Retinitis Pigmentosa Panel

Last modified: Mar 21, 2018


  • Is a 110 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion /diagnosis of isolated retinitis pigmentosa. The genes included on this panel are included in the Retinal Dystrophy Panel.

    For patients with syndromic retinitis pigmentosa, we recommend the Retinal Dystrophy Panel.

Analysis methods

  • PLUS
  • SEQ


3-4 weeks

Number of genes


Test code


CPT codes

SEQ 81434
DEL/DUP 81479


The Blueprint Genetics Retinitis Pigmentosa Panel (test code OP0901):

  • Is a 110 gene panel that includes assessment of selected non-coding disease-causing variants
  • Includes analysis of the MAK Alu insertion. The majority of the X-linked RP is caused by mutations in theRPGR gene, which contains a mutational hotspot at a unique 567-aa exon called ORF15 accounting for two-thirds of all disease-causing mutations. The exon ORF15, however, includes a highly repetitive, purine-rich sequence, which generally performs poorly in NGS-based assays. Blueprint Genetics custom assay has good coverage (>20x) with high mapping rates (mapping quality >20) for 100.0% of the target regions in RPGR gene. Our validation showed high mean coverage of 139X for the RPGR gene. Thus, our NGS Panel is not expected to have major limitations in detecting variants in RPGR gene including ORF15 exon.

  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

Test Specific Strength

Includes analysis of the MAK Alu insertion. The majority of the X-linked RP is caused by mutations in theRPGR gene, which contains a mutational hotspot at a unique 567-aa exon called ORF15 accounting for two-thirds of all disease-causing mutations. The exon ORF15, however, includes a highly repetitive, purine-rich sequence, which generally performs poorly in NGS-based assays. Blueprint Genetics custom assay has good coverage (>20x) with high mapping rates (mapping quality >20) for 100.0% of the target regions in RPGR gene. Our validation showed high mean coverage of 139X for the RPGR gene. Thus, our NGS Panel is not expected to have major limitations in detecting variants in RPGR gene including ORF15 exon.

ICD codes

Commonly used ICD-10 code(s) when ordering the Retinitis Pigmentosa Panel

ICD-10 Disease
H35.50 Retinitis pigmentosa

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • 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.

Please include fundus photographs, electroretinogram (ERG) findings, visual field findings and visual acuity, if available, for expert review and clinical correlation with test results

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 isolated 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 RP for 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 USH2A, which is implicated in autosomal recessive RP, RHO, accounting for approximately 28% of autosomal dominant RP and RPGR, which is estimated to explain 70% of X-linked RP. The prevalence of RP is reported to be 1:4,000 to 1:5,000.

