NF1/SPRED1 Next Generation Sequencing and Deletion/Duplication
GTR Test Accession: Help GTR000501087.7
INHERITED DISEASEDYSMORPHOLOGYINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2023-06-07
Last annual review date for the lab: 2023-06-07 LinkOut
At a Glance
Diagnosis; Screening
Neurofibromatosis, type 1; Cafe au lait spots, multiple; Legius syndrome; ...
Genes (2): Help
NF1 (17q11.2), SPRED1 (15q14)
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Patients with multiple CALMs w/wo skinfold freckling and no other …
>95% detection rate for non-founder patients who meet NIH diagnostic …
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Test short name: Help
NFSP-NG
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
CPT codes: Help
**AMA CPT codes notice
Lab contact: Help
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: Help
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
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 mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Based on applicable state law
Test strategy: Help
The DNA-based NF1/SPRED1-only by NGS involves sequencing as well as deletion/duplication analysis of the entire coding NF1 region plus the alternatively spliced exons 9br, 23a and 48a (67 exons total), as well as sequencing and deletion/duplication analysis for SPRED1. The test uses an extensively customized and optimized set of Agilent … View more
View citations (10)
  • 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.
  • Huson, SM; Hughes, RAC: The Neurofibromatoses: a Pathogenetic and Clinical Overview. London: Chapman & Hall Medical, 1994
  • 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
Conditions Help
Total conditions: 4
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 2
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Clinical Information
Test purpose: Help
Diagnosis; Screening
Clinical validity: Help
>95% detection rate for non-founder patients who meet NIH diagnostic criteria for NF1.
View citations (1)
  • 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.
Target population: Help
Patients with multiple CALMs w/wo skinfold freckling and no other typical NF1 associated features (Lisch nodules, bone abnormalities, neurofibromas, optic pathway gliomas).
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.

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
The laboratory may preform further studies on samples submitted for clinical testing only for disorders that may also help to explain the patient's phenotype.
Recommended fields not provided:
Technical Information
Test Procedure: Help
The DNA-based NF1/SPRED1-only by NGS involves sequencing as well as deletion/duplication analysis of the entire coding NF1 region plus the alternatively spliced exons 9br, 23a and 48a (67 exons total), as well as sequencing and deletion/duplication analysis for SPRED1. The test uses an extensively customized and optimized set of Agilent … View more
View citations (1)
  • Messiaen et al 2000, Messiaen and Wimmer 2005, Wimmer et al 2007, Messiaen and Wimmer, 2008
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Analytical sensitivity of next generation sequencing is typically validated using a minimum of 20 DNA samples. No false positives were detected during analysis. The test uses an extensively customized and optimized set of Agilent HaloPlex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 300bp … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Alternative Assessment

PT Provider: Help
reanalysis of internal, blinded specimens

Description of PT method: Help
Reanalysis of internally blinded specimens

Description of internal test validation method: Help
For details, please review article cited below.
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:
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.