Rhabdoid Tumor Predisposition Syndrome by Next-Generation Sequencing (RT-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
- Tumor specimens: A minimum of two anatomically distinct tumor specimens is recommended; however, a single tumor specimen may be submitted. Tumor specimens should contain at least 70% tumor content and greater than 80% nucleated cells.
- Flash-frozen tumor shipped on dry ice
- Fresh tumor or affected-tissue biopsy immersed in sterile culture media, such as PBS or RPMI
- Formalin-fixed, paraffin-embedded tumor block for SMARCB1 analysis only: specimen should have a surface area of at least 5 mm2, or include three to six loose paraffin curls measuring 30–50 µm thick; do not submit slides
Turnaround Time
- Blood, saliva, or DNA: Average of 30 working days
- Fresh or frozen tumor or FFPE tumor block: Average of 50 working days
Price, CPT Codes, and Z Code
- Institutional/self-pay price for blood, saliva, or DNA: $1,000 USD
- Institutional/self-pay price for fresh or frozen tumor or FFPE tumor block: $1,500 USD
- CPT codes: 81479 × 2
- Z code: ZB68B
Candidates for Testing
Patients with rhabdoid tumors, with or without confirmed SMARCB1 loss identified by immunohistochemistry.
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
Rhabdoid tumors are rare, aggressive childhood cancers that most commonly develop in the kidney as malignant rhabdoid tumors or in the central nervous system as atypical teratoid/rhabdoid tumors. These tumors may occur sporadically or as part of hereditary Rhabdoid Tumor Predisposition Syndrome. Compared with isolated sporadic rhabdoid tumors, the hereditary form is associated with an increased risk of developing multiple tumors at younger ages and schwannomas that typically present during adulthood. Germline pathogenic variants in both SMARCB1 and SMARCA4 have been associated with Rhabdoid Tumor Predisposition Syndrome.
Test Description
The Rhabdoid Tumor Predisposition Syndrome by NGS assay includes sequencing of SMARCB1 and, for blood, saliva, and extracted DNA specimens, SMARCA4. Deletion/duplication analysis of the entire coding region of SMARCB1 is also included.
The test uses customized target enrichment followed by Illumina paired-end sequencing. Each coding exon plus approximately 50 bp of flanking intronic sequence is analyzed. The 5′ and 3′ untranslated regions are not included. Sanger sequencing is performed as needed.
Average sequencing coverage is approximately 1,100×, with 91% of coding regions covered at ≥350× and 95% covered at ≥200×. The minimum coverage for remaining regions is greater than 30×.
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.
View references for this testing.
Other Related Test Options
For more information, test requisition forms, or collection kits, please contact the UAB Medical Genomics Laboratory at 205-934-5562 or medgenomics@uabmc.edu.