Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing
Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing
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DOI：
10.1016/j.cancergen.2019.08.005
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发表时间：
2019-11-01
期刊：
影响因子：
1.9
通讯作者：
Ma, Edmond S. K.
中科院分区：
文献类型：
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作者：
Au, Chun Hang;Ho, Dona N.;Ma, Edmond S. K.
染色体易位的检测是急性髓性白血病（AML）诊断和治疗的关键组成部分。靶向RNA下一代测序（Targeted RNA generation sequencing， NGS）作为一种强大的临床实用工具正在兴起，但它依赖于潜在DNA易位中RNA转录物的表达。在这里，我们展示了纳米孔长读测序在快速检测具有精确断点的DNA易位方面的临床应用。在一名新诊断的AML患者中，常规的核型分型显示易位t(10;12)(q22;p13)，但RNA NGS检测到来自已知的隐性易位t(5;11)（q35;p15）的NUP98-NSD1融合转录物。快速无pcr纳米孔全基因组测序获得26194 bp的测序读数，并发现t（10;12）断点为DUSP13和GRIN2B头对头结构。这种易位被归类为客运结构变异。测序还获得了20,709 bp的测序读数，并揭示了驱动NUP98-NSD1融合的t（5;11）断点。鉴定的DNA断点还可以作为分子监测的标记，此外还可以通过数字PCR表达融合转录物，并通过NGS进行序列突变。我们说明，第三代纳米孔测序是DNA易位检测的简单和低成本的工作流程。(C) 2019作者。Elsevier Inc.出版。
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 kary-otyping 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. (C) 2019 The Authors. Published by Elsevier Inc.