diagnosis of vitreoretinopathy. The genes on this panel are included in the Retinal Dystropy Panel. About Vitreoretinopathy Vitreoretinal diseases are characterised by the degeneration of the vitreous and retina of the eye. Several types of vitreoretinopathies exist giving rise to a spectrum of phenotypic presentations such as retinal detachment, optically empty vitreous, fibrillary condensation, cataract, and neovascularization. The condition includes familial exudative vitreoretinopathy, snowflake vitreoretinal degeneration, Norrie disease, Wagner syndrome, Stickler syndrome and Knobloch syndrome. The vitreoretinopathies may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. For instance, autosomal dominant familial exudative vitreoretinopathy (FEVR) is caused by mutations in FZD4; LRP5 has been associated with both autosomal dominant and recessive cases and NDP with X-linked FEVR. The clinical presentation and the disease course can be highly variable. The prevalence of FEVR is unknown, but it is a rare disorder. Availability 4 weeks Gene Set Description Genes in the Vitreoretinopathy Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ATOH7 Persistent hyperplastic primary vitreous, autosomal recessive AR 4 9 BEST1 Vitreoretinochoroidopathy, Microcornea, Rod-cone dystrophy, Posterior AD/AR 62 318 staphyloma, Bestrophinopathy, Vitelliform macular dystrophy, Cataract, Retinitis pigmentosa, Macular dystrophy, vitelliform, adult-onset, Retinitis pigmentosa 50, Macular dystrophy, vitelliform 2, Best macular dystrophy, Bestrophinopathy, autosomal recessive CAPN5 Vitreoretinopathy, neovascular inflammatory AD 3 12 COL11A1 Marshall syndrome, Fibrochondrogenesis, Stickler syndrome type 2 AD/AR 34 94 COL11A2 Weissenbacher-Zweymuller syndrome, Deafness, AD/AR 29 57 Otospondylomegaepiphyseal dysplasia, Fibrochondrogenesis, Stickler syndrome type 3 (non-ocular) COL18A1 Knobloch syndrome AR 27 31 COL2A1 Avascular necrosis of femoral head, Rhegmatogenous retinal AD 180 561 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 https://blueprintgenetics.com/ COL9A1 Stickler syndrome recessive type, Multiple epiphyseal dysplasia type 6 AD/AR 9 6 (EDM6) COL9A2 Stickler syndrome, Multiple epiphyseal dysplasia type 2 (EDM2) AD/AR 7 12 COL9A3 Multiple epihyseal dysplasia type 3 (EDM3), Stickler syndrome recessive AD/AR 10 14 type CTC1 Cerebroretinal microangiopathy with calcifications and cysts AR 21 33 CTNNB1 Exudative vitreoretinopathy 7, Mental retardation, autosomal dominant AD 90 51 19 FZD4 Retinopathy of prematurity, Exudative vitreoretinopathy AD/Digenic 14 90 KCNJ13 Snowflake vitreoretinal degeneration, Leber congenital amaurosis AD/AR 6 10 KIF11 Microcephaly AD 39 69 LRP5* Van Buchem disease, Osteoporosis-pseudoglioma syndrome, AD/AR/Digenic 57 196 Hyperostosis, endosteal, Osteosclerosis, Exudative vitreoretinopathy, Osteopetrosis late-onset form type 1, LRP5 primary osteoporosis NDP Exudative vitreoretinopathy, Norrie disease XL 31 167 NR2E3 Retinitis pigmentosa, Enhanced S-cone syndrome AD/AR 19 77 P3H2 Myopia, high, with cataract and vitreoretinal degeneration AR 7 7 RCBTB1 Retinal dystrophy with or without extraocular anomalies (RDEOA), AR 6 9 Familial exudative vitreoretinopathy RS1 Retinoschisis XL 44 262 TSPAN12 Exudative vitreoretinopathy, Retinal dysplasia and severe familial AD/AR 16 51 exudative vitreoretinopathy VCAN Wagner disease AD 11 19 ZNF408 Exudative vitreoretinopathy 6, Retinitis pigmentosa 72 AD/AR 3 9 *Some regions of the gene are 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 (#). 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 disease causing variants covered by the panel Gene Genomic location HG19 HGVS RefSeq RS-number https://blueprintgenetics.com/ BEST1 Chr11:61717900 c.-29+1G>T NM_001139443.1 BEST1 Chr11:61717904 c.-29+5G>A NM_001139443.1 COL11A1 Chr1:103386637 c.3744+437T>G NM_080629.2 COL11A1 Chr1:103488576 c.1027-24A>G NM_080629.2 COL11A1 Chr1:103491958 c.781-450T>G NM_080629.2 rs587782990 COL2A1 Chr12:48379984 c.1527+135G>A NM_001844.4 NDP ChrX:43818099 c.-207-1G>A NM_000266.3 NDP ChrX:43832545 c.-208+5G>A NM_000266.3 NDP ChrX:43832548 c.-208+2T>G NM_000266.3 NDP ChrX:43832549 c.-208+1G>A NM_000266.3 NDP ChrX:43832685 c.-343A>G NM_000266.3 rs895911086 NDP ChrX:43832722 c.-391_-380delCTCTCTCTCCCTinsGTCTCTC NM_000266.3 NDP ChrX:43832724 c.-396_-383delTCCCTCTCTCTCTC NM_000266.3 rs770996360 Test Strengths 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 Our publicly available analytic validation demonstrating complete details of test performance ~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 Test Limitations 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 d etect the following: Complex inversions Gene conversions Balanced translocations Some of the panels include the whole mitochondrial genome (please see the Panel Content section) https://blueprintgenetics.com/ 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 and see our Analytic Validation. Test Performance 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
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