Sande Christopher M, Wu Rui, Yang Guang, Sussman Robyn T, Bigdeli Ashkan, Rushton Chase, Chitturi Akshay, Patel Jay, Szankasi Philippe, Morrissette Jennifer J D, Lim Megan S, Elenitoba-Johnson Kojo S J
Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.
ARUP Laboratories, Salt Lake City, Utah.
J Mol Diagn. 2023 Feb;25(2):87-93. doi: 10.1016/j.jmoldx.2022.11.005. Epub 2022 Dec 8.
Evaluation of suspected myeloid neoplasms involves testing for recurrent, diagnostically and therapeutically relevant genetic alterations. Current molecular testing requires multiple technologies, different domains of expertise, and unconnected workflows, resulting in variable, lengthy turnaround times that can delay treatment. To address this unmet clinical need, we evaluated the Oncomine Myeloid Assay GX panel on the Ion Torrent Genexus platform, a rapid, integrated nucleic acid to report next-generation sequencing platform for detecting clinically relevant genetic aberrations in myeloid disorders. Specimens included synthetic DNA (101 targets) and RNA (9 targets) controls and real-world nucleic acid material derived from bone marrow or peripheral blood samples (40 patients). Ion Torrent Genexus results and performance indices were compared with those obtained from clinically validated genomic testing workflows in 2 separate clinical laboratories. The Ion Torrent Genexus identified 100% of DNA and RNA control variants. For primary patient specimens, the Ion Torrent Genexus reported 82 of 107 DNA variants and 19 of 19 RNA gene fusions identified on clinically validated assays, yielding an 80% overall detection rate. Reanalysis of exported, unfiltered Ion Torrent Genexus data revealed 15 DNA variants not called by the filtered on-board bioinformatics pipeline, yielding a 92% potential detection rate. These results hold promise for the implementation of an integrated next-generation sequencing system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses and accelerated time to precision therapies in myeloid neoplasms.
疑似髓系肿瘤的评估涉及对复发性、具有诊断和治疗相关性的基因改变进行检测。当前的分子检测需要多种技术、不同领域的专业知识以及互不相关的工作流程，导致周转时间可变且冗长，可能会延误治疗。为满足这一未被满足的临床需求，我们在Ion Torrent Genexus平台上评估了Oncomine Myeloid Assay GX检测板，这是一个从核酸到报告的快速集成式下一代测序平台，用于检测髓系疾病中临床相关的基因畸变。样本包括合成DNA（101个靶点）和RNA（9个靶点）对照以及来自骨髓或外周血样本的实际核酸材料（40例患者）。将Ion Torrent Genexus的结果和性能指标与在2个独立临床实验室中通过临床验证的基因组检测工作流程获得的结果进行比较。Ion Torrent Genexus识别出了100%的DNA和RNA对照变异。对于原发性患者样本，Ion Torrent Genexus报告了在临床验证检测中鉴定出的107个DNA变异中的82个以及19个RNA基因融合中的19个，总体检测率为80%。对导出的、未过滤的Ion Torrent Genexus数据进行重新分析后发现，有15个DNA变异未被过滤后的机载生物信息学管道检测到，如果算上这些变异，潜在检测率可达92%。这些结果为实施集成式下一代测序系统以快速检测基因畸变带来了希望，有助于在髓系肿瘤中实现准确的、基于基因组学的诊断并加快精准治疗的时间。
