Experiment Overview
| Repository ID: | FR-FCM-Z3ET | Experiment name: | Flow cytometry of AML and MDS patients | MIFlowCyt score: | 27.00% |
| Primary researcher: | Morteza Chalabi | PI/manager: | Morteza Chalabi | Uploaded by: | Morteza Chalabi |
| Experiment dates: | 2018-01-01 - 2021-01-01 | Dataset uploaded: | Jan 2021 | Last updated: | Jan 2021 |
| Keywords: | [flow cytometry] | Manuscripts: | |||
| Organizations: |
BRIC – University of Copenhagen, Faculty of Health and Medical Sciences, Copenhagen, (Denmark)
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| Purpose: | COMPARE, an ultra-fast and robust suite for multiparametric screening, identifies phenotypic drug responses in acute myeloid leukemia | ||||
| Conclusion: | We show that COMPARE can effectively circumvent batch effects in multidimensional screening data while showing remarkably fast clustering. Using COMPARE to analyze high-throughput flow cytometry screening of AML cells, we successfully removed various biases and grouped drugs based on their responses. COMPARE effectively revealed that groups of drugs showed similar responses even though their known mechanisms are different from each other. COMPARE was sensitive enough to capture subtle changes in drug responses. We further applied COMPARE to 25 clinical flow cytometry data sets representing AML and myelodysplastic syndrome (MDS) patients. Without prior knowledge, COMPARE could effectively group the samples based on the disease with indications that the grouping also linked to clinical outcome. Thus we conclude that COMPARE is a useful tool for exploring complex multiparametric datasets and to help interpretation of drug responses. | ||||
| Comments: | Clinical flow cytometry data using a slightly modified AML panel as described by the Euroflow Consortium from 25 bone marrow aspirates from MDS and AML patients from Rigshospitalet (Copenhagen, DK) were used for analysis. Each sample was analyzed using a total of four tubes (Euroflow AML panel tubes 1-4) with eight antibodies in each tube. Acquisition of data was performed on a FACS Canto (Becton Dickinson Immunocytometry Systems) and data analysis was done in the Infinicyt software (Cytognos, Salamanca, Spain). These are fcs files version 2 (saved as 3) so don't have embedded spillover matrix. In case of using COMPARE-suite to reproduce the result of the paper, you can only use the 5th and 6th modules as there are no negative controls: (1) we set n = 5 in the 5th module, (2) we used these channels in the 5th module: CD16:FITC-A,CD13:PE-A,CD11b:APC-A,CD10:APC-H7-A,CD35:FITC-A,CD64:PE-A,IREM2(CD300e):APC-A,CD14:APC-H7-A,CD36:FITC-A,CD105:PE-A,CD33:APC-A,CD71:APC-H7-A,CD56:PE-A,CD7:APC-A,CD19:APC-H7-A,SSC-A,CD34:PerCP-Cy5-5-A,CD117:PE-Cy7-A,HLA-DR:V450-A,CD45:V500-A | ||||
| Funding: | This work was supported through a centre grant from the Novo Nordisk Foundation (Novo Nordisk Foundation Center for Stem Cell Biology, DanStem; Grant Number NNF17CC0027852) and is also part of the Danish Research Center for Precision Medicine in Blood Cancers funded by the Danish Cancer Society (Grant number R223‐A13071) and Greater Copenhagen Health Science Partners. | ||||
| Quality control: | FCS collection for software testing | ||||
