A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia

IF 6.2 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Genome research Pub Date : 2025-02-27 DOI:10.1101/gr.279634.124

Haloom Rafehi, Liam G. Fearnley, Justin Read, Penny Snell, Kayli C. Davies, Liam Scott, Greta Gillies, Genevieve C. Thompson, Tess A. Field, Aleena Eldo, Simon Bodek, Ernest Butler, Luke Chen, John Drago, Himanshu Goel, Anna Hackett, G. Michael Halmagyi, Andrew Hannaford, Katya Kotschet, Kishore R. Kumar, Smitha Kumble, Matthew Lee-Archer, Abhishek Malhotra, Mark Paine, Michael Poon, Kate Pope, Katrina Reardon, Steven Ring, Anne Ronan, Matthew Silsby, Renee Smyth, Chloe Stutterd, Mathew Wallis, John Waterston, Thomas Wellings, Kirsty West, Christine Wools, Kathy H.C. Wu, David J. Szmulewicz, Martin B. Delatycki, Melanie Bahlo, Paul J. Lockhart

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引用次数: 0

Abstract

The cerebellar ataxias (CAs) are a heterogeneous group of disorders characterized by progressive incoordination. Seventeen repeat expansion (RE) loci have been identified as the primary genetic cause and account for >80% of genetic diagnoses. Despite this, diagnostic testing is limited and inefficient, often utilizing single gene assays. This study evaluates the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Independently, long-read sequencing with adaptive sampling (LR-AS) was performed to identify pathogenic RE. SR-GS provided a genetic diagnosis for 38% of the cohort (40/110) including seven non-RE pathogenic variants. RE causes disease in 33 individuals, with the most common condition being SCA27B (n = 24). In comparison, LR-AS identified pathogenic RE in 29 individuals. RE identification for the two methods was concordant apart from four SCA27B cases not detected by LR-AS due to low read depth. For both technologies manual review of the RE alignment enhances diagnostic outcomes. Orthogonal testing for SCA27B revealed a 15% and 0% false positive rate for SR-GS and LR-AS, respectively. In conclusion, both technologies are powerful screening tools for CA. SR-GS is a mature technology currently used by diagnostic providers, requiring only minor changes in bioinformatic workflows to enable CA diagnostics. LR-AS offers considerable advantages in the context of RE detection and characterization but requires optimization before clinical implementation.

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一项比较可编程靶向长读测序和短读基因组测序用于小脑性共济失调遗传诊断的前瞻性试验

小脑共济失调（CAs）是一种以进行性不协调为特征的异质性疾病。17个重复扩增（RE）位点已被确定为主要遗传原因，占遗传诊断的80%。尽管如此，诊断测试是有限的和低效的，通常使用单基因分析。本研究评估了长读段测序和短读段测序作为CA诊断工具的有效性。我们招募了110名临床诊断为CA的个体（48名女性，62名男性）。我们进行了短读段基因组测序（SR-GS），以鉴定与CA相关的356个基因中的致病性RE和非RE变异。采用适应性采样长读测序（LR-AS）鉴定致病性RE。SR-GS为38%的队列（40/110）提供了遗传诊断，包括7个非RE致病变异。RE导致33例患者发病，其中最常见的是SCA27B （n = 24）。相比之下，LR-AS在29例个体中鉴定出致病性RE。两种方法的RE鉴定结果一致，除了4例由于读取深度低而无法被LR-AS检测到的SCA27B病例。对于这两种技术，人工审查RE对齐可提高诊断结果。SCA27B的正交试验显示，SR-GS和LR-AS的假阳性率分别为15%和0%。总之，这两种技术都是CA的强大筛查工具。SR-GS是一种成熟的技术，目前被诊断提供商使用，只需要对生物信息学工作流程进行微小的改变就可以进行CA诊断。LR-AS在RE检测和表征方面具有相当大的优势，但在临床应用前需要进行优化。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Genome research 生物-生化与分子生物学

CiteScore

12.40

自引率

1.40%

发文量

140

审稿时长

6 months

期刊介绍： Launched in 1995, Genome Research is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are presented electronically on the journal''s web site where appropriate. The journal also provides Reviews, Perspectives, and Insight/Outlook articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context.