Maroilley Tatiana, Tarailo-Graovac Maja
Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada.
Methods Mol Biol. 2025;2968:131-150. doi: 10.1007/978-1-0716-4750-9_7.
Clinical diagnostic workflows have been focused on exome sequencing and the detection of small protein-coding variants (single-nucleotides, short insertions, and deletions) often overlooking complex genomic rearrangements (CGR). Indeed, detection of CGRs required genome rather than exome sequencing and development of advanced analytical tools. Among the available technologies for genome sequencing, short-read whole genome sequencing (srWGS) is currently the most cost-efficient technology for detecting variants as it covers most of the genome and theoretically allows the detection of the whole spectrum of genomic variations. To develop and assess new workflows for accurate detection of CGRs with srWGS, model organisms such as Caenorhabditis elegans (C. elegans) constitute an excellent biological tool that could be used in a tractable fashion. Indeed, many C. elegans strains called balancers are known to carry CGRs used to balance genomic loci. Balancer C. elegans genomes constitute then a source of known CGRs to assess analytical methods and the compact genome of C. elegans allows reduced sequencing and experimental validation costs but also reduced computational burden while testing computational approaches. Here, we present a complete workflow to detect and validate CGR breakpoints as well as guidelines to interpret their structure using srWGS developed on C. elegans balancers strains.
临床诊断流程一直聚焦于外显子组测序以及小蛋白质编码变异（单核苷酸、短插入和缺失）的检测，常常忽略了复杂基因组重排（CGR）。事实上，检测CGR需要进行基因组而非外显子组测序，并开发先进的分析工具。在现有的基因组测序技术中，短读长全基因组测序（srWGS）目前是检测变异最具成本效益的技术，因为它覆盖了大部分基因组，理论上能够检测所有类型的基因组变异。为了开发和评估利用srWGS准确检测CGR的新流程，秀丽隐杆线虫（C. elegans）等模式生物构成了一种出色的生物学工具，可方便地加以利用。实际上，许多被称为平衡子的秀丽隐杆线虫品系已知携带用于平衡基因组位点的CGR。秀丽隐杆线虫平衡子基因组于是成为评估分析方法的已知CGR来源，而且秀丽隐杆线虫紧凑的基因组可降低测序和实验验证成本，同时在测试计算方法时减轻计算负担。在此，我们展示了一个完整的流程，用于检测和验证CGR断点，以及使用基于秀丽隐杆线虫平衡子品系开发的srWGS来解释其结构的指南。
