Schwannomatosis/Multiple Schwannoma Panel by Next-Gen Sequencing (SCH-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)
- A minimum of 2 anatomically distinct tumor samples is suggested, however, a single tumor can be provided. Tumor specimens should contain at least 70% pure tumor content and >80% nucleated cells.
- Flash frozen tumor sent on dry ice
- Fresh tumor or affected tissue biopsy, immersed in sterile culture media (PBS/RPMI)
- Tumor block - should have a surface area ≥5mm squared or the specimen contains at least 3-6 loose paraffin curls (no slides) that are 30-50 microns thick.
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Average = 30 working days for blood, saliva, or DNA
Average = 40 working days for fresh/frozen tumor or tumor block*
*TAT will be extended by 20 working days if reflex to Sanger sequencing is needed due to NGS failure.
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$1,500 for blood, saliva, or DNA (USD – institutiona/self-pay price)
$2,500 for fresh/frozen tumor or tumor block (USD – institutional/self-pay)
CPT: 81406, 81405, and 81479 (x3)
Z codes: ZB67Y
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{slide=Candidates for Testing}
Patients with multiple schwannomas with or without vestibular schwannomas. This testing approach is developed to diagnose mosaic NF2, classic NF2, Schwannomatosis, and mosaic schwannomatosis
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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}Schwannomas are nerve sheath tumors which are nearly always benign but can cause significant pain. Isolated schwannomas are common in the population, but the development of multiple non-intradermal schwannomas (in the absence of bilateral vestibular schwannomas, congenital cataracts or ependymomas, typically associated with constitutional NF2) as typically seen in schwannomatosis patients, is rare. The presence of multiple non-intradermal schwannomas, in the absence of a family history of NF2-related schwannomatosis, can be found in individuals with mosaic NF2-related schwannomatosis, or in individuals carrying germline variants in either SMARCB1 or LZTR1.
People with LZTR1- and SMARCB1-related schwannomatosis do not typically develop bilateral vestibular schwannomas, ependymomas, meningiomas (typically associated with NF2-related schwannomatosis), nor neurofibromas or astrocytomas (associated with NF1). However, significant clinical overlap with NF2-related schwannomatosis exists: some SMARCB1-positive patients have developed meningiomas or a unilateral vestibular schwannoma; and some LZTR1-positive patients have been reported with a unilateral/bilateral vestibular schwannoma. Whereas schwannomatosis presents with variable expressivity, penetrance for NF2-related schwannomatosis is close to 100%, whereas non-penetrance is well documented in LZTR1- and SMARCB1-related schwannomatosis, although the exact frequency is not known.
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The Schwannomatosis/Multiple Schwannoma Panel by NGS involves the simultaneous sequencing of 3 genes: NF2, SMARCB1, and LZTR1. The test uses an extensively customized and optimized set of Agilent HaloPlex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 300bp paired-end Illumina sequencing chemistry. Each coding exon plus ~50bp of flanking intronic sequence are simultaneously sequenced. 5’ and 3’ untranslated sequences are not included. The average coverage is >1600x with 100% of the coding region ≥350x.This allows for detection of very low level mosaicism by sequencing (as low as 3% in the coding region with 95% confidence). Sanger sequencing will be utilized as needed.
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/ duplication up to 112bp. Deletion/duplication analysis for NF2, SMARCB1, and LZTR1 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.
For patients presenting with phenotypes that may overlap with these disorders, genetic analysis of the associated tumors may be beneficial in determining a diagnosis.
Tumor-based analysis can be performed on fresh or frozen tumor via next-generation sequencing. If the tumor specimen has been formalin-fixed paraffin embedded (FFPE) tumor, please review our Sanger sequencing.
REFERENCES available here.
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Other related test options:
- Next-Gen Sequencing and Deletion/Duplication analysis of NF2 only (NF2-NG)
- Rhabdoid Tumor Predisposition Syndrome by Next-Gen Sequencing (RT-NG)
For more information, test requisition forms, or sample collection and mailing kits, please call: 205-934-5562.