Abstract
Purpose
Here, we studied whether amplicon next-generation deep sequencing (NGS) could improve the detection of emerging BCR-ABL1 kinase domain mutations in chronic phase chronic myeloid leukemia (CML) patients under tyrosine kinase inhibitor (TKI) treatment and discussed the clinical relevance of such sensitive mutational detection.
Methods
For NGS data evaluation including extraction of biologically relevant low-level variants from background error noise, we established and applied a robust and versatile bioinformatics approach.
Results
Results from a retrospective longitudinal analysis of 135 samples of 15 CML patients showed that NGS could have revealed emerging resistant mutants 2–11 months earlier than conventional sequencing. Interestingly, in cases who later failed first-line imatinib treatment, NGS revealed that TKI-resistant mutations were already detectable at the time of major or deeper molecular response. Identification of emerging mutations by NGS was mirrored by BCR-ABL1 transcript level expressed either fluctuations around 0.1 %IS or by slight transcript level increase. NGS also allowed tracing mutations that emerged during second-line TKI therapy back to the time of switchover. Compound mutants could be detected in three cases, but were not found to outcompete single mutants.
Conclusions
This work points out, that next-generation deep sequencing, coupled with a robust bioinformatics approach for mutation calling, may be just in place to ensure reliable detection of emerging BCR-ABL1 mutations, allowing early therapy switch and selection of the most appropriate therapy. Further, prospective assessment of how to best integrate NGS in the molecular monitoring and clinical decision algorithms is warranted.
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Acknowledgments
This work was supported by the Internal Grant Agency of Ministry of Health of the Czech Republic Grants No. IGA NT11555 and IGA NT13899 and ERDF OPPK CZ.2.16/3.1.00/28007. The authors thank also the Interlaboratory Robustness of Next Generation Sequencing—IRON-II research consortium (supported by Roche Diagnostics) and the Czech Leukemia Study Group for Life—CELL for support to this work. T. S. and V. K. were also supported by UNCE 204021 from Charles University in Prague..
Conflict of interest
The authors report following conflict of interest disclosure: K. M. P.—Novartis and Bristol Myers-Squibb—research grant and honoraria; S. S., G. M. and M. B.—Novartis, Bristol Myers-Squibb and Ariad—consultancy; A. K.—Roche Diagnostics—honoraria and employment by AstraZeneca; A. H.—Novartis, BMS, Ariad, Pfizer—research support; H. K.—Novartis and Bristol Myers-Squibb—consultancy and honoraria Roche Diagnostics—research support.
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Katerina Machova Polakova and Vojtech Kulvait contributed equally to this manuscript.
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Machova Polakova, K., Kulvait, V., Benesova, A. et al. Next-generation deep sequencing improves detection of BCR-ABL1 kinase domain mutations emerging under tyrosine kinase inhibitor treatment of chronic myeloid leukemia patients in chronic phase. J Cancer Res Clin Oncol 141, 887–899 (2015). https://doi.org/10.1007/s00432-014-1845-6
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DOI: https://doi.org/10.1007/s00432-014-1845-6