Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques present a compelling alternative for clinical diagnostics. Here, Genomic Medicine Sweden—Rare Diseases has explored the utility of HiFi Revio long-read genome sequencing (lrGS) for digital karyotyping of SVs nationwide. The 16 samples from 13 families were collected from all Swedish healthcare regions. Prior investigations had identified 16 SVs, ranging from simple to complex rearrangements, including inversions, translocations, and copy number variants. We have established a national pipeline and a shared variant database for variant calling and filtering. Using lrGS, 14 of the 16 known SVs are detected. Of these, 13 are mapped at nucleotide resolution, and one complex rearrangement is only visible by read depth. Two Chromosome 21 rearrangements, one mosaic, remain undetected. Average read lengths are 8.3–18.8 kb with coverage exceeding 20× for all samples. De novo assembly results in a limited number of phased contigs per individual (N50 6–86 Mb), enabling direct characterization of the chromosomal rearrangements. In a national pilot study, we demonstrate the utility of HiFi Revio lrGS for analyzing chromosomal rearrangements. Based on our results, we propose a 5-year plan to expand lrGS use for rare disease diagnostics in Sweden.

中文翻译：

---

一项关于染色体重排的全国长读长测序研究揭示了隐藏的复杂性


临床遗传实验室通常需要对染色体重排/结构变异 （SV） 进行全面分析，从易位和倒位等大事件到多余环/标记染色体和小的缺失或重复。了解这些事件的复杂性及其临床后果需要精确定位断点连接并解析衍生染色体结构。这项任务通常超出了短读长测序技术的能力。相比之下，长读长测序技术为临床诊断提供了一种令人信服的替代方案。在这里，Genomic Medicine Sweden—Rare Diseases 探索了 HiFi Revio 长读基因组测序 （lrGS） 在全国范围内对 SV 进行数字核型分析的效用。来自瑞典所有医疗保健地区的 16 个家庭的 13 个样本收集。先前的调查已经确定了 16 个 SV，从简单到复杂的重排，包括倒位、易位和拷贝数变异。我们已经建立了一个国家管道和一个共享变体数据库，用于变体调用和筛选。使用 lrGS，检测到 16 个已知 SV 中的 14 个。其中，13 个以核苷酸分辨率进行定位，一个复杂的重排仅通过读取深度可见。两个 21 号染色体重排，一个嵌合体，仍未检测到。所有样品的平均读长为 8.3–18.8 kb，覆盖率超过 20×。从头组装导致每个个体的相位重叠群数量有限 （N50 6–86 Mb），能够直接表征染色体重排。在一项国家试点研究中，我们证明了 HiFi Revio lrGS 在分析染色体重排方面的效用。 根据我们的结果，我们提出了一项 5 年计划，以扩大 lrGS 在瑞典罕见病诊断中的使用。