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GTR Home > Tests > Rhabdoid Tumor Predisposition Syndrome NGS Panel

Overview

Test order codeHelp: RT-NG

Test name

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Rhabdoid Tumor Predisposition Syndrome NGS Panel (RT-NG)

Purpose of the test

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This is a clinical test intended for Help: Diagnosis, Mutation Confirmation, Risk Assessment

Condition

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How to order

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Additional information regarding the specific details needed for test submission can be found on our website
Order URL Help: https://www.uab.edu/medicine/genetics/medical-genomics-laboratory/testing-services/rhabdoid-tumor-predisposition-syndrome/rhabdoid-tumor-predisposition-syndrome-by-ngs

Specimen source

Cord blood
Fibroblasts
Fresh tissue
Frozen tissue
Isolated DNA
Peripheral (whole) blood
Saliva
Skin

Methodology

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Molecular Genetics
DDeletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
CSequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)

Summary of what is tested

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Clinical utility

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Establish or confirm diagnosis

Clinical validity

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Not provided

Testing strategy

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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 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 ~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 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. 000 Additional information regarding the specific details needed for test submission can be found on our website

Test services

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  • Clinical Testing/Confirmation of Mutations Identified Previously
  • Custom Deletion/Duplication Testing
  • Result interpretation

IMPORTANT NOTE: NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in the 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.