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 294 1105
ABHD12 Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract AR 12 18
ADIPOR1* Complement system AD/AR 4
AGBL5 Retinitis pigmentosa 75 2 9
AHI1 Joubert syndrome AR 53 84
AIPL1 Retinitis pigmentosa, Cone rod dystrophy, Leber congenital amaurosis AD/AR 8 73
ARHGEF18 Retinitis pigmentosa 78 5 5
ARL2BP Retinitis pigmentosa with or without situs inversus AR 3 4
ARL6 Bardet-Biedl syndrome, Retinitis pigmentosa AR 13 21
BBS1 Bardet-Biedl syndrome AR 48 100
BBS2 Bardet-Biedl syndrome, Retinitis pigmentosa AR 32 90
BEST1 Vitreoretinochoroidopathy, Microcornea, Rod-cone dystrophy, Posterior staphyloma, Bestrophinopathy, Vitelliform macular dystrophy, Cataract, Retinitis pigmentosa AD/AR 50 275
C1QTNF5 Late-onset retinal degeneration AD 18 4
C2ORF71 Retinitis pigmentosa AR 13 41
C8ORF37 Retinitis pigmentosa, Cone rod dystrophy AR 8 15
C21ORF2 Retinal dystrophy with or without macular staphyloma (RDMS), Spondylometaphyseal dysplasia, axial (SMDAX) 12 19
CA4 Retinitis pigmentosa 17 AD 3 8
CDHR1 Retinitis pigmentosa, Cone rod dystrophy AR 12 36
CEP290* Bardet-Biedl syndrome, Leber congenital amaurosis, Joubert syndrome, Senior-Loken syndrome, Meckel syndrome AR 96 266
CERKL Retinitis pigmentosa AR 16 33
CHM Choiroideremia XL 38 276
CLN3 Neuronal ceroid lipofuscinosis, type 3 AR 85 70
CLRN1 Retinitis pigmentosa, Usher syndrome AR 17 34
CNGA1 Retinitis pigmentosa AR 13 30
CNGB1 Retinitis pigmentosa AR 24 49
CRB1 Retinitis pigmentosa, Pigmented paravenous chorioretinal atrophy, Leber congenital amaurosis AD/AR 47 308
CRX Cone rod dystrophy, Leber congenital amaurosis AD/AR 28 93
CTNNA1 Macular dystrophy, patterned 2 AD 6 8
CWC27 Retinitis pigmentosa with or without skeletal anomalies (RPSKA) 5 7
CYP4V2 Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophy AR 31 88
DHDDS Retinitis pigmentosa AR 1 5
DHX38 Retinitis pigmentosa AR 1
EYS* Retitinis pigmentosa AR 72 277
FAM161A Retitinis pigmentosa AR 10 18
FLVCR1 Ataxia, posterior column, with retinitis pigmentosa AR 6 15
GNPTG Mucolipidosis AR 26 42
GUCY2D Cone rod dystrophy, Leber congenital amaurosis AD/AR 25 217
HGSNAT Mucopolysaccharidosis (Sanfilippo syndrome), Retinitis pigmentosa AR 24 68
HK1 Hemolytic anemia, nonspherocytic, due to hexokinase deficiency AD/AR 9 7
IDH3B Retinitis pigmentosa AR 2 2
IFT140 Short -rib thoracic dysplasia with or without polydactyly, Asphyxiating thoracic dysplasia (ATD; Jeune) AR 19 52
IMPDH1 Retinitis pigmentosa, Leber congenital amaurosis AD 7 19
IMPG2 Retinitis pigmentosa, Vitelliform macular dystrophy AD/AR 21 38
INPP5E Joubert syndrome, Mental retardation, truncal obesity, retinal dystrophy, and micropenis (MORM syndrome) AR 23 44
KIZ Retinitis pigmentosa 69 AR 3 3
KLHL7 Retinitis pigmentosa AD 9 9
LCA5 Leber congenital amaurosis AR 10 46
LRAT Retinitis pigmentosa, juvenile, Leber congenital amaurosis, Retinitis punctata albescens, Retinal-dystrophy, early-onset severe AR 7 20
MAK Retinitis pigmentosa AR 10 17
MERTK Retinitis pigmentosa AR 23 68
MFRP Microphthalmia, isolated 5, Nanophthalmos 2, Retinitis pigmentosa, autosomal recessive AR 18 29
MVK Mevalonic aciduria, Hyper-IgD syndrome AR 29 173
NEK2 Retinitis pigmentosa 67 AR 1 1
NMNAT1 Leber congenital amaurosis AR 16 69
NR2E3 Retinitis pigmentosa, Enhanced S-cone syndrome AD/AR 17 74
NRL Retinitis pigmentosa, Clumped pigmentary retinal degeneration AD/AR 7 24
OAT Gyrate atrophy of choroid and retina AR 63 70
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 133 156
PDE6A Retinitis pigmentosa AR 14 40
PDE6B Retinitis pigmentosa, Night blindness, congenital stationary AD/AR 26 117
PDE6G Retinitis pigmentosa AR 1 2
PEX1 Heimler syndrome AR 77 130
PEX2 Zellweger syndrome, Peroxisome biogenesis disorder AR 9 18
PEX7 Refsum disease, Rhizomelic CDP type 1 AR 36 52
PHYH Refsum disease AR 10 36
PITPNM3 Cone-rod dystrophy 5 AD 4
PLA2G5 Fleck retina, familial benign AR 1 7
PRCD Retinitis pigmentosa AR 3 7
PRKCG Spinocerebellar ataxia AD/AR 29 40
PROM1# Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Macular dystrophy, retinal, AD/AR 19 69
PRPF3 Retinitis pigmentosa AD 3 7
PRPF4 Retinitis pigmentosa 70 AD 2 4
PRPF6 Retinitis pigmentosa 60 AD 4 7
PRPF8 Retinitis pigmentosa AD 12 35
PRPF31 Retinitis pigmentosa AD 32 142
PRPH2 Choriodal dystrophy, central areolar, Macular dystrophy, vitelliform, Retinitis pigmentosa, Retinitis punctata albescens, Macula dystrophy, patterned AD/Digenic 42 160
RBP3 Retinitis pigmentosa AR 5 16
RBP4 Retinol dystrophy, iris coloboma, and comedogenic acne syndrome AR 6 6
RDH5 Fundus albipunctatus AR 11 50
RDH12 Retinitis pigmentosa, Leber congenital amaurosis AD/AR 21 99
REEP6 Retinitis pigmentosa 77 4 6
RGR Retinitis pigmentosa AD/AR 2 10
RHO Retinitis pigmentosa, Night blindness, congenital stationary, Retinitis punctata albescens AD/AR 56 203
RIMS1 Cone-rod dystrophy 7 AD 3 8
RLBP1 Newfoundland rod-cone dystrophy, Fundus albipunctatus, Bothnia retinal dystrophy, Retinitis punctata albescens AR 8 35
ROM1 Retinitis pigmentosa 7, digenic Digenic 3 15
RP1 Retinitis pigmentosa AD/AR 38 171
RP2 Retinitis pigmentosa XL 20 108
RPE65 Retinitis pigmentosa, Leber congenital amaurosis AR 23 181
RPGR Retinitis pigmentosa XL 62 202
RPGRIP1 Cone rod dystrophy, Leber congenital amaurosis AR 33 127
RS1 Retinoschisis XL 38 244
SAG Retinitis pigmentosa, Oguchi disease AR 6 15
SAMD11 Retinitis pigmentosa AR 2 5
SEMA4A Retinitis pigmentosa, Cone rod dystrophy AR 4 12
SLC7A14 Retinitis pigmentosa 68 AR 4 8
SNRNP200 Retinitis pigmentosa AD 6 27
SPATA7 Leber congenital amaurosis, Retitinitis pigmentosa AR 10 29
SPP2 Retinitis pigmentosa AD 1 2
TOPORS Retitinis pigmentosa AD 6 19
TTC8 Bardet-Biedl syndrome, Retinitis pigmentosa AR 5 16
TTPA Ataxia with isolated vitamin E deficiency AR 26 28
TUB Retinal dystrophy and obesity AR 1 1
TULP1 Retinitis pigmentosa, Leber congenital amaurosis AR 22 69
USH1C Deafness, Usher syndrome AR 18 48
USH2A Usher syndrome, Retinitis pigmentosa, Retinitis pigmentosa 39 AR 225 1001
VPS13B Cohen syndrome AR 231 197
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 20 28
ZNF408 Exudative vitreoretinopathy 6, Retinitis pigmentosa 72 AD/AR 3 8
ZNF513 Retinitis pigmentosa AR 1 1

