NanoRanger enables rapid single-base-pair resolution of genomic disorders.

IF 12.8 Q1 MEDICINE, RESEARCH & EXPERIMENTAL Med Pub Date : 2024-10-11 Epub Date: 2024-07-23 DOI:10.1016/j.medj.2024.07.003
Yingzi Zhang, Chongwei Bi, Seba Nadeef, Sateesh Maddirevula, Mashael Alqahtani, Fowzan S Alkuraya, Mo Li
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Abstract

Background: Delineating base-resolution breakpoints of complex rearrangements is crucial for an accurate clinical understanding of pathogenic variants and for carrier screening within family networks or the broader population. However, despite advances in genetic testing using short-read sequencing (SRS), this task remains costly and challenging.

Methods: This study addresses the challenges of resolving missing disease-causing breakpoints in complex genomic disorders with suspected homozygous rearrangements by employing multiple long-read sequencing (LRS) strategies, including a novel and efficient strategy named nanopore-based rapid acquisition of neighboring genomic regions (NanoRanger). NanoRanger does not require large amounts of ultrahigh-molecular-weight DNA and stands out for its ease of use and rapid acquisition of large genomic regions of interest with deep coverage.

Findings: We describe a cohort of 16 familial cases, each harboring homozygous rearrangements that defied breakpoint determination by SRS and optical genome mapping (OGM). NanoRanger identified the breakpoints with single-base-pair resolution, enabling accurate determination of the carrier status of unaffected family members as well as the founder nature of these genomic lesions and their frequency in the local population. The resolved breakpoints revealed that repetitive DNA, gene regulatory elements, and transcription activity contribute to genome instability in these novel recessive rearrangements.

Conclusions: Our data suggest that NanoRanger greatly improves the success rate of resolving base-resolution breakpoints of complex genomic disorders and expands access to LRS for the benefit of patients with Mendelian disorders.

Funding: M.L. is supported by KAUST Baseline Award no. BAS/1/1080-01-01 and KAUST Research Translation Fund Award no. REI/1/4742-01.

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NanoRanger 能够快速分辨基因组紊乱的单碱基对。
背景:划定复杂重排的碱基分辨率断点对于临床准确了解致病变异以及在家族网络或更广泛的人群中进行携带者筛查至关重要。然而,尽管使用短线程测序技术(SRS)进行基因检测取得了进展,但这项工作仍然成本高昂且极具挑战性:本研究采用多种长读程测序(LRS)策略,包括一种名为 "基于纳米孔的邻近基因组区域快速获取"(NanoRanger)的新型高效策略,解决了疑似同源重排的复杂基因组疾病中缺失致病断点的难题。NanoRanger不需要大量超高分子量DNA,因其易于使用和快速获取深度覆盖的大基因组感兴趣区域而脱颖而出:我们描述了一组 16 例家族病例,每例都有同基因重排,无法通过 SRS 和光学基因组图谱 (OGM) 确定断点。NanoRanger 以单碱基对的分辨率确定了断点,从而准确地确定了未受影响的家族成员的携带状态,以及这些基因组病变的创始性质及其在当地人群中的频率。分辨出的断点显示,重复 DNA、基因调控元件和转录活动导致了这些新型隐性重排基因组的不稳定性:我们的数据表明,NanoRanger 大大提高了解析复杂基因组疾病碱基分辨率断点的成功率,并扩大了 LRS 的使用范围,使孟德尔疾病患者受益:M.L. 由 KAUST Baseline Award no.BAS/1/1080-01-01 和 KAUST Research Translation Fund Award no.REI/1/4742-01。
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来源期刊
Med
Med MEDICINE, RESEARCH & EXPERIMENTAL-
CiteScore
17.70
自引率
0.60%
发文量
102
期刊介绍: Med is a flagship medical journal published monthly by Cell Press, the global publisher of trusted and authoritative science journals including Cell, Cancer Cell, and Cell Reports Medicine. Our mission is to advance clinical research and practice by providing a communication forum for the publication of clinical trial results, innovative observations from longitudinal cohorts, and pioneering discoveries about disease mechanisms. The journal also encourages thought-leadership discussions among biomedical researchers, physicians, and other health scientists and stakeholders. Our goal is to improve health worldwide sustainably and ethically. Med publishes rigorously vetted original research and cutting-edge review and perspective articles on critical health issues globally and regionally. Our research section covers clinical case reports, first-in-human studies, large-scale clinical trials, population-based studies, as well as translational research work with the potential to change the course of medical research and improve clinical practice.
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