Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq
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 ap...
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2021
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oai:doaj.org-article:982c0d93ba4e444ea8df66af214376912021-11-21T12:42:52ZPathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq10.1038/s41525-021-00258-w2056-7944https://doaj.org/article/982c0d93ba4e444ea8df66af214376912021-11-01T00:00:00Zhttps://doi.org/10.1038/s41525-021-00258-whttps://doaj.org/toc/2056-7944Abstract 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.R. KosterR. D. BrandãoD. TserpelisC. E. P. van RoozendaalC. N. van OosterhoudK. B. M. ClaesA. D. C. PaulussenM. SinnemaM. VreeburgV. van der SchootC. T. R. M. StumpelM. P. G. BroenL. SpruijtM. C. J. JongmansS. A. J. Lesnik ObersteinA. S. PlompM. Misra-IsrieF. A. DuijkersM. J. LouwersR. SzklarczykK. W. J. DerksH. G. BrunnerA. van den WijngaardM. van GeelM. J. BlokNature PortfolioarticleMedicineRGeneticsQH426-470ENnpj Genomic Medicine, Vol 6, Iss 1, Pp 1-10 (2021) |
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DOAJ |
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DOAJ |
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Medicine R Genetics QH426-470 |
| spellingShingle |
Medicine R Genetics QH426-470 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. Szklarczyk K. W. J. Derks H. G. Brunner A. van den Wijngaard M. van Geel M. J. Blok Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| description |
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 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. |
| format |
article |
| author |
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. Szklarczyk K. W. J. Derks H. G. Brunner A. van den Wijngaard M. van Geel M. J. Blok |
| author_facet |
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. Szklarczyk K. W. J. Derks H. G. Brunner A. van den Wijngaard M. van Geel M. J. Blok |
| author_sort |
R. Koster |
| title |
Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| title_short |
Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| title_full |
Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| title_fullStr |
Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| title_full_unstemmed |
Pathogenic neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq |
| title_sort |
pathogenic neurofibromatosis type 1 (nf1) rna splicing resolved by targeted rnaseq |
| publisher |
Nature Portfolio |
| publishDate |
2021 |
| url |
https://doaj.org/article/982c0d93ba4e444ea8df66af21437691 |
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