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Machine Learning of Bone Marrow Histopathology Identifies Genetic and Clinical Determinants in Patients with MDS
Authors
Tero A. Aittokallio
Oscar E. Brück
+9 more
Freja T. Ebeling
Helena R. Hohtari
Aleksandr Ianevski
Panu E. Kovanen
Soili I. Kytölä
Susanna E. Lallukka-Brück
Satu M. Mustjoki
Kimmo V. Porkka
Pedro M. Ramos
Publication date
22 March 2021
Publisher
Doi
Cite
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on
PubMed
Abstract
Publisher Copyright: ©2021 American Association for Cancer Research.In myelodysplastic syndrome (MDS) and myeloproliferative neoplasm (MPN), bone marrow (BM) histopathology is assessed to identify dysplastic cellular morphology, cellularity, and blast excess. Yet, other morphologic findings may elude the human eye. We used convolutional neural networks to extract morphologic features from 236 MDS, 87 MDS/MPN, and 11 control BM biopsies. These features predicted genetic and cytogenetic aberrations, prognosis, age, and gender in multivariate regression models. Highest prediction accuracy was found for TET2 [area under the receiver operating curve (AUROC) = 0.94] and spliceosome mutations (0.89) and chromosome 7 monosomy (0.89). Mutation prediction probability correlated with variant allele frequency and number of affected genes per pathway, demonstrating the algorithms' ability to identify relevant morphologic patterns. By converting regression models to texture and cellular composition, we reproduced the classical del(5q) MDS morphology consisting of hypolobulated megakaryocytes. In summary, this study highlights the potential of linking deep BM histopathology with genetics and clinical variables. SIGNIFICANCE: Histopathology is elementary in the diagnostics of patients with MDS, but its high-dimensional data are underused. By elucidating the association of morphologic features with clinical variables and molecular genetics, this study highlights the vast potential of convolutional neural networks in understanding MDS pathology and how genetics is reflected in BM morphology.See related commentary by Elemento, p. 195.Peer reviewe
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Last time updated on 19/12/2022