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Junctional Epidermolysis Bullosa via the COL17A1 Gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
974 COL17A1$2110.00 81479 Add to Order
Targeted Testing

For ordering targeted known variants, please proceed to our Targeted Variants landing page.

Turnaround Time

The great majority of tests are completed within 18 days.

Clinical Sensitivity

One study reported that the COL17A1 gene mutations were found in 98.8% (85/86 alleles) of the 43 JEB patients with either reduced or absent collagen XVII expression (Kiritsi et al. J Med Genet 48:450-457, 2011).

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Deletion/Duplication Testing via aCGH

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
600 COL17A1$690.00 81479 Add to Order
Pricing Comment

# of Genes Ordered

Total Price

1

$690

2

$730

3

$770

4-10

$840

11-30

$1,290

31-100

$1,670

Over 100

Call for quote

Turnaround Time

The great majority of tests are completed within 28 days.

Clinical Features

The collagen protein XVII (also known as BP180 and BPAG2) encoded by COL17A1 is essential for cohesion between dermal-epidermal junction, as it is a key component of hemidesmosomes needed to hold stratified epithelia to the basal membrane. Junctional epidermolysis bullosa (JEB), one of the four major types of epidermolysis bullosa (EB), is a clinically and genetically heterogeneous skin/mucosa separation disorder characterized by blister formation induced by mild trauma. COL17A1 mutations often cause the mild type of JEB (Non-Herlitz JEB, OMIM#226650), however in some cases, COL17A1 null mutations were also reported in the neonatal lethal form (Herlitz JEB, OMIM#226700). Variki et al. studied 20 cases with COL17A1 mutations; seven of them had generalized blisters, hematuria, anemia and growth retardation, one of the seven patients had pseudosyndactly and wrist/ankle abnormalities, which mimic the features of dystrophic epidermolysis bullosa (Varki et al. J Med Genet 43:641-652, 2006). Other common clinical features in JEB are enamel defects, nail dystrophy and alopecia. It should be noted that clinical manifestations overlap significantly among different types of EB because at least 12 other genes encoding the multiprotein cohesion complex in skin contribute to epidemolysis bullosa (EB) (Fine et al. J Am Acad Derm 58:931-950, 2008; Laimer et al. Dermatol Clin 28:55-60, 2010). Therefore, clinically suspected EB patients can be evaluated by skin biopsy to help with clinical  diagnosis and direct genetic testing.

Genetics

Junctional Epidermolysis Bullosa (JEB) is an autosomal recessive disorder caused by mutations in LAMA3, LAMB3, LAMC2 and COL17A1. Mutations in COL17A1 account for ~12% of reported pathogenic mutations related to JEB (Pfendner et al. GeneReviews, 2008). Collagen XVII, a transmembrane protein of the hemidesmosome, contains an intracellular noncollagenous domain (exons 2 to 17), and an extracellular collagenous domain (exons 18 to 56) (Giudice et al. J Invest Dermatol 99:243-250,1992; McGrath et al. Nat Genet 11:83-86, 1995; Gatalica et al. Am. J. Hum. Genet 60:352-365, 1997, Varki et al. 2006, Pfendner et al. GeneReviews, 2008). Most known mutations (>80%) result in truncated proteins (nonsense, small deletions/insertions and splicing). Two recurring mutations (p.Gly803X and p.Arg1226X) comprise 7% and 10% of the reported COL17A1 mutations, respectively (Kiritsi et al. J Med Genet 48:450-457, 2011). A heterozygous variant c.1880G>T, p.G627V in COL17A1 was reported in an autosomal dominant JEB patient with an enamel defect (Almaani et al. Br J Dermatol 160:1094-1097, 2009). Mutations in COL17A1 were also identified in a patient affected with epidermolysis bullosa simplex (Pasmooij et al. Br J Dermatol 151:669-674, 2004).

Testing Strategy

Collagen XVII is coded by exons 2-56 of the COL17A1 gene on chromosome 10q24.3. Testing involves the PCR amplifications from genomic DNA and bidirectional sequencing of the coding exons and ~20bp of adjacent noncoding sequences. We will also sequence any single exon (Test #100) or pair of exons (Test #200) in family members of patients with known mutations or to confirm research results.

