Macular Dystrophy Panel

Updated
Summary
  • Is a 28 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion / diagnosis of macular dystrophy. The genes on this panel are included in the Retinal Dystrophy Panel.

    Is not ideal for the investigation of isolated age-related macular dystrophy.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

28

Test code

OP0101

Panel size

Small

CPT codes
81479

Summary

The Blueprint Genetics Macular Dystrophy Panel (test code OP0101):

Test Specific Strength

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 Macular Dystrophy Panel

ICD-10 Disease
H35.50 Macular dystrophy
H35.50 Best vitelliform macular dystrophy
H35.50 Adult-onset foveomacular dystrophy
H35.50 Fundus albipunctatus

Sample Requirements

  • Blood (min. 1ml) in an EDTA tube
  • Extracted DNA, min. 2 μg in TE buffer or equivalent
  • Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)

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. Read more about our sample requirements here.

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

Macular dystrophy is a rare ocular disorder that affects the central area of the retina called the macula. The macula is responsible for sharp central vision, which is needed for detailed tasks, such as reading, driving, and recognizing faces. Best vitelliform macular dystrophy is an autosomal dominant disorder characterized by bilateral yellow "egg-yolk" appearance of the macula. It is slowly progressive disease with onset generally in childhood and sometimes in later teenage years. Affected individuals initially have normal vision followed by decreased central visual acuity and metamorphopsia. Individuals retain normal peripheral vision and dark adaptation. Best vitelliform macular dystrophy is caused by mutations in BEST1. The prevalence is estimated to be between 1:5,000 and 1:67,000 in northern Sweden and Denmark, respectively. Adult vitelliform macular dystrophy (AVMD) is characterized by the presence of bilateral, small, circular, yellow, symmetrical, subretinal lesions with drusen-like deposits. It shows significant phenotypic overlap with Best vitelliform macular dystrophy and affects mainly middle-aged individuals. Variability in the clinical presentation is a characteristic feature. Mutations in the PRPH2 gene cause a variety of retinal disorders, including AVMD. Stargardt disease or fundus flavimaculatus is a progressive form of juvenile macular degeneration with considerable clinical and genetic heterogeneity. Stargardt disease is caused by mutations in ABCA4, and the inheritance pattern is autosomal recessive. Variants in ELOVL4 are associated with autosomal dominant Stargardt disease 3. Worldwide prevalence of Stargardt disease is estimated at 1:8,000 – 1:10,000.

Genes in the Macular Dystrophy 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 308 1231
BEST1 Vitreoretinochoroidopathy, Microcornea, Rod-cone dystrophy, Posterior 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 AD/AR 62 318
C1QTNF5 Late-onset retinal degeneration AD 27 7
CDH3 Hypotrichosis, congenital, with juvenile macular dystrophy, Ectodermal dysplasia, ectrodactyly, and macular dystrophy syndrome AR 7 30
CERKL Retinitis pigmentosa AR 20 37
CNGB3 Macular degeneration, juvenile, Achromatopsia AR 115 124
CRB1 Retinitis pigmentosa, Pigmented paravenous chorioretinal atrophy, Leber congenital amaurosis AR 54 334
CRX Cone rod dystrophy, Leber congenital amaurosis AD/AR 30 106
CTNNA1 Macular dystrophy, patterned 2 AD 6 10
DRAM2 Cone-rod dystrophy 21 AR 8 10
EFEMP1 Doyne honeycomb degeneration of retina, Malattia leventinese AD 2 8
ELOVL4 Stargardt disease, Icthyosis, spastic quadriplegia, and mental retardation, Spinocerebellar ataxia AD/AR 13 14
IMPG1 Macular dystrophy, vitelliform AD/AR 9 11
IMPG2 Retinitis pigmentosa, Vitelliform macular dystrophy AD/AR 25 40
KCNV2 Retinal cone dystrophy AR 16 94
MFSD8 Ceroid lipofuscinosis, neuronal AR 27 47
NMNAT1# Leber congenital amaurosis AR 20 74
PRDM13 Macular dystrophy, retinal 1, North Carolina type AD 7
PROM1 Stargardt disease, Retinitis pigmentosa, Cone rod dystrophy, Macular dystrophy, retinal, AD/AR 22 80
PRPH2 Choriodal dystrophy, central areolar, Macular dystrophy, vitelliform, Retinitis pigmentosa, Retinitis punctata albescens, Macula dystrophy, patterned AD/AR 48 176
RAX2 Cone rod dystrophy AD/AR 5 4
RDH12 Retinitis pigmentosa, Leber congenital amaurosis AD/AR 23 102
RDH5 Fundus albipunctatus AR 11 51
RLBP1 Newfoundland rod-cone dystrophy, Fundus albipunctatus, Bothnia retinal dystrophy, Retinitis punctata albescens AR 9 37
RP1L1 Occult macular dystrophy, Retinitis pigmentosa AD/AR 7 48
RPGR Retinitis pigmentosa, Cone-rod dystrophy, X-linked, 1, Macular degeneration, X-linked atrophic, Retinitis pigmentosa 3 XL 79 218
RS1 Retinoschisis XL 44 262
TIMP3 Sorsby fundus dystrophy AD 6 17

