Cone Rod Dystrophy Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: OP0401

The Blueprint Genetics Cone Rod Dystrophy Panel is a 32 gene test for genetic diagnostics of patients with clinical suspicion of cone rod dystrophy.

The panel covers genes associated with autosomal recessive, autosomal dominant and X-linked forms of cone rod dystrophy. This panel is included in the Retinal Dystrophy Panel.

About Cone Rod Dystrophy

Cone rod dystrophies (CRD) are inherited retinal dystrophies characterized by cone dysfunction followed by rod photoreceptor degeneration. Fundus examination shows pigment deposits and retinal atrophy in the macular region of the retina. In contrast to typical retinitis pigmentosa (RP, rod cone dystrophy) resulting from the primary loss in rod photoreceptors and later followed by the secondary loss in cone photoreceptors, CRDs reflect the opposite sequence of events. Predominant symptoms of CRDs are decreased visual acuity, color vision defects, photoaversion and decreased sensitivity in the central visual field, later followed by progressive loss in peripheral vision and night blindness. The clinical course of CRDs is generally more severe and rapid than that of RP, leading to earlier legal blindness and disability. CRDs are most frequently nonsyndromic, but they may also be part of several syndromes, such as Bardet-Biedl syndrome. Nonsyndromic CRDs can be inherited in an autosomal dominant, autosomal recessive or X-linked manner. The two major causative genes involved in the pathogenesis of CRDs are ABCA4 (autosomal recessive CRD, also implicated in Stargardt disease) and GUCY2D (autosomal dominant CRD). The prevalence of CRDs is estimated at 1:40,000.

Availability

Results in 3-4 weeks.

Genes in the Cone Rod Dystrophy Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ABCA4Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Retinal dystrophy, early-onset severe, Fundus flavimaculatusAR2031012
ADAM9Cone rod dystrophyAR59
AIPL1Retinitis pigmentosa, Cone rod dystrophy, Leber congenital amaurosisAD/AR873
BEST1Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma, VitreoretinochoroidopathyAD/AR31269
C8ORF37Retinitis pigmentosa, Cone rod dystrophyAR4
CABP4Night blindness, congenital stationaryAR410
CACNA1FAland Island eye disease, Cone rod dystrophy, Night blindness, congenital stationaryXL18142
CACNA2D4Retinal cone dystrophyAR19
CDHR1Retinitis pigmentosa, Cone rod dystrophyAR933
CERKLRetinitis pigmentosaAR1026
CLN3Ceroid lipofuscinosis, neuronalAR6964
CNGA3Leber congenital amaurosis, AchromatopsiaAR16141
CNGB3Macular degeneration, juvenile, AchromatopsiaAR1463
CNNM4Jalili syndromeAR918
CRB1Retinitis pigmentosa, Pigmented paravenous chorioretinal atrophy, Leber congenital amaurosisAD/AR31291
CRXCone rod dystrophy, Leber congenital amaurosisAD/AR2287
CYP4V2Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophyAR3075
FBLN5Cutis laxa, Macular degeneration, age-relatedAD/AR1321
GNAT2AchromatopsiaAR411
GUCA1ACone dystrophy 3/Cone rod dystrophyAD516
GUCY2DCone rod dystrophy, Leber congenital amaurosisAD/AR18214
KCNV2Retinal cone dystrophyAR1387
MERTKRetinitis pigmentosaAR1859
PDE6CCone dystrophyAR1833
PDE6HRetinal cone dystrophy, AchromatopsiaAD/AR22
PROM1Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Macular dystrophy, retinal,AD/AR1058
PRPH2Choriodal dystrophy, central areolar, Macular dystrophy, vitelliform, Retinitis pigmentosa, Retinitis punctata albescens, Macula dystrophy, patternedAD/Digenic28157
RAX2Cone rod dystrophyAD54
RDH5Fundus albipunctatusAR1150
RPGRRetinitis pigmentosaXL41184
RPGRIP1Cone rod dystrophy, Leber congenital amaurosisAR23117
SEMA4ARetinitis pigmentosa, Cone rod dystrophyAR213

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.

Blueprint Genetics offers a comprehensive cone rod dystrophy panel that covers classical genes associated with cone rod dystrophy, Jalili syndrome and Stargardt disease. 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.

Please see our latest validation report showing sensitivity and specificity for SNPs and indels, sequencing depth, % of the nucleotides reached at least 15x coverage etc. If the Panel is not present in the report, data will be published when the Panel becomes available for ordering. 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. All the Panels available for ordering have sensitivity and specificity higher than > 0.99 to detect single nucleotide polymorphisms and a high sensitivity for indels ranging 1-19 bp. 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. Detection limit for Del/Dup analysis varies through the genome from one to six exon Del/Dups depending on exon size, sequencing coverage and sequence content.

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.

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ICD & CPT codes

CPT codes

SEQ81434
DEL/DUP81479


ICD codes

Commonly used ICD-10 codes when ordering the Cone Rod Dystrophy Panel

ICD-10Disease
H35.50Cone rod dystrophy

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.