Retinitis Pigmentosa 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: OP0901

The Blueprint Genetics Retinitis Pigmentosa Panel is an 80 gene test for genetic diagnostics of patients with clinical suspicion of retinitis pigmentosa.

The panel covers genes associated with autosomal recessive, autosomal dominant and X-linked forms of retinitis pigmentosa (RP). Clinical utility of this panel is estimated to be 57% for patients with autosomal recessive or dominant RP and 85% for patients with X-linked RP. Differential diagnosis includes choroideremia, gyrate atrophy of choroid and retina and X-linked retinoschisis. For patients with syndromic RP, we recommend to choose Retinal Dystrophy Panel.

About Retinitis Pigmentosa

Retinitis pigmentosa (RP) is a group of inherited disorders in which abnormalities of the photoreceptors (rods and cones) or the retinal pigment epithelium lead to progressive visual loss. RP can be classified as nonsyndromic or syndromic. Nonsyndromic RP is extremely heterogeneous, both clinically and genetically, and it may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. Autosomal dominant RP is estimated to account for 15-25% of cases, autosomal recessive 5-20% and X-linked 5-15% (GeneReviews). Sporadic cases are common (40-50%). Severity is partly correlated with the pattern of inheritance with X-linked cases having the most severe course. The major causative genes are RHO, accounting for approximately 28% of autosomal dominant RP and RPGR, which is estimated to explain 70% of X-linked RP. Prevalence of RP is reported to be 1:4,000 to 1:5,000. The major forms of syndromic RP are Usher syndrome and Bardet-Biedl syndrome.

Availability

Results in 3-4 weeks.

Genes in the Retinitis Pigmentosa Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ABCA4Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Retinal dystrophy, early-onset severe, Fundus flavimaculatusAR2031012
ABHD12Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataractAR1015
AIPL1Retinitis pigmentosa, Cone rod dystrophy, Leber congenital amaurosisAD/AR873
ARL6Bardet-Biedl syndrome, Retinitis pigmentosaAR921
BBS1Bardet-Biedl syndromeAR1992
BBS2Bardet-Biedl syndrome, Retinitis pigmentosaAR3084
BEST1Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma, VitreoretinochoroidopathyAD/AR31269
C2ORF71Retinitis pigmentosaAR11
C8ORF37Retinitis pigmentosa, Cone rod dystrophyAR4
CDHR1Retinitis pigmentosa, Cone rod dystrophyAR933
CEP290*Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndromeAR79252
CERKLRetinitis pigmentosaAR1026
CHMChoiroideremiaXL26268
CLN3Ceroid lipofuscinosis, neuronalAR6964
CLRN1Retinitis pigmentosa, Usher syndromeAR1432
CNGA1Retinitis pigmentosaAR1027
CNGB1Retinitis pigmentosaAR1233
CRB1Retinitis pigmentosa, Pigmented paravenous chorioretinal atrophy, Leber congenital amaurosisAD/AR31291
CRXCone rod dystrophy, Leber congenital amaurosisAD/AR2287
CYP4V2Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophyAR3075
DHDDSRetinitis pigmentosaAR13
EYS*Retitinis pigmentosaAR44234
FAM161ARetitinis pigmentosaAR714
FLVCR1Ataxia, posterior column, with retinitis pigmentosaAR412
GNPTGMucolipidosisAR2242
GUCY2DCone rod dystrophy, Leber congenital amaurosisAD/AR18214
HK1Hemolytic anemia, nonspherocytic, due to hexokinase deficiencyAR58
IDH3BRetinitis pigmentosaAR22
IMPDH1Retinitis pigmentosa, Leber congenital amaurosisAD620
IMPG2Retinitis pigmentosaAR1623
KLHL7Retinitis pigmentosaAD77
LCA5Leber congenital amaurosisAR745
LRATRetinitis pigmentosa, juvenile, Leber congenital amaurosis, Retinitis punctata albescens, Retinal-dystrophy, early-onset severeAR718
MAKRetinitis pigmentosaAR913
MERTKRetinitis pigmentosaAR1859
MVKMevalonic aciduria, Hyper-IgD syndromeAR27168
NMNAT1Leber congenital amaurosisAR1164
NR2E3Retinitis pigmentosa, Enhanced S-cone syndromeAD/AR1274
NRLRetinitis pigmentosa, Clumped pigmentary retinal degenerationAD/AR721
OATGyrate atrophy of choroid and retinaAR6269
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL129148
PANK2Hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration, Neurodegeneration with brain iron accumulationAD/AR17148
PDE6ARetinitis pigmentosaAR740
PDE6BRetinitis pigmentosa, Night blindness, congenital stationaryAD/AR19100
PDE6GRetinitis pigmentosaAR12
PEX1Heimler syndromeAR34121
PEX2Zellweger syndrome, Peroxisome biogenesis disorderAR818
PEX7Refsum diseaseAR1751
PHYHRefsum diseaseAR936
PRCDRetinitis pigmentosaAR36
PROM1Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Macular dystrophy, retinal,AD/AR1058
PRPF3Retinitis pigmentosaAD34
PRPF8Retinitis pigmentosaAD933
PRPF31Retinitis pigmentosaAD21122
PRPH2Choriodal dystrophy, central areolar, Macular dystrophy, vitelliform, Retinitis pigmentosa, Retinitis punctata albescens, Macula dystrophy, patternedAD/Digenic28157
RBP3Retinitis pigmentosaAR311
RDH5Fundus albipunctatusAR1150
RDH12Retinitis pigmentosa, Leber congenital amaurosisAD/AR2095
RGRRetinitis pigmentosaAD/AR18
RHORetinitis pigmentosa, Night blindness, congenital stationary, Retinitis punctata albescensAD/AR50197
RLBP1Newfoundland rod-cone dystrophy, Fundus albipunctatus, Bothnia retinal dystrophy, Retinitis punctata albescensAR733
RP1Retinitis pigmentosaAD/AR21149
RP2Retinitis pigmentosaXL14104
RPE65Retinitis pigmentosa, Leber congenital amaurosisAR16170
RPGRRetinitis pigmentosaXL41184
RPGRIP1Cone rod dystrophy, Leber congenital amaurosisAR23117
RS1RetinoschisisXL24235
SAGRetinitis pigmentosa, Oguchi diseaseAR514
SEMA4ARetinitis pigmentosa, Cone rod dystrophyAR213
SNRNP200Retinitis pigmentosaAD623
SPATA7Leber congenital amaurosis, Retitinitis pigmentosaAR1029
TOPORSRetitinis pigmentosaAD416
TTC8Bardet-Biedl syndrome, Retinitis pigmentosaAR516
TTPAAtaxia with isolated vitamin E deficiencyAR1928
TULP1Retinitis pigmentosa, Leber congenital amaurosisAR1966
USH1CDeafness, Usher syndromeAR1345
USH2AUsher syndromeAR147924
VPS13BCohen syndromeAR128184
WDR19Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndromeAD/AR1625
ZNF513Retinitis pigmentosaAR11
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

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 retinitis pigmentosa panel that covers classical genes associated with choroideremia, gyrate atrophy of choroid and retina, retinitis pigmentosa, Stargardt disease and x-linked retinoschisis. 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 Retinitis Pigmentosa Panel

ICD-10Disease
H35.50Retinitis pigmentosa

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.