* Some, or all, of the gene is 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).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), 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 Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ABCA4 Chr1:94526934 c.1938-619A>G NM_000350.2
ABCA4 Chr1:94525509 c.2160+584A>G NM_000350.2
ABCA4 Chr1:94576926 c.302+68C>T NM_000350.2 rs761188244
ABCA4 Chr1:94509799 c.3050+370C>T NM_000350.2
ABCA4 Chr1:94493272 c.4539+1729G>T NM_000350.2
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 Chr1:94492937 c.4539+2064C>T NM_000350.2
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
ABCA4 Chr1:94566773 c.570+1798A>G NM_000350.2
ABCA4 Chr1:94468019 c.6148-471C>T NM_000350.2
ABCA4 Chr1:94578638 c.67-16T>A NM_000350.2
BBS1 Chr11:66291682 c.1110+329C>T NM_024649.4 rs571170303
BBS1 Chr11:66291105 c.951+58C>T NM_024649.4
BEST1 Chr11:61717900 c.-29+1G>T NM_001139443.1
BEST1 Chr11:61717904 c.-29+5G>A NM_001139443.1
C21ORF2 Chr21:45750232 c.1000-23A>T NM_001271441.1
CA4 Chr17:58236874 c.*89G>A NM_000717.3
CEP290 Chr12:88494960 c.2991+1655A>G NM_025114.3 rs281865192
CEP290 Chr12:88462434 c.6012-12T>A NM_025114.3 rs752197734
CHM ChrX:85220593 c.315-1536A>G NM_000390.2
CHM ChrX:85223644 c.315-4587T>A NM_000390.2
CLN3 Chr16:28497984 c.461-13G>C NM_000086.2 rs386833721
DHDDS Chr1:26774026 c.441-24A>G NM_024887.3 rs764831063
EYS Chr6:66417023 c.-448+5G>A NM_001142800.1
GNPTG Chr16:1412562 c.610-16_609+28del NM_032520.4 rs193302853
GUCY2D Chr17:7906220 c.-9-137T>C NM_000180.3
HK1 Chr10:71038467 c.-390-3818G>C NM_033500.2 rs397514654
HK1 Chr10:71038447 c.-390-3838G>C NM_033500.2 rs797044964
HK1 Chr10:71075518 c.27+14901A>G NM_033500.2 rs187500777
IMPDH1 Chr7:128043703 c.402+57G>A NM_000883.3 rs72624951
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
PRPH2 Chr6:42666249 c.829-4C>G NM_000322.4
RPE65 Chr1:68910577 c.246-11A>G NM_000329.2
RPGR ChrX:38160137 c.1059+363G>A NM_001034853.1
RPGRIP1 Chr14:21795769 c.2711-13G>T NM_020366.3 rs369991630
USH2A Chr1:216596610 c.-259G>T NM_206933.2
USH2A Chr1:215821092 c.14583-20C>G NM_206933.2
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
USH2A Chr1:215967783 c.9959-4159A>G NM_206933.2

