Tuberous Sclerosis Complex Panel by Next-Generation Sequencing (TSCP-NG)
Information for Ordering
Acceptable Specimen Types
- Fresh blood sample: 3–6 mL EDTA; no time limitations associated with receipt
- Saliva: OGD-575 DNA Genotek collection kit; kits are provided upon request
- DNA extracted from lymphocyte cells: minimum volume of 25 µL containing 3 µg of DNA; A260/A280 ratio ≥1.8; must be extracted in a CLIA-certified or equivalent laboratory
- Flash-frozen tumor shipped on dry ice
- Fresh tumor or affected-tissue biopsy immersed in sterile culture media, such as PBS or RPMI
Turnaround Time
- Blood, saliva, or DNA: Average of 30 working days
- Fresh or frozen tumor: Average of 50 working days
Price, CPT Codes, and Z Code
- Institutional/self-pay price for blood, saliva, or DNA: $1,500 USD
- Institutional/self-pay price for fresh or frozen tumor: $2,500 USD
- CPT codes: 81479, 81406, and 81405
- Z code: ZB68E
Candidates for Testing
Patients with clinical features suggestive of tuberous sclerosis complex.
Specimen Shipping and Handling
Please refer to the specimen requirements listed above.
Blood, saliva, DNA, fresh tumor, and fresh-tissue biopsy specimens should be shipped at room temperature unless otherwise directed by the laboratory. Flash-frozen tumor specimens must be shipped on dry ice.
Specimens must be packaged to prevent breakage. Absorbent material must be included to contain liquids if breakage occurs. Specimens must also be shipped in double watertight containers, such as a specimen pouch placed inside the shipping company’s diagnostic envelope.
To request a collection kit, please complete the Collection Kit Request Form.
Please complete the Fresh/Frozen Tumor Submission Checklist when submitting tumor specimens.
Before shipping a specimen, please contact the UAB Medical Genomics Laboratory by email at medgenomics@uabmc.edu or by phone at 205-934-5562. Please provide the specimen type, shipment date, and package tracking number so the laboratory can help ensure proper and timely receipt.
Required Forms
About
Disorder Background
Tuberous sclerosis complex is a rare autosomal dominant disorder involving abnormalities of the skin, brain, kidneys, heart, and lungs. Central nervous system tumors are common in patients with tuberous sclerosis complex.
Heterozygous pathogenic variants can be identified in approximately 75%–90% of individuals who meet the clinical diagnostic criteria for tuberous sclerosis complex. Among individuals in whom a pathogenic variant is identified, variants in TSC1 and TSC2 account for approximately 31% and 69% of cases, respectively.
Test Description
The Tuberous Sclerosis Complex Panel by NGS involves simultaneous sequencing of two genes: TSC1 and TSC2.
Average coverage is greater than 1,600×, with more than 99% of the coding region covered at ≥350× and more than 99% covered at ≥200×. The minimum coverage for remaining regions is greater than 30×.
This coverage permits detection of low-level mosaicism. Variants may be detected at approximately an 8% variant allele fraction across all regions analyzed by NGS. More than 99% of the coding region has deeper coverage that permits detection of substitution variants at approximately a 3% variant allele fraction.
Variant and copy-number calls are generated using a validated bioinformatics pipeline capable of detecting single-nucleotide variants, insertions, deletions, and frameshifts caused by deletions or duplications up to 112 bp.
Deletion/duplication analysis of TSC1 and TSC2 is included because copy-number variants are part of the disease-associated variant spectrum for these genes.
Relevant family members of a proband with a novel or previously identified variant of uncertain significance may be offered targeted analysis at no additional charge when accurate phenotypic information is provided by a healthcare professional to assist with variant interpretation. There is no limit to the number of qualifying relatives who may be tested.
Analysis may be performed by next-generation sequencing on fresh or flash-frozen affected-tissue specimens.
View references for this testing.
For more information, test requisition forms, or collection kits, please contact the UAB Medical Genomics Laboratory at 205-934-5562 or medgenomics@uabmc.edu.