长读测序通过鉴定 EYS 基因中的阿鲁逆转录质子插入提高了视网膜色素变性的基因诊断水平

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY Mobile DNA Pub Date : 2024-05-04 DOI:10.1186/s13100-024-00320-1
Elena Fernández-Suárez, María González-del Pozo, Cristina Méndez-Vidal, Marta Martín-Sánchez, Marcela Mena, Belén de la Morena-Barrio, Javier Corral, Salud Borrego, Guillermo Antiñolo
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引用次数: 0

摘要

在某些人群中,常染色体隐性色素性视网膜炎(arRP)的主要病因是 EYS 的双叶变体。EYS 是视网膜中表达量最大的基因之一(约 2 Mb),其结构变异(SV)是常见的致病原因。然而,使用短线程测序(SRS)鉴定这些变异并不总是可行的。在这里,我们在 MinION 测序平台(Oxford Nanopore Technologies)上利用 EYS 的自适应采样进行了靶向长读测序(T-LRS),以明确诊断一个 arRP 家族,该家族的患病个体(n = 3)携带 EYS 基因 32-33 外显子的杂合致病性缺失。由于这是一个在我们的队列中另外三个家系中发现的复发性变异,我们还旨在从核苷酸水平上描述已知缺失的特征,以评估可能的奠基人效应。A 家系的 T-LRS 发现了 EYS 第 43 编码外显子(chr6(GRCh37):g.64430524_64430525ins352)中的杂合子 AluYa5 插入物,该插入物与之前发现的缺失以复合杂合子的形式与疾病分离。使用 IGV 对以前的 SRS 对齐进行目测发现,有几个读数含有软剪切碱基,同时在 Alu 插入位点的覆盖率略有下降。这促使我们使用 grep 命令开发了一个简化程序,以便从 SRS 数据中调查该变异在我们队列中的复发情况。此外,LRS 还将 CNV 定性为跨越 EYS 32-33 外显子的约 56.4kb 缺失(chr6(GRCh37):g.64764235_64820592del)。通过对这四个家庭进行桑格测序和关联分析,进一步鉴定的结果与创始变异一致。据我们所知,这是第一份关于 EYS 编码序列中的移动元素插入可能导致一个家族出现 arRP 的报告。我们的研究凸显了 LRS 技术在表征和鉴定隐性致病 SV(如逆转录转座子插入)方面的价值,这些 SV 对罕见病病因发病机制的贡献可能被低估。
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Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
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. 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. 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.
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
期刊最新文献
International congress on transposable elements (ICTE 2024) in Saint Malo: breaking down transposon waves and their impact. Accelerating de novo SINE annotation in plant and animal genomes. Association of hyperactivated transposon expression with exacerbated immune activation in systemic lupus erythematosus. Widespread HCD-tRNA derived SINEs in bivalves rely on multiple LINE partners and accumulate in genic regions. Correction: Transposon-derived introns as an element shaping the structure of eukaryotic genomes.
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