Retinitis Pigmentosa Panel

  • bpg-method PLUS
  • bpg-method SEQ
  • bpg-method DEL/DUP

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. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more: http://blueprintgenetics.com/faqs/#prenatal

Genes in the Retinitis Pigmentosa Panel and their clinical significance
Gene Associated phenotypes Inheritance ClinVar HGMD
ABCA4 Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Retinal dystrophy, early-onset severe, Fundus flavimaculatus AR 203 1012
ABHD12 Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract AR 10 15
AIPL1 Retinitis pigmentosa, Cone rod dystrophy, Leber congenital amaurosis AD/AR 8 73
ARL6 Bardet-Biedl syndrome, Retinitis pigmentosa AR 9 21
BBS1 Bardet-Biedl syndrome AR 19 92
BBS2 Bardet-Biedl syndrome, Retinitis pigmentosa AR 30 84
BEST1 Vitreoretinochoroidopathy, Microcornea, Rod-cone dystrophy, Posterior staphyloma, Bestrophinopathy, Vitelliform macular dystrophy, Cataract, Retinitis pigmentosa AD/AR 31 269
C2ORF71 Retinitis pigmentosa AR 11
C8ORF37 Retinitis pigmentosa, Cone rod dystrophy AR 4
CDHR1 Retinitis pigmentosa, Cone rod dystrophy AR 9 33
CEP290* Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndrome AR 79 252
CERKL Retinitis pigmentosa AR 10 26
CHM Choiroideremia XL 26 268
CLN3 Ceroid lipofuscinosis, neuronal AR 69 64
CLRN1 Retinitis pigmentosa, Usher syndrome AR 14 32
CNGA1 Retinitis pigmentosa AR 10 27
CNGB1 Retinitis pigmentosa AR 12 33
CRB1 Retinitis pigmentosa, Pigmented paravenous chorioretinal atrophy, Leber congenital amaurosis AD/AR 31 291
CRX Cone rod dystrophy, Leber congenital amaurosis AD/AR 22 87
CYP4V2 Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophy AR 30 75
DHDDS Retinitis pigmentosa AR 1 3
EYS* Retitinis pigmentosa AR 44 234
FAM161A Retitinis pigmentosa AR 7 14
FLVCR1 Ataxia, posterior column, with retinitis pigmentosa AR 4 12
GNPTG Mucolipidosis AR 22 42
GUCY2D Cone rod dystrophy, Leber congenital amaurosis AD/AR 18 214
HK1 Hemolytic anemia, nonspherocytic, due to hexokinase deficiency AD/AR 5 8
IDH3B Retinitis pigmentosa AR 2 2
IMPDH1 Retinitis pigmentosa, Leber congenital amaurosis AD 6 20
IMPG2 Retinitis pigmentosa, Vitelliform macular dystrophy AD/AR 16 23
KLHL7 Retinitis pigmentosa AD 7 7
LCA5 Leber congenital amaurosis AR 7 45
LRAT Retinitis pigmentosa, juvenile, Leber congenital amaurosis, Retinitis punctata albescens, Retinal-dystrophy, early-onset severe AR 7 18
MAK Retinitis pigmentosa AR 9 13
MERTK Retinitis pigmentosa AR 18 59
MVK Mevalonic aciduria, Hyper-IgD syndrome AR 27 168
NMNAT1 Leber congenital amaurosis AR 11 64
NR2E3 Retinitis pigmentosa, Enhanced S-cone syndrome AD/AR 12 74
NRL Retinitis pigmentosa, Clumped pigmentary retinal degeneration AD/AR 7 21
OAT Gyrate atrophy of choroid and retina AR 62 69
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 129 148
PANK2 Hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration, Neurodegeneration with brain iron accumulation AD/AR 17 148
PDE6A Retinitis pigmentosa AR 7 40
PDE6B Retinitis pigmentosa, Night blindness, congenital stationary AD/AR 19 100
PDE6G Retinitis pigmentosa AR 1 2
PEX1 Heimler syndrome AR 34 121
PEX2 Zellweger syndrome, Peroxisome biogenesis disorder AR 8 18
PEX7 Refsum disease, Rhizomelic CDP type 1 AR 17 51
PHYH Refsum disease AR 9 36
PRCD Retinitis pigmentosa AR 3 6
PROM1 Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Macular dystrophy, retinal, AD/AR 10 58
PRPF3 Retinitis pigmentosa AD 3 4
PRPF8 Retinitis pigmentosa AD 9 33
PRPF31 Retinitis pigmentosa AD 21 122
PRPH2 Choriodal dystrophy, central areolar, Macular dystrophy, vitelliform, Retinitis pigmentosa, Retinitis punctata albescens, Macula dystrophy, patterned AD/Digenic 28 157
RBP3 Retinitis pigmentosa AR 3 11
RDH5 Fundus albipunctatus AR 11 50
RDH12 Retinitis pigmentosa, Leber congenital amaurosis AD/AR 20 95
RGR Retinitis pigmentosa AD/AR 1 8
RHO Retinitis pigmentosa, Night blindness, congenital stationary, Retinitis punctata albescens AD/AR 50 197
RLBP1 Newfoundland rod-cone dystrophy, Fundus albipunctatus, Bothnia retinal dystrophy, Retinitis punctata albescens AR 7 33
RP1 Retinitis pigmentosa AD/AR 21 149
RP2 Retinitis pigmentosa XL 14 104
RPE65 Retinitis pigmentosa, Leber congenital amaurosis AR 16 170
RPGR Retinitis pigmentosa XL 41 184
RPGRIP1 Cone rod dystrophy, Leber congenital amaurosis AR 23 117
RS1 Retinoschisis XL 24 235
SAG Retinitis pigmentosa, Oguchi disease AR 5 14
SEMA4A Retinitis pigmentosa, Cone rod dystrophy AR 2 13
SNRNP200 Retinitis pigmentosa AD 6 23
SPATA7 Leber congenital amaurosis, Retitinitis pigmentosa AR 10 29
TOPORS Retitinis pigmentosa AD 4 16
TTC8 Bardet-Biedl syndrome, Retinitis pigmentosa AR 5 16
TTPA Ataxia with isolated vitamin E deficiency AR 19 28
TULP1 Retinitis pigmentosa, Leber congenital amaurosis AR 19 66
USH1C Deafness, Usher syndrome AR 13 45
USH2A Usher syndrome, Retinitis pigmentosa AR 147 924
VPS13B Cohen syndrome AR 128 184
WDR19 Retinitis pigmentosa, Nephronophthisis, Short -rib thoracic dysplasia with or without polydactyly, Senior-Loken syndrome, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 1, Cranioectodermal dysplasia (Levin-Sensenbrenner) type 2, Asphyxiating thoracic dysplasia (ATD; Jeune) AD/AR 16 25
ZNF513 Retinitis pigmentosa AR 1 1

