RNA-based NF1 and gDNA-based SPRED1 Testing on Blood (NFSP-R)

Information for Ordering

• Fresh blood sample (3-6 ml EDTA; must be received within 60-72 hours of collection)

*Saliva or DNA are NOT acceptable specimens*

22 working days

$2,000 (USD- institutional/self-pay price)

CPT: 88230, 81408, 81479 (x2), and 81405

Z code: ZB6AJ

Patients who need the most sensitive and specific test with the fastest turnaround time.

Please find specimen requirement specifications above.

All submitted specimens must be sent at room temperature. DO NOT ship on ice.

Specimens must be packaged to prevent breakage and absorbent material must be included in the package to absorb liquids in the event that breakage occurs. Also, the package must be shipped in double watertight containers (e.g. a specimen pouch + the shipping company’s diagnostic envelope).

To request a sample collection kit, please click here or email medgenomics@uabmc.edu to complete the specimen request form.

Please contact the MGL (via email at medgenomics@uabmc.edu, or via phone at 205-934-5562) prior to sample shipment and provide us with the date of shipment and tracking number of the package so that we can better ensure receipt of the samples.

About

Germline loss-of-function variants in SPRED1, a negative regulator of the RAS-MAPK pathway, cause a neurofibromatosis type 1-like phenotype, first described in 2007 (Legius syndrome). Patients present with multiple café-au-lait spots with or without skinfold freckling. Other typical NF1 associated features (Lisch nodules, bone abnormalities, neurofibromas, optic pathway gliomas) are systematically absent. However, in some individuals Noonan-like features have been reported. 

In individuals with CALMs with or without freckling and no other specific distinguishing features, the NIH criteria cannot reliably distinguish NF1 from Legius syndrome. In such patients, a correct diagnosis has important implications for prognosis, counseling, and potential prenatal genetic diagnosis.  Based on a cross-sectional study we estimate that patients presenting sporadically with these pigmentary signs only will carry a variant in the NF1 gene in ~43% of cases and in the SPRED1 gene in ~1.3% of cases. When such patients have a family history of CALMs with or without freckling and no additional NF1-related criteria, an NF1 variant will be found in ~73% of cases and in the SPRED1 gene in ~19% of cases.
SPRED1 is a member of the SPROUTY/SPRED family of proteins that act as negative regulators of RAS-RAF interaction and mitogen-activated protein kinase (MAPK) signaling.

The RNA-based NF1 and DNA-based SPRED1 testing on blood requires a fresh EDTA blood sample, to arrive in the lab <60-70 hours after blood draw. DNA is extracted and in addition, a short term phytohemagglutinin-stimulated lymphocyte culture is initiated and used as starting material to extract RNA. The complete NF1 coding region is analyzed by a cascade of complementary variant detection techniques, including RT-PCR, direct sequencing of cDNA fragments, microsatellite marker analysis and copy number analysis by MLPA, enabling identification of the variant in ~95% of non-founder patients fulfilling the NIH diagnostic criteria.
RNA-based NF1 testing allows finding deep intronic splice variants through their observed effect on splicing. These splice variants would not be detected if a “simple” exon-by-exon DNA-based (NGS/Sanger) sequencing approach is used. During the >15 years we have offered comprehensive RNA-based NF1 testing on blood, we have identified >65 different locations harboring deep intronic splice variants: together they account for 2.5% of all pathogenic variants identified in the NF1 UAB cohort. Please note that all known deep intronic splice variants have been incorporated in the customized UAB NGS available assays.

In addition, all coding exons and flanking intronic sequences of the SPRED1 gene are analyzed by bidirectional sequencing and deletion/duplication analysis is performed using MLPA. 

REFERENCES available here.


Other related test options:


For more information, test requisition forms, or sample collection and mailing kits, please call: 205-934-5562.

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