本研究旨在探讨全基因组测序（WGS）作为唯一的方法用于检测B细胞急性淋巴细胞白血病（ALL）中与临床相关的基因组异常，并旨在取代现有的诊断方法。为此，我们评估了150个bp配对末端WGS（90倍白血病/ 30倍生殖细胞系）的分析性能。选择了一组88个回顾性的B细胞ALL样本，以代表已建立的ALL亚型，以及缺乏分层标志物的ALL样本（称为B-other ALL）。无论是配对白血病/生殖细胞系（L/N）（n = 64）的分析，还是仅白血病（L-only）（n = 88）的分析，均能检测到当前ALLTogether试验方案中所需的所有类型的异常，包括非整倍体、结构变异和局部拷贝数异常。此外，与SoC的比较显示完全一致，并且使用两种方法将所有患者正确分配到正确的遗传亚型中。值得注意的是，WGS可以将39个B-other ALL样本中的35个分配到最新ALL分类中考虑的一组新出现的遗传亚型之一。我们进一步研究了高（90倍; n = 58）和低（30倍; n = 30）覆盖率对诊断产量的影响，并观察到与SoC完全一致的结果；低覆盖率能够检测到所有相关病变。对WGS结果进行对ALL中反复重排的一系列基因的过滤，有助于有效提取临床相关信息。然而，由于高度重复的D4Z4区域中嵌入了多个DUX4基因的副本，检测DUX4重排需要额外的定制分析。我们得出结论，WGS作为独立方法的诊断性能令人瞩目，并可以在B细胞ALL的诊断设置中检测到所有临床相关的基因组事件。版权所有© 2023 Rezayee, Eisfeldt, Skaftason, Öfverholm, Sayyab, Syvänen, Maqbool, Lilljebjörn, Johansson, Olsson-Arvidsson, Pietras, Staffas, Palmqvist, Fioretos, Cavelier, Fogelstrand, Nordlund, Wirta, Rosenquist和Barbany。

The suitability of whole-genome sequencing (WGS) as the sole method to detect clinically relevant genomic aberrations in B-cell acute lymphoblastic leukemia (ALL) was investigated with the aim of replacing current diagnostic methods.For this purpose, we assessed the analytical performance of 150 bp paired-end WGS (90x leukemia/30x germline). A set of 88 retrospective B-cell ALL samples were selected to represent established ALL subgroups as well as ALL lacking stratifying markers by standard-of-care (SoC), so-called B-other ALL.Both the analysis of paired leukemia/germline (L/N)(n=64) as well as leukemia-only (L-only)(n=88) detected all types of aberrations mandatory in the current ALLTogether trial protocol, i.e., aneuploidies, structural variants, and focal copy-number aberrations. Moreover, comparison to SoC revealed 100% concordance and that all patients had been assigned to the correct genetic subgroup using both approaches. Notably, WGS could allocate 35 out of 39 B-other ALL samples to one of the emerging genetic subgroups considered in the most recent classifications of ALL. We further investigated the impact of high (90x; n=58) vs low (30x; n=30) coverage on the diagnostic yield and observed an equally perfect concordance with SoC; low coverage detected all relevant lesions.The filtration of the WGS findings with a short list of genes recurrently rearranged in ALL was instrumental to extract the clinically relevant information efficiently. Nonetheless, the detection of DUX4 rearrangements required an additional customized analysis, due to multiple copies of this gene embedded in the highly repetitive D4Z4 region. We conclude that the diagnostic performance of WGS as the standalone method was remarkable and allowed detection of all clinically relevant genomic events in the diagnostic setting of B-cell ALL.Copyright © 2023 Rezayee, Eisfeldt, Skaftason, Öfverholm, Sayyab, Syvänen, Maqbool, Lilljebjörn, Johansson, Olsson-Arvidsson, Pietras, Staffas, Palmqvist, Fioretos, Cavelier, Fogelstrand, Nordlund, Wirta, Rosenquist and Barbany.