Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene

Background: Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structu...

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Autores: Fernández Suárez, Elena, González del Pozo, María, Méndez Vidal, Cristina, Martín Sánchez, Marta, Mena, Marcela, Morena Barrio, Belén de la, Corral, Javier, Borrego, Salud, Antiñolo Gil, Guillermo
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universidad de Sevilla (US)
Repositorio:idUS. Depósito de Investigación de la Universidad de Sevilla
OAI Identifier:oai:idus.us.es:11441/178869
Acceso en línea:https://hdl.handle.net/11441/178869
https://doi.org/10.1186/s13100-024-00320-1
Access Level:acceso abierto
Palabra clave:Alu insertion
CNV
EYS
Inherited retinal diseases
Long-read sequencing
Nanopore sequencing
Retinitis pigmentosa
Retrotransposon
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spelling Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS geneFernández Suárez, ElenaGonzález del Pozo, MaríaMéndez Vidal, CristinaMartín Sánchez, MartaMena, MarcelaMorena Barrio, Belén de laCorral, JavierBorrego, SaludAntiñolo Gil, GuillermoAlu insertionCNVEYSInherited retinal diseasesLong-read sequencingNanopore sequencingRetinitis pigmentosaRetrotransposonBackground: Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32–33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. Results: T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32–33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. Conclusions: To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated.BioMed CentralCirugíaInstituto de Salud Carlos IIIGobierno de EspañaEuropean Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER)Junta de AndalucíaFundación Isabel GemioFundación CajasolCIBERERMMS2024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttps://hdl.handle.net/11441/178869https://doi.org/10.1186/s13100-024-00320-1reponame:idUS. Depósito de Investigación de la Universidad de Sevillainstname:Universidad de Sevilla (US)InglésMobile DNA, 15, 9.PI21-00244PEER-0501–2019FGEMIO-2019–01FI19/00091ERF02MOV/2023RH-0049–2021https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-024-00320-1info:eu-repo/semantics/openAccessoai:idus.us.es:11441/1788692026-06-17T12:51:07Z
dc.title.none.fl_str_mv Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
title Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
spellingShingle Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
Fernández Suárez, Elena
Alu insertion
CNV
EYS
Inherited retinal diseases
Long-read sequencing
Nanopore sequencing
Retinitis pigmentosa
Retrotransposon
title_short Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
title_full Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
title_fullStr Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
title_full_unstemmed Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
title_sort Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
dc.creator.none.fl_str_mv Fernández Suárez, Elena
González del Pozo, María
Méndez Vidal, Cristina
Martín Sánchez, Marta
Mena, Marcela
Morena Barrio, Belén de la
Corral, Javier
Borrego, Salud
Antiñolo Gil, Guillermo
author Fernández Suárez, Elena
author_facet Fernández Suárez, Elena
González del Pozo, María
Méndez Vidal, Cristina
Martín Sánchez, Marta
Mena, Marcela
Morena Barrio, Belén de la
Corral, Javier
Borrego, Salud
Antiñolo Gil, Guillermo
author_role author
author2 González del Pozo, María
Méndez Vidal, Cristina
Martín Sánchez, Marta
Mena, Marcela
Morena Barrio, Belén de la
Corral, Javier
Borrego, Salud
Antiñolo Gil, Guillermo
author2_role author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Cirugía
Instituto de Salud Carlos III
Gobierno de España
European Commission (EC). Fondo Europeo de Desarrollo Regional (FEDER)
Junta de Andalucía
Fundación Isabel Gemio
Fundación Cajasol
CIBERER
MMS
dc.subject.none.fl_str_mv Alu insertion
CNV
EYS
Inherited retinal diseases
Long-read sequencing
Nanopore sequencing
Retinitis pigmentosa
Retrotransposon
topic Alu insertion
CNV
EYS
Inherited retinal diseases
Long-read sequencing
Nanopore sequencing
Retinitis pigmentosa
Retrotransposon
description Background: Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32–33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. Results: T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32–33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. Conclusions: To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated.
publishDate 2024
dc.date.none.fl_str_mv 2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/11441/178869
https://doi.org/10.1186/s13100-024-00320-1
url https://hdl.handle.net/11441/178869
https://doi.org/10.1186/s13100-024-00320-1
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Mobile DNA, 15, 9.
PI21-00244
PEER-0501–2019
FGEMIO-2019–01
FI19/00091
ERF02MOV/2023
RH-0049–2021
https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-024-00320-1
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:idUS. Depósito de Investigación de la Universidad de Sevilla
instname:Universidad de Sevilla (US)
instname_str Universidad de Sevilla (US)
reponame_str idUS. Depósito de Investigación de la Universidad de Sevilla
collection idUS. Depósito de Investigación de la Universidad de Sevilla
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,81155

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