Bioscience Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
Med. 2024 Oct 11;5(10):1307-1325.e3. doi: 10.1016/j.medj.2024.07.003. Epub 2024 Jul 23.
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.
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.
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.
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.
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.
准确理解致病性变异体并在家族网络或更广泛的人群中进行携带者筛查，需要对复杂重排的碱基分辨率断点进行描绘。然而，尽管使用短读长测序（SRS）进行遗传检测取得了进展，但这项任务仍然具有成本高和挑战性大的特点。
本研究通过采用多种长读长测序（LRS）策略，包括一种名为基于纳米孔的快速获取相邻基因组区域（NanoRanger）的新策略，解决了具有疑似纯合重排的复杂基因组疾病中缺失的致病断点分辨率的挑战。NanoRanger 不需要大量超高分子量 DNA，其易于使用且能快速获取大的感兴趣基因组区域，并具有深度覆盖。
我们描述了一个 16 个家族性病例的队列，每个病例都存在纯合重排，这些重排通过 SRS 和光学基因组图谱（OGM）都无法确定断点。NanoRanger 以单碱基分辨率确定了断点，从而能够准确确定未受影响的家族成员的携带者状态，以及这些基因组病变的起源及其在当地人群中的频率。解析的断点表明，重复 DNA、基因调控元件和转录活性导致了这些新型隐性重排中的基因组不稳定性。
我们的数据表明，NanoRanger 大大提高了复杂基因组疾病碱基分辨率断点解析的成功率，并为孟德尔疾病患者提供了更多获得 LRS 的机会。
M.L. 得到 KAUST 基线奖（BAS/1/1080-01-01）和 KAUST 研究转化基金奖（REI/1/4742-01）的支持。
