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Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families
BACKGROUND: Variants identified through parent–child trio-WES yield up to 28–55% positive diagnostic rate across a variety of Mendelian disorders, there remain numerous patients who do not receive a genetic diagnosis. Studies showed that some aberrant splicing variants, which are either not readily...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188693/ https://www.ncbi.nlm.nih.gov/pubmed/34107977 http://dx.doi.org/10.1186/s12920-021-01008-8 |
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author | Li, Qiang Wang, Yiting Pan, Yijun Wang, Jia Yu, Weishi Wang, Xiaodong |
author_facet | Li, Qiang Wang, Yiting Pan, Yijun Wang, Jia Yu, Weishi Wang, Xiaodong |
author_sort | Li, Qiang |
collection | PubMed |
description | BACKGROUND: Variants identified through parent–child trio-WES yield up to 28–55% positive diagnostic rate across a variety of Mendelian disorders, there remain numerous patients who do not receive a genetic diagnosis. Studies showed that some aberrant splicing variants, which are either not readily detectable by WES or could be miss-interpreted by regular detecting pipelines, are highly relevant to human diseases. METHODS: We retrospectively investigated the negative molecular diagnostics through trio-WES for 15 genetically undiagnosed patients whose clinical manifestations were highly suspected to be genetic disorders with well-established genotype–phenotype relationships. We scrutinized the synonymous variants from WES data and Sanger sequenced the suspected intronic region for deep intronic variants. The functional consequences of variants were analyzed by in vitro minigene experiments. RESULTS: Here, we report two abnormal splicing events, one of which caused exon truncating due to the activation of cryptic splicing site by a synonymous variant; the other caused partial intron retention due to the generation of splicing sites by a deep intronic variant. CONCLUSIONS: We suggest that, despite initial negative genetic test results in clinically highly suspected genetic diseases, the combination of predictive bioinformatics and functional analysis should be considered to unveil the genetic etiology of undiagnosed rare diseases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-021-01008-8. |
format | Online Article Text |
id | pubmed-8188693 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-81886932021-06-10 Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families Li, Qiang Wang, Yiting Pan, Yijun Wang, Jia Yu, Weishi Wang, Xiaodong BMC Med Genomics Research BACKGROUND: Variants identified through parent–child trio-WES yield up to 28–55% positive diagnostic rate across a variety of Mendelian disorders, there remain numerous patients who do not receive a genetic diagnosis. Studies showed that some aberrant splicing variants, which are either not readily detectable by WES or could be miss-interpreted by regular detecting pipelines, are highly relevant to human diseases. METHODS: We retrospectively investigated the negative molecular diagnostics through trio-WES for 15 genetically undiagnosed patients whose clinical manifestations were highly suspected to be genetic disorders with well-established genotype–phenotype relationships. We scrutinized the synonymous variants from WES data and Sanger sequenced the suspected intronic region for deep intronic variants. The functional consequences of variants were analyzed by in vitro minigene experiments. RESULTS: Here, we report two abnormal splicing events, one of which caused exon truncating due to the activation of cryptic splicing site by a synonymous variant; the other caused partial intron retention due to the generation of splicing sites by a deep intronic variant. CONCLUSIONS: We suggest that, despite initial negative genetic test results in clinically highly suspected genetic diseases, the combination of predictive bioinformatics and functional analysis should be considered to unveil the genetic etiology of undiagnosed rare diseases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-021-01008-8. BioMed Central 2021-06-09 /pmc/articles/PMC8188693/ /pubmed/34107977 http://dx.doi.org/10.1186/s12920-021-01008-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Li, Qiang Wang, Yiting Pan, Yijun Wang, Jia Yu, Weishi Wang, Xiaodong Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title | Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title_full | Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title_fullStr | Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title_full_unstemmed | Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title_short | Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
title_sort | unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188693/ https://www.ncbi.nlm.nih.gov/pubmed/34107977 http://dx.doi.org/10.1186/s12920-021-01008-8 |
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