通过重新分析线粒体疾病的全外显子测序数据提高诊断率。

IF 3.2 4区 医学 Q2 CLINICAL NEUROLOGY
Catarina Olimpio, Ida Paramonov, Leslie Matalonga, Steven Laurie, Katherine Schon, Kiran Polavarapu, Janbernd Kirschner, Ulrike Schara-Schmidt, Hanns Lochmüller, Patrick F Chinnery, Rita Horvath
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引用次数: 0

摘要

背景:线粒体疾病的遗传诊断因其遗传和表型的复杂性而变得复杂。新一代测序技术大大提高了这些疾病的诊断率。10 年前,有文献报道了一组患有多种呼吸链缺陷的个体,通过全外显子组测序(WES),诊断率为 60%,但仍有 40% 的个体未被诊断:我们的目的是通过重新分析这批 10 年前疑似线粒体疾病患者中未确诊部分的 WES 数据,确定基因诊断结果:WES数据由RD-Connect基因组-表型组分析平台(GPAP)利用其标准化管道进行传输和处理。在 RD-Connect GPAP 上对变异进行优先排序:对 14 个个体的单体 WES 数据进行了重新分析。我们确定了 8 名患者(8/14,57%)可能或可能的基因诊断。鉴定出的变异涉及线粒体 DNA(n = 1,MT-TN)、核编码线粒体基因(n = 2,PDHA1 和 SUCLA2)以及与非线粒体疾病相关的核基因(n = 5,PNPLA2、CDC40、NBAS 和 SLC7A7)。NBAS 和 CDC40 基因的变异在原始队列发表后被确定为致病基因。我们在没有产生任何进一步基因组数据的情况下,将原始队列的诊断率提高了 15%:结论:在多组学时代,我们强调对现有 WES 数据的重新分析是对疑似线粒体疾病患者进行额外诊断的有效工具,尤其是当时间推移到新的生物信息管道出现、变异解释新工具的开发有助于变异的重新分类和扩展有关其他基因的科学知识时。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Increased Diagnostic Yield by Reanalysis of Whole Exome Sequencing Data in Mitochondrial Disease.

Background: The genetic diagnosis of mitochondrial disorders is complicated by its genetic and phenotypic complexity. Next generation sequencing techniques have much improved the diagnostic yield for these conditions. A cohort of individuals with multiple respiratory chain deficiencies, reported in the literature 10 years ago, had a diagnostic rate of 60% by whole exome sequencing (WES) but 40% remained undiagnosed.

Objective: We aimed to identify a genetic diagnosis by reanalysis of the WES data for the undiagnosed arm of this 10-year-old cohort of patients with suspected mitochondrial disorders.

Methods: The WES data was transferred and processed by the RD-Connect Genome-Phenome Analysis Platform (GPAP) using their standardized pipeline. Variant prioritisation was carried out on the RD-Connect GPAP.

Results: Singleton WES data from 14 individuals was reanalysed. We identified a possible or likely genetic diagnosis in 8 patients (8/14, 57%). The variants identified were in a combination of mitochondrial DNA (n = 1, MT-TN), nuclear encoded mitochondrial genes (n = 2, PDHA1, and SUCLA2) and nuclear genes associated with nonmitochondrial disorders (n = 5, PNPLA2, CDC40, NBAS and SLC7A7). Variants in both the NBAS and CDC40 genes were established as disease causing after the original cohort was published. We increased the diagnostic yield for the original cohort by 15% without generating any further genomic data.

Conclusions: In the era of multiomics we highlight that reanalysis of existing WES data is a valid tool for generating additional diagnosis in patients with suspected mitochondrial disease, particularly when more time has passed to allow for new bioinformatic pipelines to emerge, for the development of new tools in variant interpretation aiding in reclassification of variants and the expansion of scientific knowledge on additional genes.

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来源期刊
Journal of neuromuscular diseases
Journal of neuromuscular diseases Medicine-Neurology (clinical)
CiteScore
5.10
自引率
6.10%
发文量
102
期刊介绍: The Journal of Neuromuscular Diseases aims to facilitate progress in understanding the molecular genetics/correlates, pathogenesis, pharmacology, diagnosis and treatment of acquired and genetic neuromuscular diseases (including muscular dystrophy, myasthenia gravis, spinal muscular atrophy, neuropathies, myopathies, myotonias and myositis). The journal publishes research reports, reviews, short communications, letters-to-the-editor, and will consider research that has negative findings. The journal is dedicated to providing an open forum for original research in basic science, translational and clinical research that will improve our fundamental understanding and lead to effective treatments of neuromuscular diseases.
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