Corneal Dystrophy Panel

Updated
Summary
  • Is a 29 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion / diagnosis of corneal dystrophy.

Analysis methods
  • PLUS
Availability

4 weeks

Number of genes

29

Test code

OP1601

Panel size

Small

CPT codes
81479

Summary

The Blueprint Genetics Corneal Dystrophy Panel (test code OP1601):

ICD codes

Commonly used ICD-10 code(s) when ordering the Corneal Dystrophy Panel

ICD-10 Disease
H18.50 Corneal dystrophy
H18.55 Macular corneal dystrophy
H18.50 Meesmann corneal dystrophy
H18.50 Fuchs endothelial corneal dystrophy
H18.50 Fish-eye disease
H18.54 Lattice corneal dystrophy

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.

Corneal dystrophy refers to a heterogeneous group of bilateral genetically determined non-inflammatory corneal diseases that are usually restricted to the cornea. Clinically, the corneal dystrophies can be divided into three groups based the specific location within the cornea. It can affect primarily the corneal epithelium and its basement membrane (superficial corneal dystrophy), the corneal stroma (stromal corneal dystrophy) or Descemet membrane and the corneal endothelium (posterior corneal dystrophy). Corneal dystrophies can be caused by variants in genes such as COL8A2, ZEB1, TCF4, COL8A2, LOXHD1, SLC4A11, CHST6, TGFBI, UBIAD1, TACSTD2, and CHRDL1 and may have an autosomal dominant, autosomal recessive, or X-linked mode of inheritance. The prevalence of corneal dystrophies is variable, but all of these conditions are rare.

Genes in the Corneal Dystrophy Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
CHRDL1 Megalocornea 1, X-linked XL 8 21
CHST6 Macular dystrophy, corneal AR 11 178
COL17A1 Epithelial recurrent erosion dystrophy (ERED), Epidermolysis bullosa, junctional, non-Herlitz AD/AR 32 112
COL5A1 Ehlers-Danlos syndrome AD 101 154
COL8A2 Corneal dystrophy polymorphous posterior, 2, Corneal dystrophy, Fuchs endothelial, 1 AD 3 7
CYP4V2 Retinitis pigmentosa, Bietti crystalline corneoretinal dystrophy AR 31 94
DCN Corneal dystrophy, congenital stromal AD 4 5
FOXE3 Aphakia, congenital primary, Anterior segment mesenchymal dysgenesis, Cataract 34, Aortic aneurysm, familial thoracic AR/AD 9 29
GJA8 Cataract AD/AR 20 61
GRHL2 Ectodermal dysplasia/short stature syndrome, Deafness, autosomal dominant 28, Corneal dystrophy, posterior polymorphous AD/AR 12 12
GSN Amyloidosis, Finnish type AD 3 13
KERA Cornea plana 2, autosomal recessive AR 8 15
KRT12 Meesmann corneal dystrophy AD 9 25
KRT3 Meesmann corneal dystrophy AD 3 4
LCAT Lecithin:cholesterol acyltransferase deficiency, Fish-eye disease AR 18 102
LOXHD1 Deafness AD/AR 26 60
MAF# Ayme-Gripp syndrome, Cataract 21, multiple types AD 21 22
NLRP3 Neonatal onset multisystem inflammatory disease (NOMID), Muckle-Wells syndrome, Chronic infantile neurologic cutaneous articular (CINCA) syndrome, Familial cold-induced autoinflammatory syndrome 1 AD 20 136
OVOL2 Corneal dystrophy, posterior polymorphous, 1 AD 4 4
PIKFYVE Corneal fleck dystrophy AD 7 13
PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, Iridogoniodysgenesis, Peters anomaly AD 23 101
PRDM5 Brittle cornea syndrome 2 AR 8 13
SLC4A11 Cryohydrocytosis, Corneal dystrophy, Fuchs endothelial 4, Corneal endothelial dystrophy 2, autosomal recessive, Corneal endothelial dystrophy and perceptive deafness AD/AR 22 95
TACSTD2 Corneal dystrophy, gelatinous drop-like AR 8 32
TCF4 Corneal dystrophy, Fuchs endothelial, Pitt-Hopkins syndrome AD 105 146
TGFBI Corneal dystrophy, Avellino, Corneal dystrophy, Thiel-Behnke, Corneal dystrophy, Groenouw, Corneal dystrophy, epithelial basement membrane, Corneal dystrophy of Bowman layer, Corneal dystrophy, Corneal dystrophy, Reis-Bucklers AD 13 70
UBIAD1 Corneal dystrophy, crystalline, of Schnyder AD 10 28
ZEB1 Corneal dystrophy, Fuchs endothelial, Corneal dystrophy, posterior polymorphous AD 8 52
ZNF469 Brittle cornea syndrome AR 34 69

* 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), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence 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 Corneal Dystrophy Panel

Gene Genomic location HG19 HGVS RefSeq RS-number
COL17A1 Chr10:105840444 c.-11-2A>G NM_000494.3
COL5A1 Chr9:137645685 c.1720-11T>A NM_000093.4 rs863223444
COL5A1 Chr9:137680989 c.2647-12A>G NM_000093.4
COL5A1 Chr9:137686903 c.2701-25T>G NM_000093.4 rs765079080
COL5A1 Chr9:137726806 c.5137-11T>A NM_000093.4 rs183495554
GRHL2 Chr8:102505149 c.20+133delA NM_024915.3
GRHL2 Chr8:102505272 c.20+257delT NM_024915.3
GRHL2 Chr8:102505561 c.20+544G>T NM_024915.3
LCAT Chr16:67976512 c.524-22T>C NM_000229.1 rs794726664
OVOL2 Chr20:18038552 c.-274T>G NM_021220.2 rs869320630
OVOL2 Chr20:18038585 c.-307T>C NM_021220.2 rs869320629
OVOL2 Chr20:18038617 NM_021220.2
OVOL2 Chr20:18038648 c.-370T>C NM_021220.2 rs869320628
PITX2 Chr4:111538758 c.*520_*522delTAT NM_000325.5 rs561702585,rs775662096
PITX2 Chr4:111539855 c.412-11A>G NM_000325.5
PITX2 Chr4:111559138 c.-1214_-1213delAT NM_153426.2
SLC4A11 Chr20:3211931 c.1077+26_1077+44delCGGCAGGGTCGGCGGGGGC NM_001174090.1

Added and removed genes from the panel

Genes added Genes removed
GRHL2
NLRP3

Test Strengths

The strengths of this test include:
  • CAP 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 ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
  • 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

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 genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).

Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.

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 99.2% (7,745/7,806) >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%
     
Size range (0.1-47 Mb) 100% (25/25)
     
The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics
     
Mean sequencing depth 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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