RNA-Based NF1 and Genomic DNA-Based SPRED1 Testing on Blood (NFSP-R)
Information for Ordering
Acceptable Specimen Types
- Fresh blood sample: 3–6 mL EDTA; must be received within 60–72 hours of collection
- Saliva and extracted DNA are not acceptable specimens.
Whole blood specimens submitted for RNA-based testing must be received within 60–72 hours of collection to maintain lymphocyte viability.
Turnaround Time
Average turnaround time: 22 working days
Price, CPT Codes, and Z Code
- Institutional/self-pay price: $2,000 USD
- CPT codes: 88230, 81408, 81479 × 2, and 81405
- Z code: ZB6AJ
Candidates for Testing
Patients requiring the most sensitive and specific combined testing of NF1 and SPRED1 with the fastest available turnaround time.
Specimen Shipping and Handling
Please refer to the specimen requirements listed above.
All submitted specimens must be shipped at room temperature. Do not ship specimens on ice.
Because this specimen must be received within 60–72 hours of collection, please plan shipment carefully and avoid delays that could affect specimen viability.
Specimens must be packaged to prevent breakage. Absorbent material must be included to contain liquids if breakage occurs. Specimens must also be shipped in double watertight containers, such as a specimen pouch placed inside the shipping company’s diagnostic envelope.
To request a collection kit, please complete the Collection Kit Request Form .
Before shipping a specimen, please contact the UAB Medical Genomics Laboratory by email at medgenomics@uabmc.edu or by phone at 205-934-5562. Please provide the collection date, shipment date, and package tracking number so the laboratory can help ensure proper and timely receipt.
Required Forms
About
Disorder Background
Germline loss-of-function variants in SPRED1, a negative regulator of the RAS/MAPK pathway, cause a neurofibromatosis type 1-like phenotype known as Legius syndrome.
Individuals with Legius syndrome may present with multiple café-au-lait macules, with or without skinfold freckling. Other typical NF1-associated features, such as Lisch nodules, bone abnormalities, neurofibromas, and optic pathway gliomas, are generally absent. Noonan-like features have been reported in some individuals.
In individuals with café-au-lait macules, with or without freckling, and no other distinguishing clinical features, diagnostic criteria may not reliably distinguish NF1 from Legius syndrome. An accurate diagnosis has important implications for prognosis, counseling, and potential prenatal genetic diagnosis.
Based on a cross-sectional study, patients presenting sporadically with pigmentary findings alone carry a variant in the NF1 gene in approximately 43% of cases and a variant in the SPRED1 gene in approximately 1.3% of cases. When patients have a family history of café-au-lait macules, with or without freckling, and no additional NF1-related criteria, an NF1 variant is identified in approximately 73% of cases and a SPRED1 variant in approximately 19% of cases.
SPRED1 is a member of the SPROUTY/SPRED family of proteins, which act as negative regulators of RAS-RAF interaction and mitogen-activated protein kinase signaling.
Test Description
This test requires a fresh EDTA blood specimen received within 60–72 hours of collection to maintain lymphocyte viability.
The RNA-based NF1 and genomic DNA-based SPRED1 blood test requires a fresh EDTA blood specimen. DNA is extracted, and a short-term phytohemagglutinin-stimulated lymphocyte culture is established to provide RNA for analysis.
The complete NF1 coding region is evaluated using complementary variant-detection methods, including RT-PCR, direct sequencing of cDNA fragments, microsatellite marker analysis, and MLPA copy-number analysis. This approach identifies the causative variant in approximately 95% of non-founder patients who meet NIH diagnostic criteria.
RNA-based NF1 testing enables identification of deep intronic splice variants through their observed effects on RNA splicing. These variants may not be detected using conventional exon-by-exon DNA-based sequencing alone.
During more than 15 years of comprehensive RNA-based NF1 testing, the UAB Medical Genomics Laboratory has identified more than 65 locations harboring deep intronic splice variants. Together, these account for approximately 2.5% of all pathogenic NF1 variants identified in the UAB cohort. All currently known deep intronic splice variants have been incorporated into the laboratory’s customized DNA-based NGS assays.
In addition, all coding exons and flanking intronic sequences of SPRED1 are analyzed by bidirectional sequencing, and deletion/duplication analysis is performed using MLPA.
View references for this testing .
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 and Deletion/Duplication Analysis (RAS-NG)
- RNA-Based NF1/SPRED1 Testing on Affected Tissues (NF14N/NF14C)
For more information, test requisition forms, or collection kits, please contact the UAB Medical Genomics Laboratory at 205-934-5562 or medgenomics@uabmc.edu.