Epidermolysis Bullosa Panel

Last modified: Jun 12, 2018

Summary

  • Is a 24 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of congenital epidermolysis bullosa.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

3-4 weeks

Number of genes

24

Test code

DE0301

CPT codes

SEQ 81406
DEL/DUP 81479
SEQ 81479

Summary

The Blueprint Genetics Epidermolysis Bullosa Panel (test code DE0301):

  • Is a 24 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Epidermolysis Bullosa Panel

ICD-10 Disease
Q81.8 Congenital epidermolysis bullosa

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.

Epidermolysis bullosa (EB) is a group of inherited diseases that are characterised by blistering lesions on the skin and mucous membranes, most commonly appearing at sites of friction and minor trauma such as the feet and hands. In some subtypes, blisters may also occur on internal organs, such as the oesophagus, stomach and respiratory tract, without any apparent friction. There are 4 major types of EB based on different sites of blister formation within the skin structure: Epidermolysis bullosa simplex (EBS), Junctional epidermolysis bullosa (JEB), Dystrophic epidermolysis bullosa (DEB), and Kindler syndrome (KS). EBS is usually characterized by skin fragility and rarely mucosal epithelia that results in non-scarring blisters caused by mild or no trauma. The four most common subtypes of EBS are: 1) localized EBS (EBS-loc; also known as Weber-Cockayne type), 2) Dowling-Meara type EBS (EBS-DM), 3) other generalized EBS(EBS, gen-nonDM; also known as Koebner type) and 4) EBS-with mottled pigmentation (EBS-MP). Skin biopsy from fresh blister is considered mandatory for diagnostics of generalized forms of EBS. The prevalence of EBS is is estimated to be 1:30,000 - 50,000. EBS-loc is the most prevalent, EBS-DM and EBS-gen-nonDM are rare, and EBS-MP is even rarer. Penetrance is 100% for known KRT5 and KRT14 mutations. Location of the mutations within functional domains of KRT5and KRT14 has shown to predict EBS phenotype. JEB is characterized by fragility of the skin and mucous membranes, manifest by blistering with little or no trauma. Blistering may be severe and granulation tissue can form on the skin around the oral and nasal cavities, fingers and toes, and internally around the upper airway. JEB is caused by mutations in LAMB3 (70% of all JEB), COL17A1 (12%), LAMC2 (9%), and LAMA3 (9%). DEB is caused by COL7A1 mutations and can be either dominantly (DDEB) or recessively (RDEB). DDEB is usually mild. Blistering may be localized to the hands, feet, elbows and knees or it may be generalized. RDEB is typically more generalized and severe than DDEB. KS is very rare and involves all layers of the skin with extreme fragility.

