全基因组测序在基因问题尚未解决的意大利遗传性视网膜疾病患者中发现了难以捉摸的变体。

IF 3.3 Q2 GENETICS & HEREDITY
HGG Advances Pub Date : 2024-07-18 Epub Date: 2024-05-29 DOI:10.1016/j.xhgg.2024.100314
Roberta Zeuli, Marianthi Karali, Suzanne E de Bruijn, Kim Rodenburg, Margherita Scarpato, Dalila Capasso, Galuh D N Astuti, Christian Gilissen, María Rodríguez-Hidalgo, Javier Ruiz-Ederra, Francesco Testa, Francesca Simonelli, Frans P M Cremers, Sandro Banfi, Susanne Roosing
{"title":"全基因组测序在基因问题尚未解决的意大利遗传性视网膜疾病患者中发现了难以捉摸的变体。","authors":"Roberta Zeuli, Marianthi Karali, Suzanne E de Bruijn, Kim Rodenburg, Margherita Scarpato, Dalila Capasso, Galuh D N Astuti, Christian Gilissen, María Rodríguez-Hidalgo, Javier Ruiz-Ederra, Francesco Testa, Francesca Simonelli, Frans P M Cremers, Sandro Banfi, Susanne Roosing","doi":"10.1016/j.xhgg.2024.100314","DOIUrl":null,"url":null,"abstract":"<p><p>Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.</p>","PeriodicalId":34530,"journal":{"name":"HGG Advances","volume":null,"pages":null},"PeriodicalIF":3.3000,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225895/pdf/","citationCount":"0","resultStr":"{\"title\":\"Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients.\",\"authors\":\"Roberta Zeuli, Marianthi Karali, Suzanne E de Bruijn, Kim Rodenburg, Margherita Scarpato, Dalila Capasso, Galuh D N Astuti, Christian Gilissen, María Rodríguez-Hidalgo, Javier Ruiz-Ederra, Francesco Testa, Francesca Simonelli, Frans P M Cremers, Sandro Banfi, Susanne Roosing\",\"doi\":\"10.1016/j.xhgg.2024.100314\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.</p>\",\"PeriodicalId\":34530,\"journal\":{\"name\":\"HGG Advances\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.3000,\"publicationDate\":\"2024-07-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225895/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"HGG Advances\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1016/j.xhgg.2024.100314\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/5/29 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q2\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"HGG Advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1016/j.xhgg.2024.100314","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/5/29 0:00:00","PubModel":"Epub","JCR":"Q2","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

遗传性视网膜疾病(IRDs)是一组罕见的单基因疾病,具有高度遗传异质性(在 280 多个致病基因中发现了致病变异)。IRD的基因诊断率约为60%,这主要归功于新一代测序(NGS)方法的常规应用,如广泛的基因面板或全外显子组分析。有报道称,全基因组测序(WGS)可揭示结构变异(SV)和深部内含子变异(DIV)等难以捉摸的变异,从而提高诊断率。我们对 33 例疑似常染色体隐性 IRD 的未确诊病例进行了 WGS 检测,旨在确定非编码区的致病基因变异或检测在初步筛查中未发现的 SV。大多数入选病例(30/33,90.9%)携带与临床表现相关的基因单倍致病变异,因此我们首先分析了这些候选基因的非编码区。如果这种方法未能发现其他致病变异,我们就将 SV 和 DIV 的搜索范围扩大到所有 IRD 相关基因。总的来说,我们在 11 名患者(11/33,33.3%)中发现了缺失的致病变异。这些变异包括 ABCA4、CEP290 和 RPGRIP1 中的三个 DIV;PROM1 中的一个非典型剪接位点 (NCSS) 变异以及 EYS、PCDH15 和 USH2A 中的三个 SV(大缺失)。对于之前未报道的 CEP290 中的 DIV 和 PROM1 中的 NCCS 变异,我们通过对患者来源 RNA 的反转录 (RT)-PCR 验证了其对剪接的影响。这项研究证明了 WGS 作为一种多合一检测方法在鉴定标准 NGS 诊断方法遗漏的致病变异方面的能力和临床实用性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients.

Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
HGG Advances
HGG Advances Biochemistry, Genetics and Molecular Biology-Molecular Medicine
CiteScore
4.30
自引率
4.50%
发文量
69
审稿时长
14 weeks
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信