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Segmental Overgrowth Disorders - NGS panel
Clinical Genetic Test
Help
offered by
Amsterdam UMC Genome Diagnostics
View lab's test page
LinkOut
GTR Test Accession: Help GTR000552540.4
INHERITED DISEASEDYSMORPHOLOGYMUSCULOSKELETAL ... View more
Last updated in GTR: 2021-04-08
View version history
Last annual review date for the lab: 2024-04-16 LinkOut
At a Glance
Test purpose: Help
Diagnosis
Conditions (4): Help
CLOVES syndrome; Megalencephaly-capillary malformation-polymicrogyria syndrome; Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 more...
Genes (13): Help
AKT1 (14q32.33); AKT3 (1q43-44); GNA11 (19p13.3); GNAQ (9q21.2); HRAS (11p15.5) more...
Methods (1): Help
Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Target population: Help
Not provided
Clinical validity: Help
Not provided
Clinical utility: Help
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Amsterdam UMC Genome Diagnostics
View lab's website
View lab's test page
Test short name: Help
SO
Specimen Source: Help
  • Buccal swab
  • Cell culture
  • Fibroblasts
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Peripheral (whole) blood
  • Saliva
Who can order: Help
  • Health Care Provider
  • Licensed Physician
Test Order Code: Help
D00454
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
To order a test, complete and submit the test from our website. Please visit our website for the latest panel update.
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
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
No
Test strategy: Help
This panel targets 8 genes associated with overgrowth. NGS is performed with high coverage (>500x). The bioinformatic pipeline is designed to detect low mosaicism. Both an affected tissue and a peripheral blood sample is requested for comparative analysis.
View citations (1)
  • Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, Warman ML. Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Am J Hum Genet. 2012;90(6):1108-15. doi:10.1016/j.ajhg.2012.05.006. Epub 2012 May 31. PMID: 22658544.
Pre-test genetic counseling required: Help
Yes
Post-test genetic counseling required: Help
Yes
Recommended fields not provided:
Lab contact for this test
Conditions Help
Total conditions: 4
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 13
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 1
Method Category Help
Test method Help
Instrument *
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)
  • Kurek KC, Luks VL, Ayturk UM, Alomari AI, Fishman SJ, Spencer SA, Mulliken JB, Bowen ME, Yamamoto GL, Kozakewich HP, Warman ML. Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome. Am J Hum Genet. 2012;90(6):1108-15. doi:10.1016/j.ajhg.2012.05.006. Epub 2012 May 31. PMID: 22658544.

Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
The 5-classes classification method (Alamut)

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Not provided.
Recommended fields not provided:
Clinical validity, Target population, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Will the lab re-contact the ordering physician if variant interpretation changes?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Platform:
Illumina MiSeq
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This NGS panel is designed to detect low mosaicism. Sequencing is done with a high coverage (>500x). The bioinformatic pipeline is modified to make detection of low mosaic variants possible. Mosaicism as low as 1% is detected.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
European Molecular Genetics Quality Network, EMQN
VUS:
Software used to interpret novel variations Help
Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions

Laboratory's policy on reporting novel variations Help
The laboratory reports class 3 (unknown pathogenicity), class 4 (likely pathogenic) and class 5 (certainly pathogenic) variants.
Recommended fields not provided:
Test Confirmation, Assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: Not Applicable
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.