Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq
Koster, R.; Brandão, R. D.; Tserpelis, D.; van Roozendaal, C. E.P.; van Oosterhoud, C. N.; Claes, K. B.M.; Paulussen, A. D.C.; Sinnema, M.; Vreeburg, M.; van der Schoot, V.; Stumpel, C. T.R.M.; Broen, M. P.G.; Spruijt, L.; Jongmans, M. C.J.; Lesnik Oberstein, S. A.J.; Plomp, A. S.; Misra-Isrie, M.; Duijkers, F. A.; Louwers, M. J.; Szklarczyk, R.; Derks, K. W.J.; Brunner, H. G.; van den Wijngaard, A.; van Geel, M.; Blok, M. J.
(2021) npj Genomic Medicine, volume 6, issue 1, pp. 1 - 10
(Article)
Abstract
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
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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.
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Keywords: Genetics(clinical), Genetics, Molecular Biology, Journal Article
ISSN: 2056-7944
Publisher: Nature Publishing Group
Note: Publisher Copyright: © 2021, The Author(s).
(Peer reviewed)