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Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms

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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.

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Acknowledgements

Thermo Fisher Scientific (Waltham, MA, USA) provided technical support for Ion Torrent sequencing in this study but was not involved in data collection or manuscript preparation.

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Authors and Affiliations

  1. Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea

    Joonhong Park, Hoon Seok Kim, Jong-Mi Lee, Jin Jung, Yonggoo Kim & Myungshin Kim

  2. Catholic Genetic Laboratory Center, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea

    Joonhong Park, Hoon Seok Kim, Jong-Mi Lee, Jin Jung, Dain Kang, Hayoung Choi, Gun Dong Lee, Jungok Son, Yonggoo Kim & Myungshin Kim

  3. Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea

    Silvia Park, Byung‐Sik Cho & Hee‐Je Kim

  4. Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea

    Seongkoo Kim, Jae Wook Lee, Nack-Gyun Chung & Bin Cho

  5. Thermo Fisher Scientific, Waltham, MA, USA

    Hua Zhang & Nickolay A. Khazanov

  6. Thermo Fisher Scientific Solutions, Seoul, Republic of Korea

    Jongpill Choi & Jae-Won Jung

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  1. Joonhong Park
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Corresponding authors

Correspondence to Yonggoo Kim or Myungshin Kim.

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Funding

This research was supported by a Grant (18172MFDS182) from the Korean Ministry of Food and Drug Safety in 2020.

Conflict of interest

HZ, NAK, JC, and J-WJ are employed at Thermo Fisher, which provided only technical support for this research. JP, HSK, J-ML, JJ, DK, HC, GDL, JS, SP, B-SC, H-JK, SK, JWL, N-GC, BC, YK, and MK have no conflicts of interest that are directly relevant to the content of this article.

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Park, J., Kim, H.S., Lee, JM. et al. Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms. Mol Diagn Ther 24, 579–592 (2020). https://doi.org/10.1007/s40291-020-00484-5

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