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Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases

High throughput sequencing technologies have revolutionized the identification of mutations responsible for a diverse set of Mendelian disorders, including inherited retinal disorders (IRDs). However, the causal mutations remain elusive for a significant proportion of patients. This may be partially...

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Autores principales: Qian, Xinye, Wang, Jun, Wang, Meng, Igelman, Austin D., Jones, Kaylie D., Li, Yumei, Wang, Keqing, Goetz, Kerry E., Birch, David G., Yang, Paul, Pennesi, Mark E., Chen, Rui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7960924/
https://www.ncbi.nlm.nih.gov/pubmed/33737949
http://dx.doi.org/10.3389/fgene.2021.647400
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author Qian, Xinye
Wang, Jun
Wang, Meng
Igelman, Austin D.
Jones, Kaylie D.
Li, Yumei
Wang, Keqing
Goetz, Kerry E.
Birch, David G.
Yang, Paul
Pennesi, Mark E.
Chen, Rui
author_facet Qian, Xinye
Wang, Jun
Wang, Meng
Igelman, Austin D.
Jones, Kaylie D.
Li, Yumei
Wang, Keqing
Goetz, Kerry E.
Birch, David G.
Yang, Paul
Pennesi, Mark E.
Chen, Rui
author_sort Qian, Xinye
collection PubMed
description High throughput sequencing technologies have revolutionized the identification of mutations responsible for a diverse set of Mendelian disorders, including inherited retinal disorders (IRDs). However, the causal mutations remain elusive for a significant proportion of patients. This may be partially due to pathogenic mutations located in non-coding regions, which are largely missed by capture sequencing targeting the coding regions. The advent of whole-genome sequencing (WGS) allows us to systematically detect non-coding variations. However, the interpretation of these variations remains a significant bottleneck. In this study, we investigated the contribution of deep-intronic splice variants to IRDs. WGS was performed for a cohort of 571 IRD patients who lack a confident molecular diagnosis, and potential deep intronic variants that affect proper splicing were identified using SpliceAI. A total of six deleterious deep intronic variants were identified in eight patients. An in vitro minigene system was applied to further validate the effect of these variants on the splicing pattern of the associated genes. The prediction scores assigned to splice-site disruption positively correlated with the impact of mutations on splicing, as those with lower prediction scores demonstrated partial splicing. Through this study, we estimated the contribution of deep-intronic splice mutations to unassigned IRD patients and leveraged in silico and in vitro methods to establish a framework for prioritizing deep intronic variant candidates for mechanistic and functional analyses.
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spelling pubmed-79609242021-03-17 Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases Qian, Xinye Wang, Jun Wang, Meng Igelman, Austin D. Jones, Kaylie D. Li, Yumei Wang, Keqing Goetz, Kerry E. Birch, David G. Yang, Paul Pennesi, Mark E. Chen, Rui Front Genet Genetics High throughput sequencing technologies have revolutionized the identification of mutations responsible for a diverse set of Mendelian disorders, including inherited retinal disorders (IRDs). However, the causal mutations remain elusive for a significant proportion of patients. This may be partially due to pathogenic mutations located in non-coding regions, which are largely missed by capture sequencing targeting the coding regions. The advent of whole-genome sequencing (WGS) allows us to systematically detect non-coding variations. However, the interpretation of these variations remains a significant bottleneck. In this study, we investigated the contribution of deep-intronic splice variants to IRDs. WGS was performed for a cohort of 571 IRD patients who lack a confident molecular diagnosis, and potential deep intronic variants that affect proper splicing were identified using SpliceAI. A total of six deleterious deep intronic variants were identified in eight patients. An in vitro minigene system was applied to further validate the effect of these variants on the splicing pattern of the associated genes. The prediction scores assigned to splice-site disruption positively correlated with the impact of mutations on splicing, as those with lower prediction scores demonstrated partial splicing. Through this study, we estimated the contribution of deep-intronic splice mutations to unassigned IRD patients and leveraged in silico and in vitro methods to establish a framework for prioritizing deep intronic variant candidates for mechanistic and functional analyses. Frontiers Media S.A. 2021-03-02 /pmc/articles/PMC7960924/ /pubmed/33737949 http://dx.doi.org/10.3389/fgene.2021.647400 Text en Copyright © 2021 Qian, Wang, Wang, Igelman, Jones, Li, Wang, Goetz, Birch, Yang, Pennesi and Chen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Qian, Xinye
Wang, Jun
Wang, Meng
Igelman, Austin D.
Jones, Kaylie D.
Li, Yumei
Wang, Keqing
Goetz, Kerry E.
Birch, David G.
Yang, Paul
Pennesi, Mark E.
Chen, Rui
Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title_full Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title_fullStr Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title_full_unstemmed Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title_short Identification of Deep-Intronic Splice Mutations in a Large Cohort of Patients With Inherited Retinal Diseases
title_sort identification of deep-intronic splice mutations in a large cohort of patients with inherited retinal diseases
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7960924/
https://www.ncbi.nlm.nih.gov/pubmed/33737949
http://dx.doi.org/10.3389/fgene.2021.647400
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