Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
Mol Diagn Ther. 2020 Oct;24(5):579-592. doi: 10.1007/s40291-020-00484-5.
Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies.
Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms.
Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis.
All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA correlated well with clinical data, whereas those of FLT3-ITDs were significantly lower than with fragment analysis (P = 0.008). Together, OMA showed strong ability to identify RNA gene fusions (Kappa agreement 0.961), except one RUNX1-MECOM. The MECOM gene was highly expressed in all five samples with MECOM-associated rearrangements, including inv(3), t(3;3), and t(3;21).
OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.
新一代测序（NGS）面板最近已被引入，以有效地检测血液系统恶性肿瘤中的遗传变异。
我们的目的是评估商业化的 Oncomine™髓系研究检测（OMA）在髓系肿瘤中的性能。
使用了经认证的参考材料和临床研究样本，包括 60 个基因组 DNA 和 56 个 RNA 样本。NGS 是使用 OMA 进行的，它能够通过 Ion S5 XL 测序仪检测 40 个目标基因、29 个基因融合和 5 个表达目标基因和 5 个表达控制基因。分析数据与通过核型分析、逆转录聚合酶链反应（PCR）、荧光原位杂交、Sanger 测序、定制 NGS 面板和片段分析获得的临床数据进行比较。
除了我们预计 OMA 不会检测到的三个（两个 ASXL1 和一个 CEBPA）突变外，所有参考材料的目标均被检测到。在临床搜索样本中，OMA 满意地鉴定了 DNA 变体，包括 90 个单核苷酸变体（SNVs）、48 个小插入和缺失（indels）和 8 个 FLT3 内部串联重复（ITDs）（Kappa 一致性 0.938）。OMA 测量的 SNVs 和 indels 的变异等位基因频率与临床数据密切相关，而 FLT3-ITDs 的频率明显低于片段分析（P=0.008）。总体而言，OMA 具有很强的识别 RNA 基因融合的能力（Kappa 一致性 0.961），除了一个 RUNX1-MECOM。在所有五个具有 MECOM 相关重排的样本中，包括 inv（3）、t（3;3）和 t（3;21），MECOM 基因均高度表达。
OMA 显示出出色的分析和潜在的临床性能，可能是传统分子检测的良好替代品。
