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Scalable prediction of acute myeloid leukemia using high-dimensional machine learning and blood transcriptomics

Warnat-Herresthal, Stefanie; Perrakis, Konstantinos; Taschler, Bernd; Becker, Matthias; Baßler, Kevin; Beyer, Marc; Günther, Patrick; Schulte-Schrepping, Jonas; Seep, Lea; Klee, Kathrin; Ulas, Thomas; Haferlach, Torsten; Mukherjee, Sach; Schultze, Joachim L.

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Authors

Stefanie Warnat-Herresthal

Bernd Taschler

Matthias Becker

Kevin Baßler

Marc Beyer

Patrick Günther

Jonas Schulte-Schrepping

Lea Seep

Kathrin Klee

Thomas Ulas

Torsten Haferlach

Sach Mukherjee

Joachim L. Schultze



Abstract

Acute myeloid leukemia (AML) is a severe, mostly fatal hematopoietic malignancy. We were interested in whether transcriptomic-based machine learning could predict AML status without requiring expert input. Using 12,029 samples from 105 different studies, we present a large-scale study of machine learning-based prediction of AML in which we address key questions relating to the combination of machine learning and transcriptomics and their practical use. We find data-driven, high-dimensional approaches—in which multivariate signatures are learned directly from genome-wide data with no prior knowledge—to be accurate and robust. Importantly, these approaches are highly scalable with low marginal cost, essentially matching human expert annotation in a near-automated workflow. Our results support the notion that transcriptomics combined with machine learning could be used as part of an integrated -omics approach wherein risk prediction, differential diagnosis, and subclassification of AML are achieved by genomics while diagnosis could be assisted by transcriptomic-based machine learning.

Citation

Warnat-Herresthal, S., Perrakis, K., Taschler, B., Becker, M., Baßler, K., Beyer, M., …Schultze, J. L. (2020). Scalable prediction of acute myeloid leukemia using high-dimensional machine learning and blood transcriptomics. iScience, 23(1), Article 100780. https://doi.org/10.1016/j.isci.2019.100780

Journal Article Type Article
Acceptance Date Dec 12, 2019
Online Publication Date Dec 18, 2019
Publication Date Jan 24, 2020
Deposit Date Jun 10, 2020
Publicly Available Date Jun 18, 2020
Journal iScience
Publisher Cell Press
Peer Reviewed Peer Reviewed
Volume 23
Issue 1
Article Number 100780
DOI https://doi.org/10.1016/j.isci.2019.100780
Related Public URLs https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6992905/

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