Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms
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ORIGINAL RESEARCH ARTICLE
Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms Joonhong Park1,2 · Hoon Seok Kim1,2 · Jong‑Mi Lee1,2 · Jin Jung1,2 · Dain Kang2 · Hayoung Choi2 · Gun Dong Lee2 · Jungok Son2 · Silvia Park3 · Byung‐Sik Cho3 · Hee‐Je Kim3 · Seongkoo Kim4 · Jae Wook Lee4 · Nack‑Gyun Chung4 · Bin Cho4 · Hua Zhang5 · Nickolay A. Khazanov5 · Jongpill Choi6 · Jae‑Won Jung6 · Yonggoo Kim1,2 · Myungshin Kim1,2
© Springer Nature Switzerland AG 2020
Abstract Introduction Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. Objectives Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. Methods 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. Results 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). Conclusion OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.
Key Points This article outlines the analytical performance and potential clinical performance of the Oncomine™ myeloid research assay, which targets both DNA and RNA Electronic supplementary material The online version of this article (https://doi.org/10.1007/s40291-020-00484-5) contains supplementary material, which is available to authorized users. * Yonggoo Kim [email protected]
Oncomine™ myeloid research assay showed excellent identification of single nucleotide variations, insertions and/or deletions, and gene fusions MECOM gene expression could be useful to verify the MECOM-associated rearrangements
* Myungshin Kim [email protected] Extended author information available
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