An R‐Derived FlowSOM Process to Analyze Unsupervised Clustering of Normal and Malignant Human Bone Marrow Classical Flow Cytometry Data

• Published in: Cytometry. Part A Vol. 95; no. 11; pp. 1191 - 1197
• Main Authors: Lacombe, Francis, Lechevalier, Nicolas, Vial, Jean Philippe, Béné, Marie C.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.11.2019; Wiley Subscription Services, Inc
• Subjects: Bone marrow; Clustering; Computer programs; Flow cytometry; FlowSOM; Hematology; Hematopoiesis; machine learning; Minimal residual disease; MRD; Software; FlowSOM; flow cytometry; machine learning; MRD; bone marrow
• ISSN: 1552-4922; 1552-4930; 1552-4930
• DOI: 10.1002/cyto.a.23897

Multiparameter flow cytometry (MFC) is a powerful and versatile tool to accurately analyze cell subsets, notably to explore normal and pathological hematopoiesis. Yet, mostly supervised subjective strategies are used to identify cell subsets in this complex tissue. In the past few years, the implementation of mass cytometry and the big data generated have led to a blossoming of new software solutions. Their application to classical MFC in hematology is however still seldom reported. Here, we show how one of these new tools, the FlowSOM R solution, can be applied, together with the Kaluza® software, to a new delineation of hematopoietic subsets in normal human bone marrow (BM). We thus combined the unsupervised discrimination of cell subsets provided by FlowSOM and their expert‐driven node‐by‐node assignment to known or new hematopoietic subsets. We also show how this new tool could modify the MFC exploration of hematological malignancies both at diagnosis (Dg) and follow‐up (FU). This can be achieved by direct comparison of merged listmodes of reference normal BM, Dg, and FU samples of a representative acute myeloblastic case tested with the same immunophenotyping panel. This provides an immediate unsupervised evaluation of minimal residual disease. © 2019 International Society for Advancement of Cytometry