* 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 Macular Dystrophy Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
ABCA4 Chr1:94461770 c.6730-19G>A NM_000350.2 rs375179475
ABCA4 Chr1:94468019 c.6148-471C>T NM_000350.2
ABCA4 Chr1:94481967 c.5197–557G>T 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 Chr1:94484082 c.5196+1056A>G NM_000350.2
ABCA4 Chr1:94492936 c.4539+2065C>G NM_000350.2
ABCA4 Chr1:94492937 c.4539+2064C>T NM_000350.2
ABCA4 Chr1:94492973 c.4539+2028C>T NM_000350.2 rs869320785
ABCA4 Chr1:94493000 c.4539+2001G>A NM_000350.2
ABCA4 Chr1:94493073 c.4539+1928C>T NM_000350.2
ABCA4 Chr1:94493272 c.4539+1729G>T NM_000350.2
ABCA4 Chr1:94493895 c.4539 +1106C>T NM_000350.2
ABCA4 Chr1:94493901 c.4539+1100A>G NM_000350.2
ABCA4 Chr1:94496509 c.4253+43G>A NM_000350.2
ABCA4 Chr1:94508465 c.3191–11T>A NM_000350.2
ABCA4 Chr1:94509047 c.3051-16T>A NM_000350.2
ABCA4 Chr1:94509799 c.3050+370C>T NM_000350.2
ABCA4 Chr1:94510683 c.2919-383C>T NM_000350.2
ABCA4 Chr1:94525509 c.2160+584A>G NM_000350.2
ABCA4 Chr1:94526934 c.1938-619A>G NM_000350.2
ABCA4 Chr1:94527698 c.1937+435C>G NM_000350.2
ABCA4 Chr1:94528120 c.1937+13T>G NM_000350.2
ABCA4 Chr1:94546780 c.859-506G>C NM_000350.2
ABCA4 Chr1:94546814 c.859–540C>G NM_000350.2
ABCA4 Chr1:94549781 c.769–784C>T NM_000350.2
ABCA4 Chr1:94561127 c.768+3223C>T NM_000350.2
ABCA4 Chr1:94566773 c.570+1798A>G NM_000350.2
ABCA4 Chr1:94576926 c.302+68C>T NM_000350.2 rs761188244
ABCA4 Chr1:94577158 c.161–23T>G NM_000350.2
ABCA4 Chr1:94578638 c.67-16T>A NM_000350.2
ABCA4 Chr14:21793564 c.2367+23delG NM_020366.3
BEST1 Chr11:61717900 c.-29+1G>T NM_001139443.1
BEST1 Chr11:61717904 c.-29+5G>A NM_001139443.1
NMNAT1 Chr1:10003560 c.-70A>T NM_022787.3
NMNAT1 Chr1:10003561 c.-69C>T NM_022787.3
NMNAT1 Chr1:10003580 c.-57+7T>G NM_022787.3
PRDM13 Chr6:100040906 c.-14005G>T .
PRDM13 Chr6:100040987 c.-13924G>C .
PRDM13 Chr6:100041040 c.-13871C>T .
PRDM13 Chr6:100046783 c.-8128A>C NM_021620.3
PRDM13 Chr6:100046804 c.-8107T>C NM_021620.3
PROM1 Chr4:15989860 c.2077-521A>G NM_006017.2 rs796051882
RDH5 Chr12:56114302 c.-33+2dupT NM_002905.3
RPGR ChrX:38128234 NM_000328.2
RPGR ChrX:38160137 c.1059+363G>A NM_001034853.1

Added and removed genes from the panel

Genes added Genes removed
KCNV2
NMNAT1

Test Strengths

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 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
  • 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 below ‘Non-coding disease causing variants covered by this panel’)
  • 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

The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: NMNAT1 (NM_001297779:5). Genes with suboptimal coverage in our assay are marked with number sign (#). 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 (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • 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 macular dystrophy panel covers classical genes associated with macular dystrophy, best vitelliform macular dystrophy, adult-onset foveomacular dystrophy and fundus albipunctatus. 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 high-quality, clinical grade NGS sequencing assay for panels.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.89% (99,153/99,266) >99.9999
Insertions, deletions and indels by sequence analysis
1-10 bps 96.9% (7,563/7,806) >99.9999
11-50 bps 99.13% (2,524/2,546) >99.9999
Copy number variants (exon level dels/dups)
1 exon level deletion (heterozygous) 100% (20/20) NA
1 exon level deletion (homozygous) 100% (5/5) NA
1 exon level deletion (het or homo) 100% (25/25) NA
2-7 exon level deletion (het or homo) 100% (44/44) NA
1-9 exon level duplication (het or homo) 75% (6/8) NA
Simulated CNV detection
5 exons level deletion/duplication 98.7% 100.00%
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 143X
Nucleotides with >20x sequencing coverage (%) 99.86%

Bioinformatics

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 and regulatory 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 including, 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, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the 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 is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call.
Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed 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, abstracts and variant databases used to help ordering providers 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. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. 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.

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