Acute myeloid leukemia (AML) is caused by genetic aberrations that also govern the prognosis of patients and guide risk-adapted and targeted therapy. Genetic aberrations in AML are structurally diverse and currently detected by different diagnostic assays. This study sought to establish whole transcriptome RNA sequencing as single, comprehensive, and flexible platform for AML diagnostics. We developed HAMLET (Human AML Expedited Transcriptomics) as bioinformatics pipeline for simultaneous detection of fusion genes, small variants, tandem duplications, and gene expression with all information assembled in an annotated, user-friendly output file. Whole transcriptome RNA sequencing was performed on 100 AML cases and HAMLET results were validated by reference assays and targeted resequencing. The data showed that HAMLET accurately detected all fusion genes and overexpression of EVI1 irrespective of 3q26 aberrations. In addition, small variants in 13 genes that are often mutated in AML were called with 99.2% sensitivity and 100% specificity, and tandem duplications in FLT3 and KMT2A were detected by a novel algorithm based on soft-clipped reads with 100% sensitivity and 97.1% specificity. In conclusion, HAMLET has the potential to provide accurate comprehensive diagnostic information relevant for AML classification, risk assessment and targeted therapy on a single technology platform.

中文翻译：

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通过全转录组RNA测序对急性髓细胞白血病进行综合诊断。

急性髓细胞性白血病（AML）是由遗传畸变引起的，遗传畸变还控制患者的预后并指导适应风险的靶向治疗。AML中的遗传畸变在结构上是多种多样的，目前可通过不同的诊断检测方法进行检测。这项研究试图建立完整的转录组RNA测序作为AML诊断的单一，全面和灵活的平台。我们开发了HAMLET（人类AML快速转录组学）作为生物信息学管道，用于同时检测融合基因，小变异，串联重复和基因表达，并将所有信息组装在带注释的用户友好输出文件中。对100例AML病例进行了完整的转录组RNA测序，并通过参考测定和靶向重测序验证了HAMLET结果。数据显示，无论3q26像差如何，HAMLET都能准确检测到所有融合基因和EVI1的过表达。此外，在AML中经常发生突变的13个基因中的小变异被称为具有99.2％的敏感性和100％的特异性，并且通过基于软剪切读取的新颖算法以100％的敏感性和97.1的新颖算法检测到FLT3和KMT2A中的串联重复。特异性百分比。总之，HAMLET有可能在单个技术平台上提供与AML分类，风险评估和靶向治疗相关的准确，全面的诊断信息。通过一种基于软剪切读段的新颖算法检测FLT3和KMT2A中的双链和双链重复，灵敏度为100％，特异性为97.1％。总之，HAMLET有可能在单个技术平台上提供与AML分类，风险评估和靶向治疗相关的准确，全面的诊断信息。通过一种基于软剪切读段的新颖算法检测FLT3和KMT2A中的双链和双链重复，灵敏度为100％，特异性为97.1％。总之，HAMLET有可能在单个技术平台上提供与AML分类，风险评估和靶向治疗相关的准确，全面的诊断信息。