Non-NF1 RASopathy 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.: GTR000551628.6
- 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 Noonan syndrome
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.Non-NF1 RASopathy NGS Panel (NNP-NG)
This is a clinical test intended for HelpPurposes or indications for the test. Lab-provided.: Diagnosis
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.: http://www.genetics.uab.edu/medgenomics
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)
- Applied Biosystems 3730 capillary sequencing instrument
- CSequence analysis of the entire coding region
- Next-Generation (NGS)/Massively parallel sequencing (MPS)
- Other
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 Non-NF1 Rasopathy panel by NGS involves the simultaneous sequencing of 17 genes: SPRED1, PTPN11, PPP1CB, BRAF, CBL, HRAS, KRAS, LZTR1, NRAS, MAP2K1, MAP2K2, RAF1, RIT1, RASA2, SHOC2, SOS1 and SOS2. The test uses a customized and optimized set of Agilent Haloplex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 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 >2000x with >98.5% of the coding region ≥350x and 99.3% ≥200x, allowing detection of very low-level mosaicism, down to 3-5% variant allele fraction respectively (regions covered by ≥350x respectively ≥200x) with 95% confidence. 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 mutations including single nucleotide substitutions, indels, and frameshifts caused by deletion/ duplication up to 112bp. Deletion/duplication analysis for LZTR1 and SPRED1 is included in this test, as such mutations are a part of the mutation spectrum for these conditions. Deletion/duplication analysis for the other 15 genes on this panel is not offered as current empirical and biological evidence is not sufficient to allow the conclusion that an altered copy number of these genes is a mechanism critical for the phenotype associated with the Rasopathies. Nevertheless, deletion/duplication analysis through aCGH analysis can be offered as a reflex test through the UAB cytogenetic laboratory (directed by Drs. A. Carroll and F. Mikhail). 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. 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
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