Indications for Test

Individuals with clinical features consistent with H-JEB, Non-Herlitz JEB. Individuals diagnosed with skin biopsy showing absent or reduced collagen XVII expression are preferred.

Gene

Official Gene Symbol OMIM ID
COL17A1 113811
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Non-Herlitz Junctional Epidermolysis Bullosa 226650

Related Tests

Name
Dystrophic Epidermolysis Bullosa (DEB) via the COL7A1 Gene
Ectodermal Dysplasia/skin Fragility Syndrome via the PKP1 Gene
Epidermolysis Bullosa Simplex (EBS) via the KRT14 Gene
Epidermolysis Bullosa Simplex (EBS) via the KRT5 Gene
Epidermolysis Bullosa with Pyloric Atresia via the ITGA6 Gene
Epidermolysis Bullosa with Pyloric Atresia via the ITGB4 Gene
Epidermolysis Bullosa with Pyloric Atresia via the PLEC Gene
Kindler Syndrome via the FERMT1 Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Almaani et al. Autosomal dominant junctional epidermolysis bullosa. Br J Dermatol 160(5):1094-1097, 2009. PubMed ID: 19120338
  • Fine et al. (2008). PubMed ID: 18374450
  • Gatalica et al. Cloning of the human type XVII collagen gene (COL17A1), and detection of novel mutations in generalized atrophic benign epidermolysis bullosa. Am J Hum Genet 60(2):352-365, 1997. PubMed ID: 9012408
  • Giudice et al. Cloning and primary structural analysis of the bullous pemphigoid autoantigen BP180. J Invest Dermatol 99(3):243-250, 1992. PubMed ID: 1324962
  • Kiritsi et al. Molecular mechanisms of phenotypic variability in junctional epidermolysis bullosa. J Med Genet 48(7):450-457, 2011. PubMed ID: 21357940
  • Laimer et al. Herlitz junctional epidermolysis bullosa. Dermatol Clin 28(1):55-60, 2010. PubMed ID: 19945616
  • McGrath et al. Mutations in the 180-kD bullous pemphigoid antigen (BPAG2), a hemidesmosomal transmembrane collagen (COL17A1), in generalized atrophic benign epidermolysis bullosa. Nat Genet 11(1):83-86, 1995. PubMed ID: 7550320
  • Pasmooij et al.  Features of epidermolysis bullosa simplex due to mutations in the ectodomain of type XVII collagen. Br J Dermatol 151(3):669-674, 2004. PubMed ID: 15377356
  • Pfendner et al. Junctional Epidermolysis Bullosa. GeneReviews, 2008 PubMed ID: 20301304
  • Varki, et al. Epidermolysis bullosa. II. (2007). PubMed ID: 16971478
Order Kits
TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.

Our ability to detect minor sequence variants, due for example to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.

Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

Deletion/Duplication Testing Via Array Comparative Genomic Hybridization

Test Procedure

Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.

Analytical Validity

PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.

Analytical Limitations

Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.

This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.

aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.

Breakpoints, if occurring outside the targeted gene, may be hard to define.

The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.

Order Kits

Ordering Options


myPrevent - Online Ordering
  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.
REQUISITION FORM
  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

SPECIMEN TYPES
WHOLE BLOOD

(Delivery accepted Monday - Saturday)

  • Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
  • For small babies, we require a minimum of 1 ml of blood.
  • Only one blood tube is required for multiple tests.
  • Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
  • During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
  • In cold weather, include an unfrozen ice pack in the shipping container as insulation.
  • At room temperature, blood specimen is stable for up to 48 hours.
  • If refrigerated, blood specimen is stable for up to one week.
  • Label the tube with the patient name, date of birth and/or ID number.

DNA

(Delivery accepted Monday - Saturday)

  • Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
  • For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
  • DNA may be shipped at room temperature.
  • Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
  • We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.

CELL CULTURE

(Delivery preferred Monday - Thursday)

  • PreventionGenetics should be notified in advance of arrival of a cell culture.
  • Culture and send at least two T25 flasks of confluent cells.
  • Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
  • Send specimens in insulated, shatterproof container overnight.
  • Cell cultures may be shipped at room temperature or refrigerated.
  • Label the flasks with the patient name, date of birth, and/or ID number.
  • We strongly recommend maintaining a local back-up culture. We do not culture cells.
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