Savara Jakub, Novosád Tomáš, Gajdoš Petr, Kriegová Eva
Department of Computer Science, VSB-Technical University of Ostrava, Ostrava, 708 00, Czech Republic.
Department of Immunology, Faculty of Medicine and Dentistry, Palacký University in Olomouc and University Hospital Olomouc, 779 00, Olomouc, Czech Republic.
Bioinformatics. 2021 Oct 25;37(20):3398-3404. doi: 10.1093/bioinformatics/btab359.
Recent studies have shown the potential of using long-read whole-genome sequencing (WGS) approaches and optical mapping (OM) for the detection of clinically relevant structural variants (SVs) in cancer research. Three main long-read WGS platforms are currently in use: Pacific Biosciences (PacBio), Oxford Nanopore Technologies (ONT) and 10x Genomics. Recently, whole-genome OM technology (Bionano Genomics) has been introduced into human diagnostics. Questions remain about the accuracy of these long-read sequencing platforms, how comparable/interchangeable they are when searching for SVs and to what extent they can be replaced or supplemented by OM. Moreover, no tool can effectively compare SVs obtained by OM and WGS.
This study compared optical maps of the breast cancer cell line SKBR3 with AnnotSV outputs from WGS platforms. For this purpose, a software tool with comparative and filtering features was developed. The majority of SVs up to a 50 kbp distance variance threshold found by OM were confirmed by all WGS platforms, and ∼99% of translocations and ∼80% of deletions found by OM were confirmed by both PacBio and ONT, with ∼70% being confirmed by 10x Genomics in combination with PacBio and/or ONT. Interestingly, long deletions (>100 kbp) were detected only by 10x Genomics. Regarding insertions, ∼74% was confirmed by PacBio and ONT, but none by 10x Genomics. Inversions and duplications detected by OM were not detected by WGS. Moreover, the tool enabled the confirmation of SVs that overlapped in the same gene(s) and was applied to the filtering of disease-associated SVs.
最近的研究表明，在癌症研究中，使用长读长全基因组测序（WGS）方法和光学图谱（OM）检测临床相关结构变异（SV）具有潜力。目前主要使用三种长读长WGS平台：太平洋生物科学公司（PacBio）、牛津纳米孔技术公司（ONT）和10x基因组学公司。最近，全基因组OM技术（Bionano基因组学）已被引入人类诊断领域。关于这些长读长测序平台的准确性、在寻找SV时它们的可比性/互换性以及它们可被OM替代或补充的程度，仍然存在问题。此外，没有工具能够有效地比较通过OM和WGS获得的SV。
本研究将乳腺癌细胞系SKBR3的光学图谱与WGS平台的AnnotSV输出进行了比较。为此，开发了一种具有比较和过滤功能的软件工具。OM发现的距离变异阈值高达50 kbp的大多数SV被所有WGS平台证实，OM发现的约99%的易位和约80%的缺失被PacBio和ONT两者证实，约70%被10x基因组学与PacBio和/或ONT联合证实。有趣的是，只有10x基因组学检测到了长缺失（>100 kbp）。关于插入，约74%被PacBio和ONT证实，但10x基因组学未证实任何插入。WGS未检测到OM检测到的倒位和重复。此外，该工具能够确认在相同基因中重叠的SV，并应用于疾病相关SV的过滤。