Genes in the Epidermolysis Bullosa Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
ATP2C1 Benign chronic pemphigus AD 17 184
CDSN Peeling skin syndrome, Hypotrichosis AD/AR 6 13
COL7A1 Nail disorder, nonsyndromic congenital, Transient bullous dermolysis of the newborn, Epidermolysis bullosa dystrophica, Epidermolysis bullosa, pretibial, Epidermolysis bullosa pruriginosa AD/AR 159 783
COL17A1 Epithelial recurrent erosion dystrophy (ERED), Epidermolysis bullosa, junctional, non-Herlitz AD/AR 32 109
DSG1 Severe dermatitis, multiple allergies, and metabolic wasting syndrome (SAM syndrome), Keratosis palmoplantaris striata I AR 13 30
DSG2 Arrhythmogenic right ventricular dysplasia, Dilated cardiomyopathy (DCM) AD 40 125
DSG4 Hypotrichosis AR 8 18
DSP Cardiomyopathy, dilated, with wooly hair, keratoderma, and tooth agenesis, Arrhythmogenic right ventricular dysplasia, familial, Cardiomyopathy, dilated, with wooly hair and keratoderma, Keratosis palmoplantaris striata II, Epidermolysis bullosa, lethal acantholytic AD/AR 155 281
DST Neuropathy, hereditary sensory and autonomic AR 9 7
EXPH5 Epidermolysis bullosa AR 2 10
FERMT1 Kindler syndrome AR 32 81
GRIP1 Fraser syndrome AR 5 17
ITGA3 Interstitial lung disease with nephrotic syndrome and epidermolysis bullosa AR 6 11
ITGA6 Epidermolysis bullosa, junctional, with pyloric stenosis AR 2 8
ITGB4 Epidermolysis bullosa simplex, Weber-Cockayne, Epidermolysis bullosa, junctional, with pyloric atresia, Epidermolysis bullosa, junctional, non-Herlitz AD/AR 24 95
KRT1 Palmoplantar keratoderma, nonepidermolytic, Ichthyosis, cyclic, with epidermolytic hyperkeratosis, Epidermolytic hyperkeratosis, Ichthyosis histrix, Curth-Macklin, Keratosis palmoplantaris striata, Palmoplantar keratoderma, epidermolytic AD 23 61
KRT5 Epidermolysis bullosa simplex, Dowling-Meara, Dowling-Degos disease, Epidermolysis bullosa simplex with migratory circinate erythema, Epidermolysis bullosa simplex with mottled pigmentation, Epidermolysis bullosa simplex, Weber-Cockayne, Epidermolysis bullosa simplex, Koebner AD 37 152
KRT14* Epidermolysis bullosa simplex, Dowling-Meara, Epidermolysis bullosa simplex, Dermatopathia pigmentosa reticularis, Epidermolysis bullosa simplex, Weber-Cockayne, Epidermolysis bullosa simplex, Koebner, Naegeli-Franceschetti-Jadassohn syndrome AD/AR 30 115
LAMA3 Epidermolysis bullosa, junctional, Herlitz, Epidermolysis bullosa, generalized atrophic benign, Laryngoonychocutaneous syndrome AR 36 54
LAMB3 Amelogenesis imperfecta, Epidermolysis bullosa, junctional, Herlitz, Epidermolysis bullosa, junctional, non-Herlitz AD/AR 65 116
LAMC2 Epidermolysis bullosa, junctional, Herlitz, Epidermolysis bullosa, junctional, non-Herlitz AR 31 40
PKP1 Ectodermal dysplasia/skin fragility syndrome AR 5 17
PLEC Muscular dystrophy, limb-girdle, Epidermolysis bullosa AR 33 98
TGM5 Peeling skin syndrome AR 10 25

* 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
ATP2C1 Chr3:130714870 c.2160-17T>C NM_001199180.1 rs117316812
COL17A1 Chr10:105840444 c.-11-2A>G NM_000494.3
COL7A1 Chr3:48632779 c.-187C>T NM_000094.3
COL7A1 Chr3:48632780 c.-188C>T NM_000094.3
COL7A1 Chr3:48626035 c.2587+40G>A NM_000094.3
COL7A1 Chr3:48616971 c.5236-23A>G NM_000094.3
COL7A1 Chr3:48613354 c.5821-19A>G NM_000094.3
COL7A1 Chr3:48602516 c.8620+26G>A NM_000094.3
COL7A1 Chr3:48629915 c.977-15G>A NM_000094.3
FERMT1 Chr20:6103422 c.-20A>G NM_017671.4 rs869312722
FERMT1 Chr20:6074846 c.1139+740G>A NM_017671.4 rs869312728
ITGA3 Chr17:48151801 c.1383-11T>A NM_005501.2
ITGB4 Chr17:73732344 c.1762-25T>A NM_000213.3
ITGB4 Chr17:73748508 c.3977-19T>A NM_000213.3
LAMB3 Chr1:209825713 c.-38+1G>A NM_000228.2
LAMB3 Chr1:209801557 c.1133-22G>A NM_000228.2 rs767847211

Added and removed genes from the panel

Genes added Genes removed

MMP1

Test strength

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
  • ~1,500 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 partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. 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 epidermolysis bullosa panel covers classical genes associated with congenital epidermolysis bullosa. 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%

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 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.