Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML). Targeted RNA next-generation sequencing (NGS) is emerging as a powerful and clinically practical tool, but it depends on expression of RNA transcript from the underlying DNA translocation. Here, we show the clinical utility of nanopore long-read sequencing in rapidly detecting DNA translocation with exact breakpoints. In a newly diagnosed patient with AML, conventional karyotyping showed translocation t(10;12)(q22;p13) but RNA NGS detected NUP98-NSD1 fusion transcripts from a known cryptic translocation t(5;11)(q35;p15). Rapid PCR-free nanopore whole-genome sequencing yielded a 26,194 bp sequencing read and revealed the t(10;12) breakpoint to be DUSP13 and GRIN2B in head-to-head configuration. This translocation was then classified as a passenger structural variant. The sequencing also yielded a 20,709 bp sequencing read and revealed the t(5;11) breakpoint of the driver NUP98-NSD1 fusion. The identified DNA breakpoints also served as markers for molecular monitoring, in addition to fusion transcript expression by digital PCR and sequence mutations by NGS. We illustrate that third-generation nanopore sequencing is a simple and low-cost workflow for DNA translocation detection.

染色体易位的检测是急性髓细胞性白血病（AML）诊断和管理中的关键组成部分。靶向RNA下一代测序（NGS）逐渐成为一种功能强大且在临床上实用的工具，但它依赖于基础DNA易位的RNA转录物的表达。在这里，我们展示了纳米孔长序列测序在快速检测具有精确断点的DNA易位中的临床实用性。在新诊断的AML患者中，常规核型分析显示易位t（10; 12）（q22; p13），但RNA NGS从已知的隐秘易位t（5; 11）（q35; p15）中检测到NUP98-NSD1融合转录本。快速无PCR的纳米孔全基因组测序产生了26194 bp的测序读数，并显示t（10; 12）断点为DUSP13和头对头配置的GRIN2B。然后将该易位归类为乘客结构变体。测序还产生了20,709 bp测序读数，并揭示了驱动程序NUP98-NSD1融合的t（5; 11）断裂点。除了通过数字PCR进行的融合转录表达和通过NGS进行的序列突变外，鉴定出的DNA断裂点还可以用作分子监测的标记。我们说明，第三代纳米孔测序是一种简单且低成本的DNA易位检测工作流程。