Next-Generation Sequencing and Deletion/Duplication Analysis of SPRED1 Only (SPD1-NG)
Information for Ordering
Acceptable Specimen Types
- Fresh blood sample: 3–6 mL EDTA; no time limitations associated with receipt
- Saliva: OGD-575 DNA Genotek collection kit; kits are provided upon request
- DNA extracted from lymphocyte cells: minimum volume of 25 µL containing 3 µg of DNA; A260/A280 ratio ≥1.8; must be extracted in a CLIA-certified or equivalent laboratory
Turnaround Time
Average turnaround time: 30 working days
Price, CPT Codes, and Z Code
- Institutional/self-pay price: $800 USD
- CPT codes: 81405 and 81479
- Z code: ZB6AC
Candidates for Testing
Patients with multiple café-au-lait macules, with or without skinfold freckling, and no other typical NF1 features, such as Lisch nodules, bone abnormalities, neurofibromas, or optic pathway gliomas, after comprehensive NF1 variant analysis.
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.
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 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 first described in 2007 and known as Legius syndrome.
Patients 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. However, Noonan-like features have been reported in some individuals.
In individuals with café-au-lait macules, with or without freckling, and no other specific distinguishing features, clinical 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 these pigmentary findings alone carry 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, a SPRED1 variant is identified 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
The DNA-based SPRED1-only NGS test includes sequencing and deletion/duplication analysis of the entire coding region of SPRED1.
The test uses a customized and optimized set of Agilent HaloPlex capture probes, followed by sequencing of overlapping amplicons within the regions of interest using 300 bp paired-end Illumina sequencing chemistry. Each coding exon plus approximately 50 bp of flanking intronic sequence is simultaneously sequenced. The 5′ and 3′ untranslated regions are not included.
Average coverage is greater than 1,600×, with more than 98% of the coding region covered at ≥350× and more than 99% covered at ≥200×. This permits detection of low-level mosaicism down to approximately 3%–5% variant allele fraction, depending on coverage, with 95% confidence.
Variant and copy-number calls are made using a specialized bioinformatics pipeline that detects single-nucleotide substitutions, insertions, deletions, and frameshifts caused by deletions or duplications up to 112 bp.
View references for this testing .
Other Related Test Options
- Next-Generation Sequencing and Deletion/Duplication Analysis of NF1 Only (NF1-NG)
- Expanded NF1 RASopathy Panel by Next-Generation Sequencing and Deletion/Duplication Analysis (RAS-NG)
- RNA-Based NF1 and Genomic DNA-Based SPRED1 Testing on Blood (NFSP-R)
- 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.