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Known Mutation Testing- NGS
Clinical Genetic Test
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offered by
UAB Medical Genomics Laboratory
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GTR Test Accession: Help GTR000576339.3
SYNDROMIC DISEASEINHERITED DISEASENERVOUS SYSTEM ... View more
Last updated in GTR: 2023-06-07
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Last annual review date for the lab: 2023-06-07 Past due LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Conditions (9): Help
Neurofibromatosis, type 1; Neurofibromatosis, familial spinal; Neurofibromatosis, type 2 more...
Genes (1): Help
NF1 (17q11.2)
Methods (1): Help
Molecular Genetics - Sequence analysis of select exons: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Target population: Help
Individuals with a confirmed familial variant concerned about their risk …
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
UAB Medical Genomics Laboratory
View lab's website
View lab's test page
Test short name: Help
KT2-NG
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
KT2-NG
View other test codes
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Lab contact: Help
Brandon Shaw, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
brandonshaw@uabmc.edu
205-934-1520
How to Order: Help
Additional information regarding the specific details needed for test submission can be found on our website
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Test additional service: Help
Custom Prenatal Testing
    OrderCode: PT2
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
Targeted Next Generation sequencing for a known familial variant or for a variant that was seen in somatic tissue to be confirmed if present in a germline tissue.
View citations (9)
  • Exhaustive mutation analysis of the NF1 gene allows identification of 95% of mutations and reveals a high frequency of unusual splicing defects. Messiaen LM, et al. Hum Mutat. 2000;15(6):541-55. doi:10.1002/1098-1004(200006)15:6<541::AID-HUMU6>3.0.CO;2-N. PMID: 10862084.
  • Pitfalls of automated comparative sequence analysis as a single platform for routine clinical testing for NF1. Messiaen LM, et al. J Med Genet. 2005;42(5):e25. PMID: 15863657.
  • Spectrum of single- and multiexon NF1 copy number changes in a cohort of 1,100 unselected NF1 patients. Wimmer K, et al. Genes Chromosomes Cancer. 2006;45(3):265-76. doi:10.1002/gcc.20289. PMID: 16283621.
  • Upadhyaya M, Huson SM, Davies M, Thomas N, Chuzhanova N, Giovannini S, Evans DG, Howard E, Kerr B, Griffiths S, Consoli C, Side L, Adams D, Pierpont M, Hachen R, Barnicoat A, Li H, Wallace P, Van Biervliet JP, Stevenson D, Viskochil D, Baralle D, Haan E, Riccardi V, Turnpenny P, Lazaro C, Messiaen L. An absence of cutaneous neurofibromas associated with a 3-bp inframe deletion in exon 17 of the NF1 gene (c.2970-2972 delAAT): evidence of a clinically significant NF1 genotype-phenotype correlation. Am J Hum Genet. 2007;80(1):140-51. doi:10.1086/510781. Epub 2006 Dec 08. PMID: 17160901.
  • Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5' splice-site disruption. Wimmer K, et al. Hum Mutat. 2007;28(6):599-612. doi:10.1002/humu.20493. PMID: 17311297.
  • Maertens O, De Schepper S, Vandesompele J, Brems H, Heyns I, Janssens S, Speleman F, Legius E, Messiaen L. Molecular dissection of isolated disease features in mosaic neurofibromatosis type 1. Am J Hum Genet. 2007;81(2):243-51. doi:10.1086/519562. Epub 2007 Jun 20. PMID: 17668375.
  • Mosaic type-1 NF1 microdeletions as a cause of both generalized and segmental neurofibromatosis type-1 (NF1). Messiaen L, et al. Hum Mutat. 2011;32(2):213-9. doi:10.1002/humu.21418. PMID: 21280148.
  • The diagnostic evaluation and multidisciplinary management of neurofibromatosis 1 and neurofibromatosis 2. Gutmann DH, et al. JAMA. 1997;278(1):51-7. PMID: 9207339.
  • Messiaen LM and Wimmer K (2008) NF1 Mutational Spectrum, in Kaufmann D (ed): Neurofibromatoses. Monogr Hum Genet. Basel, Karger, Vol 16:63-77
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Contact policy
Conditions Help
Total conditions: 9
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 1
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 select exons
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Recurrence; Risk Assessment
Target population: Help
Individuals with a confirmed familial variant concerned about their risk to inherit the variant.
View citations (1)
  • The diagnostic evaluation and multidisciplinary management of neurofibromatosis 1 and neurofibromatosis 2. Gutmann DH, et al. JAMA. 1997;278(1):51-7. PMID: 9207339.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
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? Help
Yes. Clinical information regarding the parental types is required for free of charge testing

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Research:
Is research allowed on the sample after clinical testing is complete? Help
Further studies may be performed for other disorders that may also help to explain the patient's phenotype.
Recommended fields not provided:
Clinical validity, Clinical utility, Sample negative report, Sample positive report
Technical Information
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Testing is performed in duplo by 2 independent technicians. As this is targeted testing, the proband is run as a positive control as well.
View citations (1)
  • N/A
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Alternative Assessment

PT Provider: Help
internally blinded samples
VUS:
Software used to interpret novel variations Help
Alamut, Google search, PolyPhen, SIFT, evolutionary consevation, grantham score, splicing prediction software, disorder specific databases as necessary

Laboratory's policy on reporting novel variations Help
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, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
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.