Peripheral Nerve Sheath Tumor Panel by Next-Generation Sequencing (PNT-NG)

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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: 81408, 81406, 81405, and 81479 × 4
• Z code: ZB6AE

Candidates for Testing

Patients presenting with both neurofibromas and schwannomas, or peripheral nerve sheath tumors with mixed or unconfirmed cellularity, with minimal additional findings meeting diagnostic criteria for a specific condition.

Specimen Shipping and Handling

Please refer to the specimen requirements listed above.

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

• Test Requisition Form

About

Disorder Background

Peripheral nerve sheath tumors develop from Schwann cells, which cover the peripheral nerves. These tumors may be benign or malignant, although approximately 90% are benign. Nerve sheath tumors include neurofibromas and schwannomas. They may occur as solitary lesions; however, the presence of multiple tumors may indicate a hereditary predisposition.

Neurofibromas are common benign tumors composed of a complex mixture of cell types. The presence of two or more cutaneous, subcutaneous, or plexiform neurofibromas is a diagnostic feature of neurofibromatosis type 1. Two NF1 hits are found specifically in the Schwann cells. Cutaneous neurofibromas do not undergo malignant transformation, while subcutaneous and plexiform neurofibromas may undergo malignant transformation.

Schwannomas are more homogeneously composed benign tumors. Multiple schwannomas may indicate NF2-related schwannomatosis or another schwannomatosis syndrome. The location and type of schwannomas may differ among these conditions, although overlap exists, and genetic characterization may help distinguish between them.

Some schwannomas may mimic neurofibromas and vice versa. These include myxoid schwannomas and hybrid neurofibromas/schwannomas.

A germline KRAS variant, p.K5E, has been described in a patient with multiple diffuse schwannomas. Another KRAS variant, p.G12S, was identified in one of 40 sporadic schwannomas.

Several patients with Noonan syndrome with multiple lentigines who also met diagnostic criteria for NF1 have been described with a variant in PTPN11 but not NF1. These patients had plexiform neurofibromas, large dumbbell spinal tumors, and hypertrophic peripheral nerves.

Genes included in this panel are KRAS, LZTR1, NF1, NF2, PTPN11, and SMARCB1.

Test Description

The Peripheral Nerve Sheath Tumor Panel by NGS involves simultaneous sequencing of six genes: NF1, NF2, KRAS, LZTR1, PTPN11, and SMARCB1.

The test uses a customized and optimized set of Agilent HaloPlex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 300 bp paired-end Illumina sequencing chemistry. Each coding exon plus approximately 50 bp of flanking intronic sequence is simultaneously sequenced. The 5′ and 3′ untranslated regions are not included.

The average coverage is greater than 1,600×, with more than 98% of the coding region covered at ≥350× and more than 99% covered at ≥200×. The minimum coverage for additional regions is greater than 30×. This allows detection of low-level mosaicism down to approximately 3% variant allele fraction in regions with sufficient coverage.

Variant and copy-number calls are made using a specialized bioinformatics pipeline that detects single-nucleotide substitutions, insertions, deletions, and frameshifts caused by deletions or duplications up to 112 bp.

Deletion/duplication analysis of NF1, NF2, SMARCB1, and LZTR1 is included because copy-number variants are part of the disease-associated variant spectrum for these genes. Deletion/duplication analysis is not offered for PTPN11 or KRAS because current empirical and biological evidence is insufficient to establish altered copy number as a critical disease mechanism for these conditions.

Validation of the full panel included substitutions, splice variants, insertions, deletions, duplications of 1–112 bp, and single- and multi-exon deletions and duplications. The analytical sensitivity of the NGS approach was 100% for substitutions and insertions or deletions up to 112 bp.

Relevant family members of a proband with a novel or previously identified variant of uncertain significance may be offered targeted analysis at no charge when accurate phenotypic information is provided by a healthcare professional.

For patients with overlapping phenotypes, genetic analysis of associated tumors may help establish a diagnosis. Depending on the tumor findings, tumor-based analysis may support a diagnosis of schwannomatosis, chromosome 22 involvement, or mosaic NF2-related schwannomatosis.

For patients specifically suspected of having mosaic or segmental NF1, RNA-based NF1 testing may be the preferred initial approach. Please review the RNA-Based NF1 Testing on Blood page for additional information.

Tumor-based analysis may be performed on fresh or frozen tumor specimens by next-generation sequencing. For formalin-fixed, paraffin-embedded tumor specimens, please review the available Sanger sequencing options.

View references for this testing .

Other Related Test Options

• Schwannomatosis/Multiple Schwannomas Panel by Next-Generation Sequencing (SCH-NG)
• Meningiomatosis/Multiple Meningioma Panel by Next-Generation Sequencing (MEN-NG)

For more information, test requisition forms, or collection kits, please contact the UAB Medical Genomics Laboratory at 205-934-5562 or medgenomics@uabmc.edu.

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