RNA-Based NF1/SPRED1 Testing on Cultured Cells from Affected Tissues (NF14N/NF14C)
Information for Ordering
Acceptable Specimen Types
- A minimum of two anatomically distinct 3–5 mm café-au-lait macule (CAL) punch biopsies submitted in UAB Medical Genomics Laboratory transport media.
- A minimum of two anatomically distinct fresh neurofibroma biopsies submitted in UAB Medical Genomics Laboratory transport media.
- A 3–6 mL EDTA whole blood specimen may be submitted for free targeted testing of any suspected germline (first-hit pathogenic) variant identified during biopsy-based testing.
Please contact the UAB Medical Genomics Laboratory at least one week before obtaining biopsies so the appropriate collection media can be prepared and shipped. Collection kits can be requested using the Collection Kit Request Form.
Turnaround Time
Average turnaround time: 120 working days
Price, CPT Codes, and Z Codes
- NF1-only: $2,600 USD (institutional/self-pay)
- CPT: 88233, 81408, and 81479
- Z Codes: ZB6AG (CAL biopsies); ZB67X (neurofibromas)
For CAL biopsies requiring reflex SPRED1 testing, total institutional/self-pay cost is $3,200. Additional CPT codes: 81405 and 81404.
Candidates for Testing
Patients suspected of having segmental NF1 with findings restricted to a defined body region; sporadic patients with mild or non-localized NF1 features who have no detectable NF1 variant in blood lymphocytes and may have disease caused by a postzygotic variant; and familial or sporadic patients requiring reflex testing for a first-hit pathogenic variant that was not detected by RNA- or DNA-based testing.
Specimen Shipping and Handling
Please refer to the specimen requirements listed above.
Please contact the laboratory before obtaining biopsies. We will provide individualized guidance and ship the appropriate transport media and collection materials before the procedure.
All specimens must be shipped at room temperature. Do not ship on ice.
Specimens must be packaged to prevent breakage. Include absorbent material and use double watertight packaging (for example, a specimen pouch inside the shipping company's diagnostic envelope).
To request a collection kit, please complete the Collection Kit Request Form.
Instructions for collecting and shipping café-au-lait macule biopsy specimens
Instructions for collecting and shipping neurofibroma specimens
Before shipping, please contact the UAB Medical Genomics Laboratory at medgenomics@uabmc.edu or 205-934-5562 with the shipment date and tracking number so we can help ensure timely receipt.
Required Forms
About
Disorder Background
The NF1 gene was the first gene within the RAS/MAPK pathway shown to cause an autosomal dominant disorder. Neurofibromatosis type 1 affects approximately 1 in 3,000 individuals worldwide and demonstrates marked phenotypic variability. Comprehensive RNA-based testing enables detection of deep intronic splice variants that may not be identified by DNA-only testing.
Loss-of-function variants in SPRED1 cause Legius syndrome, which shares pigmentary features with NF1 but lacks the classic tumor manifestations. Because these disorders overlap clinically, comprehensive analysis of both genes is important in selected patients.
Test Description
RNA-based NF1/SPRED1 testing on affected tissues is performed using cultured melanocytes from café-au-lait macules and cultured Schwann cells from neurofibromas.
The complete NF1 coding region is evaluated using RT-PCR, direct cDNA sequencing, microsatellite marker analysis, and MLPA copy number analysis.
RNA-based testing detects deep intronic splice variants that are not identifiable using conventional exon-by-exon DNA sequencing. During more than 15 years of testing, the UAB Medical Genomics Laboratory has identified more than 65 deep intronic splice variant locations that together account for approximately 2.5% of pathogenic NF1 variants in the UAB cohort. These known variants have since been incorporated into the laboratory's customized DNA-based NGS assays.
For patients with only pigmentary findings (café-au-lait macules with or without skinfold freckling) in whom no NF1 variants are identified, reflex SPRED1 sequencing and deletion/duplication analysis is performed to evaluate for mosaic Legius syndrome.
When disease is present, a shared first-hit pathogenic variant is typically identified in all biopsies, while a different second-hit pathogenic variant is identified in each anatomically distinct biopsy. If no pathogenic variants are identified following successful analysis of two biopsies, mosaic NF1 or Legius syndrome becomes highly unlikely (<0.2%).
REFERENCES available here.
Other Related Test Options
- Next-Generation Sequencing and Deletion/Duplication Analysis of NF1 Only (NF1-NG)
- Next-Generation Sequencing and Deletion/Duplication Analysis of NF1 and SPRED1 (NFSP-NG)
- Expanded NF1 RASopathy Panel by Next-Generation Sequencing (RAS-NG)
- RNA-Based NF1 and gDNA-Based SPRED1 Testing on Blood (NFSP-R)
For more information, test requisition forms, or collection kits, please contact the UAB Medical Genomics Laboratory at 205-934-5562 or medgenomics@uabmc.edu.