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Acute Myeloid Leukemia
Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia
Laura W. Dillon,1 Sheida Hayati,1,2 Gregory W. Roloff,1 Ilker Tunc,3 Mehdi Pirooznia,3 Antonina Mitrofanova2 and Christopher S. Hourigan1
1Laboratory of Myeloid Malignancies, Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD; 2Department of Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ and 3Bioinformatics and Computational Biology Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
ABSTRACT
Great effort is spent on developing therapies to improve the dire outcomes of those diagnosed with acute myeloid leukemia. The methods for quantifying response to therapeutic intervention have however lacked sensitivity. Patients achieving a complete remission as defined by conventional cytomorphological methods therefore remain at risk of subsequent relapse due to disease persistence. Improved risk stratification is possible based on tests designed to detect this residual leukemic burden (measurable residual disease). However, acute myeloid leukemia is a genetically diverse set of diseases, which has made it difficult to develop a single, highly reproducible, and sensitive assay for measurable residual disease. Here we present the development of a digital targeted RNA-sequencing-based approach designed to over- come these limitations by detecting all newly approved European LeukemiaNet molecular targets for measurable residual disease in acute myeloid leukemia in a single standardized assay. Iterative modifications and novel bioinformatics approaches resulted in a greater than 100-fold increase in performance compared with commercially available targeted RNA-sequencing approaches and a limit of detection as low as one leukemic cell in 100,000 cells measured, which is comparable to quanti- tative polymerase chain reaction analysis, the current gold standard for the detection of measurable residual disease. This assay, which can be customized and expanded, is the first demonstrated use of high-sensitiv- ity RNA-sequencing for measurable residual disease detection in acute myeloid leukemia and could serve as a broadly applicable standardized tool.
Introduction
Despite the achievement of a “complete remission” following therapy, patients with acute myeloid leukemia (AML) remain at risk of relapse because of the per- sistence of disease that is not detected by conventional cytomorphological meth- ods.1 Risk stratification of such patients is possible based on tests designed to detect this residual leukemic burden (termed measurable residual disease; MRD).1- 6 The importance of MRD testing in AML for prognostic risk stratification has become increasingly evident, such that the AML response criteria were substan- tively updated in 2017 by the introduction of the category of complete remission without MRD.4
A variety of technologies, such as real-time quantitative polymerase chain reac- tion (qPCR) analysis and flow cytometry, focusing on the identification of recur- rent molecular abnormalities or leukemia-associated immune phenotypes, have been developed for MRD detection in AML.7 The mutational and clonal hetero- geneity of AML provides a wide variety of targets for molecular MRD tracking,
Ferrata Storti Foundation
Haematologica 2019 Volume 104(2):297-304
Correspondence:
hourigan@nih.gov
Received: July 26 2018. Accepted: August 28, 2018. Pre-published: August 31, 2018.
doi:10.3324/haematol.2018.203133
Check the online version for the most updated information on this article, online supplements, and information on authorship & disclosures: www.haematologica.org/content/104/2/297
©2019 Ferrata Storti Foundation
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