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HelpTest Code LAB1844 Encephalocraniocutaneous lipomatosis (ECCL) and Oculoectodermal syndrome (OES) Sequencing
Clinical System Name
ECCL/OES Sequencing
Description
Encephalocraniocutaneous lipomatosis (ECCL) and Oculoectodermal syndrome (OES) are sporadic neurocutaneous disorders caused by somatic mutations in FGFR1 and KRAS. OES is characterized by congenital abnormalities of the scalp (cutis aplasia and focal alopecia) and eyes (eyelid skin tags, colobomas, epibulbar dermoids). In addition to these features, individuals with ECCL have CNS lipomas. An increased risk of low-grade gliomas is associated with these disorders. The causative mutations are not present in blood-derived DNA, so testing of biopsied tissue (skin or other affected tissue) is required.
Reported Gene List for ECCL/OES Sequencing (2 genes): FGFR1, KRAS
Sample Requirements
Samples MUST have two of the following to be accepted as properly labeled: first & last name, outside medical record number, unique accession number, or date of birth.
- If both frozen tissue and FFPE tissue are available, frozen tissue from an affected site is preferred. Tissue sampled from an affected site is preferred over non-affected tissue.
| Sample | Requirement | Important notes | |
| Fresh frozen tissue (-70C) |
25-50 mg in a sterile container. |
A copy of the pathology report is recommended.
Specify tissue source and site on requisition. |
|
| Skin biopsy |
2-4 mm punch biopsy of skin collected under sterile conditions in a sterile vial, frozen with no media.
Also acceptable, refrigerate with 1-3 mL of tissue transport medium. |
DO NOT use formaldehyde, formalin, alcohol, or 5% dextrose.
Specify tissue source and site on requisition. |
|
| FFPE (Formalin-Fixed Paraffin-Embedded) Slides or Scrolls |
|
To send FFPE scrolls:
|
A copy of the pathology report is required.
Minimum acceptable tissue area is 10 square millimeters (total of 1 cubic millimeter of tissue). Tissue sections should contain as much lesional tissue as possible.
Note that deletion/duplication analysis cannot be performed on FFPE tissue at this time. |
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To send FFPE slides:
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| Extracted DNA |
2-5 mcg DNA from tissue
DNA concentration minimum 50 µg/mL (40uL minimum volume); 260/280 ratio 1.70-2.00. |
Isolation of nucleic acids for clinical testing must be performed in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS. | |
Processing Instructions
| Specimen Type | Description |
Temperature |
Storage instructions |
| Extracted DNA | DNA aliquot tube | Refrigerate | Molecular Genetics box in CPA refrigerator #2 |
| Slides or scrolls | Glass slides or sterile tube | Room temp | Place in CPA Cytogenetics room temp box with requisition |
| Fresh frozen tissue | Frozen aliquot of 15-50 mg tissue | Frozen | CPA -70 freezer (SNP array/Molecular box) |
| Skin biopsy | Sterile container | Frozen | CPA -70 freezer (SNP array/Molecular box) |
| In medium | Refrigerate | Molecular Genetics box in CPA refrigerator #2 |
Off-site collection: Transport DNA, slides or scrolls at room temperature via overnight shipping. Transport fresh frozen tissue on dry ice.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Tissue - Fresh Frozen | -70 C | years |
| Tissue - FFPE Slides | RT | years |
| Extracted DNA | -20 C or -70 C | years |
Availability
| STAT | Performed | TAT |
|---|---|---|
| Contact lab | Monday - Friday | 4-8 weeks |
Performing Laboratory
Seattle Children's Laboratory
Department
Department: Molecular Genetics Laboratory
Phone: 206-987-3872
Lab Client Services: 206-987-2617
Lab Genetic Counselor: LabGC@seattlechildrens.org
CPT Codes
81479
Methodology
Method: Next Generation Sequencing technology using an Illumina NextSeq instrument. Target region includes coding exons and a minimum of 10 bp of flanking intron boundaries of the genes tested. Target enrichment performed using a custom Integrated DNA Technologies (IDT) panel.
Average coverage >1,000x, depth of coverage for all target regions is at least 20x.
Limitations:
This method can detect single nucleotide variants, small deletions, and small insertions in the regions targeted. Some exons cannot be efficiently captured due to sequence homology or sequence properties. This method will not detect large insertions and deletions, complex indels, structural variants, or copy number variants. Variants located outside of targeted regions will not be detected. Mosaic variants present at <20% may not be reliably detected, and detection sensitivity of mosaic variants is dependent on the nature of the variant. Recurrent hotspot variants can be detected at lower levels of mosaicism but sensitivity will be affected by DNA quality and quantity.
Reference Range
Interpretive report will be provided. Variants are not reported if they are considered benign or likely benign.
Special Instructions
Link to: Genetics Home Reference ECCL
Other References:
- Bennett JT et al. Mosaic Activating Mutations in FGFR1 Cause Encephalocraniocutaneous Lipomatosis. Am J Hum Genet. 2016 Mar 3;98(3):579-587.
- Boppudi S et al. Specific mosaic KRAS mutations affecting codon 146 cause oculoectodermal syndrome and encephalocraniocutaneous lipomatosis. Clin Genet. 2016 Oct;90(4):334-42.
- Chacon-Camacho OF et al. Expansion of the phenotypic spectrum and description of molecular findings in a cohort of patients with oculocutaneous mosaic RASopathies. Mol Genet Genomic Med. 2019 May;7(5):e625.
- Bavle A et al. Encephalocraniocutaneous Lipomatosis. J Pediatr Hematol Oncol. 2018 Oct;40(7):553-554.
Requisition
Clinical Utility
Genetic testing of individuals can be helpful in confirming a specific diagnosis. Since the prognosis and treatment of these conditions varies greatly, and they are a relatively rare group of conditions, genetic testing may guide management of these patients. Note that due to the mosaic nature of some of these conditions, a blood-based genetic test may be of limited clinical utility. Genetic counseling is recommended.