RASopathy NGS Panel - Clinical Genetic Test - GTR

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RASopathy NGS Panel

Clinical Genetic Test

offered by

Medical Genomics Laboratory

View lab's test page

GTR Test Accession: GTR000551630.6

INHERITED DISEASEDYSMORPHOLOGYMUSCULOSKELETAL ... View more

Last updated in GTR: 2023-06-07

Last annual review date for the lab: 2023-06-07

At a Glance

Test purpose:

Diagnosis

Conditions (8):

Noonan syndrome; Cardiofaciocutaneous syndrome 1; Costello syndrome; ...

Genes (18):

BRAF (7q34), CBL (11q23.3), HRAS (11p15.5), KRAS (12p12.1), LZTR1 (22q11.21), ...

Methods (2):

Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...

Target population:

Patients with clinical features suggestive of either NS, NSML, CFC, …

Clinical validity:

Not provided

Clinical utility:

Establish or confirm diagnosis

Ordering Information

Offered by:

Medical Genomics Laboratory
View lab's website
View lab's test page

Test short name:

RAS-NG

Specimen Source:

Cord blood
Fresh tissue
Frozen tissue
Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician
Nurse Practitioner
Physician Assistant

Test Order Code:

RAS-NG
View other test codes

CPT codes:

81442
81479

**AMA CPT codes notice

Lab contact:

Brandon Shaw, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
brandonshaw@uabmc.edu
205-934-1520
Bryce Brown, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
ebfincher@uabmc.edu
205-934-5525

Contact Policy:

Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.

How to Order:

Additional information regarding the specific details needed for test submission can be found on our website
Order URL

Test service:

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

Informed consent required:

Based on applicable state law

Test strategy:

The Expanded NF1-Rasopathy panel by NGS involves the simultaneous sequencing of 18 genes: NF1, SPRED1, LZTR1, PTPN11, PPP1CB, BRAF, CBL, HRAS, KRAS, NRAS, MAP2K1, MAP2K2, RAF1, RIT1, RASA2, SHOC2, SOS1 and SOS2. The test uses the same approach as detailed previously (see: NF1-only by NGS). The average coverage is ~2000x … The Expanded NF1-Rasopathy panel by NGS involves the simultaneous sequencing of 18 genes: NF1, SPRED1, LZTR1, PTPN11, PPP1CB, BRAF, CBL, HRAS, KRAS, NRAS, MAP2K1, MAP2K2, RAF1, RIT1, RASA2, SHOC2, SOS1 and SOS2. The test uses the same approach as detailed previously (see: NF1-only by NGS). The average coverage is ~2000x with >98.5% of the coding region ≥350x and >99.4% ≥200x, allowing detection of very low-level mosaicism, down to 3-5% variant allele fraction 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 variants including single nucleotide substitutions, indels, and frameshifts caused by deletion/ duplication up to 112bp. Deletion/duplication analysis for NF1, SPRED1, and LZTR1 is included in this test, as such variants are a part of the variant 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.
Based on >15 years of experience with comprehensive RNA-based NF1 testing, we designed the customized and optimized NGS NF1-component of the assay to comprise all regions encountered through analysis of >15,000 unrelated individuals including >8,100 NF1-variant-positive individuals carrying 1 out of >3,100 different unique NF1 variants identified in the UAB MGL cohort. Included in the NGS assay are the regions covering >65 different deep intronic splice variants (which reside beyond the +/-50 intronic base pairs that flank all exons). Validation of the full panel included, besides substitutions (missense, nonsense, splice variants), the most challenging variants such as insertions/deletions/duplications of 1-112bp (~25% of the UAB NF1 cohort) and one-to-multiple exon deletions/duplications (~2.8% of the UAB NF1 cohort). 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. Single exon deletions/duplications are present in ~0.45% of NF1-positive patients from the UAB cohort with 9% of these individuals being mosaic (~0.045% of all in the UAB NF1-positive cohort). Detection of Alu/LINE insertions, identified in 0.25% of patients from the UAB NF1-positive cohort, has not yet been validated using the current NGS approach.
With the largest dataset of NF1 genotypes matched with phenotypes, any genotype-phenotype correlations identified will be reported in real time. Confirmatory testing of reportable variants is performed using orthogonal methods as needed. For novel NF1 variants of unknown significance, we offer free of charge targeted RNA-based testing to assess the effect of the variant on splicing and enhance the correct classification/ interpretation of this novel variant. Relevant family members of a proband with a (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 in such families.
Mosaicism is often present in sporadic patients with an NF1 microdeletion and has important repercussions for counseling. Free of charge evaluation by FISH analysis on 200 interphase chromosomes is offered free of charge in such cases. View more

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test development

Conditions

Total conditions: 8

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 18

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 2

Method Category

Test method

Instrument

Deletion/duplication analysis

Multiplex Ligation-dependent Probe Amplification (MLPA)

Applied Biosystems 3730 capillary sequencing instrument

Sequence analysis of select exons

Next-Generation (NGS)/Massively parallel sequencing (MPS)

Other

Clinical Information

Test purpose:

Diagnosis

Clinical utility:

Establish or confirm diagnosis

View citations (1)

https://www.uab.edu/medicine/genetics/medical-genomics-laboratory/testing-services/nf1-legius-syndrome-and-rasopathies/ras-ng

Target population:

Patients with clinical features suggestive of either NS, NSML, CFC, NF1, Legius syndrome or Noonan-like syndrome; patients with a clinical diagnosis of any of these syndromes that previously tested negative in a subset of the genes included in this panel; patients with a diagnosis of Costello syndrome but no HRAS … View more

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
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?
Yes.

Will the lab re-contact the ordering physician if variant interpretation changes?
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:

Tests performed
Entire test performed in-house

Analytical Validity:

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 ~2000x with >98.5% of the coding region ≥350x and >99.4% ≥200x, allowing detection of very low-level mosaicism, down to 3-5% variant allele fraction … View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Alternative Assessment

VUS:

Software used to interpret novel variations
Alamut, Google search, PolyPhen, SIFT, evolutionary consevation, grantham score, splicing prediction software, disorder specific databases as necessary

Laboratory's policy on reporting novel variations
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:

Category: Not Applicable

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View MAP2K1 variations in ClinVar

View PTPN11 variations in ClinVar

RefSeqGene

Consumer resources:

Genetic Alliance

MedlinePlusGenetics (GHR)

NCATS Office of Rare Diseases Research (GARD)

MedlinePlus

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.