Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq

R Koster, R D Brandão, D Tserpelis, C E P van Roozendaal, C N van Oosterhoud, K B M Claes, A D C Paulussen, M Sinnema, M Vreeburg, V van der Schoot, C T R M Stumpel, M P G Broen, L Spruijt, M C J Jongmans, S A J Lesnik Oberstein, A S Plomp, M Misra-Isrie, F A Duijkers, M J Louwers, R SzklarczykK W J Derks, H G Brunner, A van den Wijngaard, M van Geel, M J Blok

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Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. For this method RNA was extracted from lymphocytes, followed by targeted RNAseq. Next, an in-house developed tool (QURNAs) was used to calculate the enrichment score (ERS) for each splicing event. This method was thoroughly tested using two different patient cohorts with known pathogenic splice-variants in NF1. In both cohorts all 56 normal reference transcript exon splice junctions, 24 previously described and 45 novel non-reference splicing events were detected. Additionally, all expected pathogenic splice-variants were detected. Eleven patients with NF1 symptoms were subsequently tested, three of which have a known NF1 DNA variant with a putative effect on RNA splicing. This effect could be confirmed for all 3. The other eight patients were previously without any molecular confirmation of their NF1-diagnosis. A deep-intronic pathogenic splice variant could now be identified for two of them (25%). These results suggest that targeted RNAseq can be successfully used to detect pathogenic RNA splicing variants in NF1.

Original languageEnglish
Article number95
Pages (from-to)95
Number of pages10
Issue number1
Publication statusPublished - 15 Nov 2021

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