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Molecular characterization of triple-negative myeloproliferative neoplasms by next-generation sequencing

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Abstract

The role of next-generation sequencing (NGS) in identifying mutations in the driver, epigenetic regulator, RNA splicing, and signaling pathway genes in myeloproliferative neoplasms (MPNs) has contributed substantially to our understanding of the disease pathogenesis as well as disease evolution. NGS aids in determining the clonal nature of the disease in a subset of these disorders where mutations in the driver genes are not detected. There is a paucity of real-world data on the utility of this test in the characterization of triple-negative myeloproliferative neoplasms (TN-MPN). In this study, 46 samples of TN-MPN (essential thrombocythemia (ET) = 17; primary myelofibrosis (PMF) = 23; & myeloproliferative neoplasm unclassified (MPN-u) = 6) were screened for markers of clonality using targeted NGS. Among these, 25 (54.3%) patients had mutations that would help determine the clonal nature of the disease. Eight of the 17 TN-ET (47%) and 13 of the 23 TN-PMF (56.5%) patients had noncanonical mutations in the driver genes and mutations in the genes involved in epigenetic regulation. Identification of mutations categorized as high molecular markers (HMR) in 2 patients helped classify them as PMF with high risk according to the MIPSS 70 scoring system. A novel mutation in the MPIG6B (C6orf25) gene associated with childhood myelofibrosis was detected in a 14-year-old girl. The presence of clonal hematopoiesis could be confirmed in four of the six MPN-u patients in this cohort. This study demonstrates the utility of NGS in improving the characterization of TN-MPN by establishing clonality and detecting noncanonical mutations in driver genes, thereby aiding in clinical decision-making.

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Data availability

All data relevant to the study are included in the article or uploaded as a supplementary file. Additional clinical and genetic data, if required, are available on reasonable request.

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Acknowledgements

We acknowledge Dr. Shaji Ramachandran Velayudan, CMC Vellore, and Dr. Vivek Gopalan and Medgenome laboratories for their help with the bioinformatic analysis of the data. Technical assistance provided by Ms. Hemamalini Suresh and Ms. Bhuvaneswari is greatly appreciated.

Funding

This study was funded by internal research grants from CMC, Vellore (IRB: 12942 & 11800) and Wellcome DBT India Alliance research grant (IA/CPHS/18/1/503930). P. B. and U. K. are supported by the Wellcome DBT India Alliance (IA/S/15/1/501842) and (IA/CPHE/17/1/503351), respectively. A. V. is supported by the Department of Biotechnology Junior research fellowship (DBT/2018/CMC/1138).

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Authors and Affiliations

  1. Department of Haematology, Christian Medical College, Vellore, Tamil Nadu, India

    Madhavi Maddali, Arvind Venkatraman, Uday Prakash Kulkarni, Sathya Mani, Anu Korula, Fouzia N A, Sharon Anbumalar Lionel, Sushil Selvarajan, Aby Abraham, Biju George, Vikram Mathews & Poonkuzhali Balasubramanian

  2. Department of Pathology, Christian Medical College, Vellore, Tamil Nadu, India

    Santhosh Raj, Elanthenral Sigamani & Marie Therese Manipadam

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  1. Madhavi Maddali
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection, and analysis were performed by Madhavi Maddali, Arvind Venkatraman, and Uday Prakash Kulkarni. The first draft of the manuscript was written by Madhavi Maddali and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Conceptualization: M. M., V. M., P. B.

Methodology: M. M., A. V., S. M.

Formal analysis and investigation: M. M., A. V., U. K., S. M.

Writing—original draft preparation: M. M., U. K., P. B.

Writing—review and editing: A. K., F. N. A., S. L., S. S., A. A., B. G., V. M.

Funding acquisition: M. M., V. M.

Resources: B. G., E. S., M. T. M., S. R., A. A., S. L., S. S., U. K., V. M.

Supervision: P. B.

Corresponding author

Correspondence to Poonkuzhali Balasubramanian.

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The present study is a retrospective analysis using DNA extracted from EDTA blood samples collected for routine molecular diagnostics in our institution from patients suspected of myeloproliferative neoplasms. No additional personal or clinical details were collected from any patient for this study. All procedures performed in this study involving human participants were as per the ethical standards of the institutional research committee. The research and the laboratory tests have been conducted following the World Medical Association Code of Ethics (Declaration of Helsinki, 1964).

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The authors declare no competing interests.

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Maddali, M., Venkatraman, A., Kulkarni, U.P. et al. Molecular characterization of triple-negative myeloproliferative neoplasms by next-generation sequencing. Ann Hematol 101, 1987–2000 (2022). https://doi.org/10.1007/s00277-022-04920-w

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