Rhabdoid Tumor Predisposition Syndrome by Next-Gen Sequencing (RT-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. (SMARCB1 only)
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{slide=Turnaround Time}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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$1000 for blood, saliva, or DNA (USD – institutional/self-pay price)
$1,500 for fresh/frozen tumor or tumor block (USD – institutional/self-pay)
CPT: 81479 (x2)
Z code: ZB68B
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{slide=Candidates for Testing}
Patients with rhabdoid tumors with or without confirmed SMARCB1-loss identified by immunohistochemistry staining.
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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}Rhabdoid tumors are rare, aggressive childhood cancers that most often develop in the kidney (Malignant Rhabdoid Tumor, MRT) and central nervous system (Atypical Teratoid/Rhabdoid Tumor, AT/RT). These lesions can occur spontaneously or as part of hereditary Rhabdoid Tumor Predisposition Syndrome (RTPS). In comparison to sporadic isolated rhabdoid tumors, the syndromic form is associated with an increased risk of developing multiple tumors at younger ages and schwannomas (benign nerve sheath tumors) that present primarily in adulthood. (Sevenet N. et al, 1999: Hum. Mol. Genet. 8:2359-68). Both SMARCB1 and SMARCA4 have been associated with rhabdoid tumor predisposition syndrome.
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{slide=Test Description}The Rhabdoid Tumor Predisposition Syndrome by NGS involves sequencing of SMARCB1 [and SMARCA4 when testing on blood, saliva, or extracted DNA] as well as deletion/duplication analysis of the entire coding region of SMARCB1. 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. Sanger sequencing will be utilized as needed.
The average coverage is ~1100x with 91% of the coding regions ≥350x and 95% ≥200x. The minimum coverage for any additional areas is >30x. 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.
REFERENCES available here.
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Other related test options:
For more information, test requisition forms, or sample collection and mailing kits, please call: 205-934-5562.