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- Title
Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A.
- Authors
Steward, Charles A.; Roovers, Jolien; Suner, Marie-Marthe; Gonzalez, Jose M.; Uszczynska-Ratajczak, Barbara; Pervouchine, Dmitri; Fitzgerald, Stephen; Viola, Margarida; Stamberger, Hannah; Hamdan, Fadi F.; Ceulemans, Berten; Leroy, Patricia; Nava, Caroline; Lepine, Anne; Tapanari, Electra; Keiller, Don; Abbs, Stephen; Sanchis-Juan, Alba; Grozeva, Detelina; Rogers, Anthony S.
- 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.
- Publication
NPJ Genomic Medicine, 2019, Vol 4, Issue 1, pN.PAG
- ISSN
2056-7944
- Publication type
Article
- DOI
10.1038/s41525-019-0106-7