*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.

Gene Genomic location HG19 HGVS RefSeq RS-number Comment Reference
ABCA4 Chr1:94576926 c.302+68C>T NM_000350.2 rs761188244
ABCA4 Chr1:94493073 c.4539+1928C>T NM_000350.2
ABCA4 Chr1:94493000 c.4539+2001G>A NM_000350.2
ABCA4 Chr1:94492973 c.4539+2028C>T NM_000350.2 rs869320785
ABCA4 Chr1:94484082 c.5196+1056A>G NM_000350.2
ABCA4 Chr1:94484001 c.5196+1137G>A NM_000350.2 rs778234759
ABCA4 Chr1:94484001 c.5196+1137G>T NM_000350.2
CEP290 Chr12:88494960 c.2991+1655A>G NM_025114.3 rs281865192
GNPTG Chr16:1412562 c.610-16_609+28del NM_032520.4 rs193302853
HK1 Chr10:71038467 c.-390-3818G>C NM_033500.2 rs397514654
HK1 Chr10:71038447 c.-390-3838G>C NM_033500.2 rs797044964
NMNAT1 Chr1:10003561 c.-69C>T NM_022787.3
NMNAT1 Chr1:10003560 c.-70A>T NM_022787.3
OFD1 ChrX:13773245 c.1130-22_1130-19delAATT NM_003611.2 rs312262865
OFD1 ChrX:13768358 c.935+706A>G NM_003611.2 rs730880283
PEX7 Chr6:137143759 c.-45C>T NM_000288.3 rs267608252
PROM1 Chr4:15989860 c.2077-521A>G NM_006017.2 rs796051882
PRPF31 Chr19:54633399 c.1374+654C>G NM_015629.3
USH2A Chr1:216247476 c.5573-834A>G NM_206933.2
USH2A Chr1:216064540 c.7595-2144A>G NM_206933.2 rs786200928
USH2A Chr1:216039721 c.8845+628C>T NM_206933.2

The strengths of this test include:

  • Blueprint Genetics is one of the few laboratories worldwide with CAP and ISO-15189 accreditation for NGS panels and CLIA certification
  • Superior sequencing quality
  • Careful selection of genes based on current literature, our experience and the most current mutation databases
  • Transparent and easy access to quality and performance data at the patient level that are accessible via our Nucleus portal
  • Transparent and reproducible analytical validation for each panel (see Test performance section; for complete details, see our Analytic Validation)
  • Sequencing and high resolution del/dup analysis available in one test
  • Inclusion of non-coding disease causing variants where clinically indicated (please see individual Panel descriptions)
  • Interpretation of variants following ACMG variant classification guidelines
  • Comprehensive clinical statement co-written by a PhD geneticist and a clinician specialist

 

This test does not detect the following:

  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Variants in regulatory or non-coding regions of the gene unless otherwise indicated (please see Non-coding disease causing variants covered by the panel). This mean for instance intronic variants locating deeper than 15 nucleotides from the exon-intron boundary.

 

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
  • Disorders caused by long repetitive sequences (e.g. trinucleotide repeat expansions)

 

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.

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.

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. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. 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.

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

SEQ 81434
DEL/DUP 81479


ICD codes

Commonly used ICD-10 codes when ordering the Retinitis Pigmentosa Panel

ICD-10 Disease
H35.50 Retinitis 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.

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