Added and removed genes from the panel

Genes added Genes removed

Test strength

Includes analysis of the MAK Alu insertion. The majority of the X-linked RP is caused by mutations in theRPGR gene, which contains a mutational hotspot at a unique 567-aa exon called ORF15 accounting for two-thirds of all disease-causing mutations. The exon ORF15, however, includes a highly repetitive, purine-rich sequence, which generally performs poorly in NGS-based assays. Blueprint Genetics custom assay has good coverage (>20x) with high mapping rates (mapping quality >20) for 100.0% of the target regions in RPGR gene. Our validation showed high mean coverage of 139X for the RPGR gene. Thus, our NGS Panel is not expected to have major limitations in detecting variants in RPGR gene including ORF15 exon.

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • 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
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • 1479 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG 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 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
  • Mitochondrial DNA variants
  • 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
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

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.

The Blueprint Genetics retinitis pigmentosa panel covers classical genes associated with Stargardt disease, x-linked retinoschisis, retinitis pigmentosa, choroideremia and gyrate atrophy of choroid and retina. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
The performance presented above reached by WES with the following coverage metrics
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%


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 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. 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 such as, 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, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

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 corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

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 used, congress abstracts and mutation databases to help our customers 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 within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling. For eligible cases, Blueprint Genetics offers a no charge service to investigate the role of reported VUS (VUS Clarification Service).

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. 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 health care provider at no additional cost.