Classic view of this page
Rhabdoid Tumor Predisposition Syndrome NGS Panel
Clinical Genetic Test
Help
offered by
UAB Medical Genomics Laboratory
View lab's test page
LinkOut
GTR Test Accession: Help GTR000551656.5
CANCERINHERITED DISEASEINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2023-06-07
View version history
Last annual review date for the lab: 2023-06-07 Past due LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation; Risk Assessment
Conditions (5): Help
Rhabdoid tumor predisposition syndrome 1; Atypical teratoid rhabdoid tumor; Malignant rhabdoid tumor, somatic more...
Genes (2): Help
SMARCA4 (19p13.2); SMARCB1 (22q11.23)
Methods (2): Help
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
Patients with rhabdoid tumors with or without confirmed SMARCB1-loss identified …
Clinical validity: Help
Not provided
Clinical utility: Help
Establish or confirm diagnosis
Ordering Information
Offered by: Help
UAB Medical Genomics Laboratory
View lab's website
View lab's test page
Test short name: Help
RT-NG
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
RT-NG
View other test codes
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Lab contact: Help
Brandon Shaw, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
brandonshaw@uabmc.edu
205-934-1520
Contact Policy: Help
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
How to Order: Help
Additional information regarding the specific details needed for test submission can be found on our website
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Result interpretation
Test development: Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
The Rhabdoid Tumor Predisposition Syndrome by NGS involves sequencing of SMARCB1 [and SMARCA4 when testing on blood, fresh/frozen tumor, 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 … View more
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Conditions Help
Total conditions: 5
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 2
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument *
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Risk Assessment
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)

Target population: Help
Patients with rhabdoid tumors with or without confirmed SMARCB1-loss identified by immunohistochemistry staining
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
In order to further investigate a VUS, the laboratory will: 1. Review software predictions (SIFT, PolyPhen, etc) 2. Review internal database to compare against alterations seen in >10,000 alleles previously tested in laboratory 3. Offer free of charge family studies for any individuals that would provide useful information for interpretation

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Yes.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Clinical validity, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Analytical sensitivity of next generation sequencing is typically validated using a minimum of 20 DNA samples. No false positives were detected during analysis. The average coverage is ~1500x with 93.1% of the coding regions ≥350x and 96.67% ≥200x. The minimum coverage for any additional areas is >30x. Variant and copy … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations Help
Alamut, Google search, PolyPhen, SIFT, evolutionary consevation, grantham score, splicing prediction software, disorder specific databases as necessary

Laboratory's policy on reporting novel variations Help
The laboratory will issue an interim report summarizing what is currently known about the variant and familial studies will be offered. Upon completion of the familial studies, a final report will be provided with a conclusion of what is suspected for the alteration.
Recommended fields not provided:
Test Confirmation, Assay limitations, Description of internal test validation method, Citations for Analytical validity, PT Provider, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.