Tuberous Sclerosis Complex NGS panel
- GTR Test IDHelpEach Test is a specific, orderable test from a particular laboratory, and is assigned a unique GTR accession number. The format is GTR00000001.1, with a leading prefix 'GTR' followed by 8 digits, a period, then 1 or more digits representing the version. When a laboratory updates a registered test, a new version number is assigned.: GTR000551658.6
- Last updated: 2023-06-07
- Test version history
Clinical testHelpIn the U.S., clinical tests must be performed under CLIA certification. When a lab uses the same methods for a test in both clinical and research settings, the test appears as two separate GTR records. for Tuberous sclerosis 1
Offered by Medical Genomics Laboratory
Overview
Test name
HelpThe name the laboratory assigns the test. Used as the default title of the page specific to the test.Tuberous Sclerosis Complex NGS panel (TSCP-NG)
This is a clinical test intended for HelpPurposes or indications for the test. Lab-provided.: Diagnosis, Mutation Confirmation, Risk Assessment
Click Indication tab for more information.
Additional information regarding the specific details needed for test submission can be found on our website
Order URL HelpLink to the laboratory webpage with information about how to order this test. Please note that clicking on this link will open a new tab in your internet browser.: https://www.uab.edu/medicine/genetics/medical-genomics-laboratory/testing-services/tuberous-sclerosis
Specimen source
Methodology
HelpThe assay's major method category (biochemical, cytogenetic or molecular genetics); method category (i.e. enzyme assay, chromosome breakage studies, targeted mutation analysis); methodology (i.e. the name of the method used) and instruments used when performing this test.- 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)
Establish or confirm diagnosis
Clinical validity
HelpHow consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. Lab-provided.Not provided
Testing strategy
HelpThe lab's suggested sequence of ordering tests based on clinical scenarios. It may include information on: reflex testing including each test component, and scenarios which prompt additional components of testing; whether lab communicates interim results or automatically proceeds to further analyses; and if any components are performed in another laboratory.The Tuberous Sclerosis Complex panel by NGS involves the simultaneous sequencing of 2 genes: TSC1 and TSC2. The average coverage is >2000x with >99% of the coding region covered at ≥350x and >99.4% ≥200x. The minimum coverage for any additional areas is >30x. This allows for detection of very low level mosiacism by sequencing (as low as 8% of the alleles in all regions analyzed by NGS; >99% of the coding region does provide deeper coverage with the ability to identify substitution variants as low as 3% of the alleles). 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 or duplication up to 112bp. Deletion/duplication analysis for TSC1 and TSC2 is included in this test, as such variants are a part of the variant spectrum for these conditions. Validation of the full panel included, besides substitutions (missense, nonsense, splice variants), the most challenging variants such as insertions/deletions/duplications of 1-112bp and one-to-multiple exon deletions/duplications. The analytical sensitivity of our NGS testing approach was 100% for substitutions as well as insertion/deletions up to 112bp. This panel has not yet been validated to identify deletions/duplications >112bp and <1 exon, but such variants have not yet been found in the UAB cohort, and therefore are likely very rare. The panel has been validated for the detection of germline (heterozygous) single-exon deletions/duplications as well as multi-exon deletions/duplications, however mosaic single-exon deletion/duplications validation is still pending. Relevant family members of a proband with any (novel or previously identified) variant of unknown significance are offered free of charge targeted analysis as long as accurate phenotypic data are provided by a health care professional to enhance the interpretation. There is no limitation to the number of relatives that can be tested free of charge. Analysis can be performed on fresh or frozen affected tissue via next-generation sequencing. 000 Additional information regarding the specific details needed for test submission can be found on our website
Test services
HelpLaboratory's order or catalog code for the test (used in the order requisition form).- 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.