Comprehensive RNA Analysis of the NF1 Gene in Classically Affected NF1 Affected Individuals Meeting NIH Criteria has High Sensitivity and Mutation Negative Testing is Reassuring in Isolated Cases With Pigmentary Features Only

Abstract

Background: The detection rate for identifying the underlyingmutation in neurocutaneous syndromes is affected bythe sensitivity of themutation test and the heterogeneity of the disease based on the diagnostic criteria. Neurofibromatosistype (NF1) has been defined for 29 years by the National Institutes for Health (NIH) criteria which include≥6 Café au Laitmacules (CAL) as a defining criterion. The discovery of SPRED1 as a cause of Legius syndromewhich ismanifested by CAL, freckling and learning difficulties has introduced substantial heterogeneity to the NIH criteria.Methods: We have defined the sensitivity of comprehensive RNA analysis on blood of presumed NF1 patientsmeetingNIH criteria with at least one nonpigmentary criterion and determined the proportion of children with ≥6 CALand no family history that has an NF1 or SPRED1 genetic variant. RNA analysis was carried out from 04/2009–12/2015 on 361 NF1 patients.Findings: A presumed causative NF1 mutation was found in 166/171 (97.08%–95% CI 94.56–99.6%) of familial casesand 182/190 (95.8%–95% CI 92.93–98.65%) sporadic de novo cases. Two of thirteen (15%)mutation negative individualshad dysembryoplastic neuroepithelial tumour (DNET) compared to 2/348 (0.6%) with an NF1 variant (p =0.007). No SPRED1 variants were found in the thirteen individuals with no NF1 variant. Of seventy-one individualswith ≥6 CAL and no non-pigmentary criterion aged 0–20 years, 47 (66.2%) had an NF1 variant six (8.5%) a SPRED1variant and 18 (25.3%) no disease causing variant. Using the 95.8% detection rate the likelihood of a child with ≥6CAL having constitutional NF1 drops from 2/3 to 1/9 after negative RNA analysis.Interpretation: RNA analysis in individuals with presumed NF1 has high sensitivity and includes a small subset withDNET without an NF1 variant. Furthermore negative analysis for NF1/SPRED1 provides strong reassurance to childrenwith ≥6 CAL that they are unlikely to have NF1