Tuberous Sclerosis Complex Panel by Next-Gen Sequencing (TSCP-NG)
Information for Ordering
{slide=Acceptable Specimen Types}• Fresh blood sample (3-6 ml EDTA; no time limitations associated with receipt)
• Saliva (OGR-575 DNA Genotek; kits are provided upon request)
• DNA (extracted from lymphocyte cells; a minimum volume of 25μL at 3μg; O.D. of 260:280nm ≥1.8; must be extracted in a CLIA or equivalent certified lab)
• Flash frozen tumor sent on dry ice
• Fresh tumor or affected tissue biopsy, immersed in sterile culture media (PBS/RPMI)
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Average = 30 working days for blood, saliva, or DNA
Average = 40 working days for fresh/frozen tumor
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$1,500 for blood, saliva, or DNA (USD – institutional/self-pay price)
$2,500 for fresh/frozen tumor (USD – institutional/self-pay)
CPT: 81479, 81406, and 81405
Z code: ZB68E
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{slide=Candidates for Testing}
Patients with clinical features suggestive of Tuberous Sclerosis Complex.
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Please find specimen requirement specifications above.
All submitted specimens must be sent at room temperature. DO NOT ship on ice.
Specimens must be packaged to prevent breakage and absorbent material must be included in the package to absorb liquids in the event that breakage occurs. Also, the package must be shipped in double watertight containers (e.g. a specimen pouch + the shipping company’s diagnostic envelope).
To request a sample collection kit, please click here or email medgenomics@uabmc.edu to complete the specimen request form.
Click here for the Fresh/Frozen Tumor Submission Checklist
Please contact the MGL (via email at medgenomics@uabmc.edu, or via phone at 205-934-5562) prior to sample shipment and provide us with the date of shipment and tracking number of the package so that we can better ensure receipt of the samples.
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Form for Customs
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About
{slide=Disorder Background}Tuberous sclerosis complex (TSC) is a rare autosomal dominant disorder involving abnormalities of the skin, brain, kidney, heart and lungs. CNS tumors are seen commonly in patients with TSC. Heterozygous pathogenic variants can be identified in 75%-90% of individuals who meet the clinical diagnostic criteria for TSC (Northrup H. et al, 2013: Ped. Neurology 49:243-4). Among those in whom a pathogenic variant can be identified, pathogenic variants in TSC1 and TSC2 are found in 31% and 69% of cases, respectively (Ozgur et al. Eur J Hum Genet. 2005;13:731–41)
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The Tuberous Sclerosis Complex panel by NGS involves the simultaneous sequencing of 2 genes: TSC1 and TSC2. The average coverage is >1600x with >99% of the coding region covered at ≥350x and >99% ≥200x. The minimum coverage for any additional areas is >30x. This allows for detection of very low level mosiacism by sequencing (as low as 8% of the alleles in all regions analyzed by NGS; >99% of the coding region does provide deeper coverage with the ability to identify substitution variants as low as 3% of the alleles). Variant and copy number calls are made using a unique bioinformatics pipeline detecting all types of variants including single nucleotide substitutions, indels and frameshifts caused by deletion or duplication up to 112bp. Deletion/duplication analysis for TSC1 and TSC2 is included in this test, as such variants are a part of the variant spectrum for these conditions.
Relevant family members of a proband with any (novel or previously identified) variant of unknown significance are offered free of charge targeted analysis as long as accurate phenotypic data are provided by a health care professional to enhance the interpretation. There is no limitation to the number of relatives that can be tested free of charge.
Analysis can be performed on fresh or frozen affected tissue via next-generation sequencing.
REFERENCES available here.
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For more information, test requisition forms, or sample collection and mailing kits, please call: 205-934-5562.