Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A

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• dc.contributor.author Steward, Charles A.
• dc.contributor.author Uszczynska-Ratajczak, Barbara
• dc.contributor.author Guigó Serra, Roderic
• dc.contributor.author Frankish, Adam
• dc.date.accessioned 2020-01-10T08:39:19Z
• dc.date.available 2020-01-10T08:39:19Z
• dc.date.issued 2019
• dc.description.abstract The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for a lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 putative transcript models. Our annotations increase the transcriptional 'footprint' of these genes by over 674 kb. Using SCN1A as a case study, due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome or a similar phenotype with a panel of exon sequences representing eight established genes and identified two de novo SCN1A variants that now - through improved gene annotation - are ascribed to residing among our exons. These two (from 122 screened people, 1.6%) molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously classified SCN1A intronic Dravet syndrome-associated variant that now lies within a deeply conserved exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders.
• dc.format.mimetype application/pdf
• dc.identifier.citation Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D et al. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A. NPJ Genom Med. 2019;4:31. DOI: 10.1038/s41525-019-0106-7
• dc.identifier.doi http://dx.doi.org/10.1038/s41525-019-0106-7
• dc.identifier.issn 2056-7944
• dc.identifier.uri http://hdl.handle.net/10230/43255
• dc.language.iso eng
• dc.publisher Nature Research
• dc.relation.ispartof NPJ Genomic Medicine. 2019;4:31
• dc.rights © The Author(s) 2019. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Medical genomics
• dc.subject.keyword Molecular medicine
• dc.title Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion