Ort to assess the reproducibility and robustness of CFP and LFP

Ort to assess the reproducibility and robustness of CFP and LFP based experiments, we tested intra-assay variability in both settings by running each sample in triplicate and calculating the coefficient of variation (CV). As shown by the descriptive statistics in Fig. 2A, the average CVs for different cell populations were similar, reflecting comparable intra-assay variability between LFP and CFP. The CV of Tregs frequencies was lower in LFP compared to CFP, suggesting that a more accurate identification of Tregs might be possible by using lyoplates. Additionally, we tested 16574785 consistent across experiments. Furthermore, when CFP and LFP based results were compared, mean cell frequency, with the exception of IL-10+ and IFN-c+ cells as in Fig. 1, were similar, as was the standard error (SE). We concluded that LFP and CFP have comparable inter-assay variability.populations were manually added to the results despite their low score. Fig. 3A shows that detection of IL-10, CD25, IFN-c, and Foxp3 positive cells differs between liquid and lyoplates. While differences in the detection of IL-10+ and IFN-c+ cells were already identified by manual analysis, differences in CD25+ and Foxp3+ cells are uniquely discovered by computational analysis. These results are confirmed by the ROC curves in Figure S4B. To confirm these findings, similar Title Loaded From File analysis was repeated in a validation cohort using new samples. The results of the ROC analysis in Figure S4C confirm the predictive power of IL-10, CD25, and Foxp3, while IFN-c was not confirmed in the validation set. A manual analysis, using the gating strategy shown in Fig. S5, confirmed the results obtained by computational analysis (Fig. 3B). Thus, computational analysis reliably analyses flow cytometry data and identifies cell populations otherwise undetected by conventional manual analysis.DiscussionIn this study we compared the performance of a conventional (liquid, CFP) versus a lyoplate-based flow cytometry platform (LFP) and the potential to integrate flow cytometry with computational data analysis to establish a robust framework to conduct biomarker discovery studies in humans. We found that LFP has a higher sensitivity for detecting key cytokines (IFN-c, IL-10) and activation markers (CD25, Foxp3) compared to CFP, while keeping comparable intra- and interassay variability. Moreover, when computational analysis was performed by using RchyOptimix, novel immunophenotypes were identified. Multicolour flow cytometry is becoming a preferential tool for immuno-monitoring and biomarker discovery in large human studies, thus requiring standardization of both experimental and analytical methods. However, available data refer to relatively small antibody cocktails and include the most common fluorochromes, thus only allowing the detection of a restricted set of markers [13,15,16]. Here, we measured for the first time 12 parameters using a LFP with and without polyclonal cell activation. Its positive performance for immunophenotyping and cytokine detection makes it a suitable alternative to CFP. LFP has the advantage of simplifying the experimental protocol, is time saving (,3 hours in each of our experiments), and allows aComputational analysis identifies novel cell populationsHig.Ort to assess the reproducibility and robustness of CFP and LFP based experiments, we tested intra-assay variability in both settings by running each sample in triplicate and calculating the coefficient of variation (CV). As shown by the descriptive statistics in Fig. 2A, the average CVs for different cell populations were similar, reflecting comparable intra-assay variability between LFP and CFP. The CV of Tregs frequencies was lower in LFP compared to CFP, suggesting that a more accurate identification of Tregs might be possible by using lyoplates. Additionally, we tested 10457188 inter-assay variability using two control samples run across multiple experiments. Fig. 2B shows the results obtained from one control sample run across four different experiments: the percentages of six cell populations investigated were 16574785 consistent across experiments. Furthermore, when CFP and LFP based results were compared, mean cell frequency, with the exception of IL-10+ and IFN-c+ cells as in Fig. 1, were similar, as was the standard error (SE). We concluded that LFP and CFP have comparable inter-assay variability.populations were manually added to the results despite their low score. Fig. 3A shows that detection of IL-10, CD25, IFN-c, and Foxp3 positive cells differs between liquid and lyoplates. While differences in the detection of IL-10+ and IFN-c+ cells were already identified by manual analysis, differences in CD25+ and Foxp3+ cells are uniquely discovered by computational analysis. These results are confirmed by the ROC curves in Figure S4B. To confirm these findings, similar analysis was repeated in a validation cohort using new samples. The results of the ROC analysis in Figure S4C confirm the predictive power of IL-10, CD25, and Foxp3, while IFN-c was not confirmed in the validation set. A manual analysis, using the gating strategy shown in Fig. S5, confirmed the results obtained by computational analysis (Fig. 3B). Thus, computational analysis reliably analyses flow cytometry data and identifies cell populations otherwise undetected by conventional manual analysis.DiscussionIn this study we compared the performance of a conventional (liquid, CFP) versus a lyoplate-based flow cytometry platform (LFP) and the potential to integrate flow cytometry with computational data analysis to establish a robust framework to conduct biomarker discovery studies in humans. We found that LFP has a higher sensitivity for detecting key cytokines (IFN-c, IL-10) and activation markers (CD25, Foxp3) compared to CFP, while keeping comparable intra- and interassay variability. Moreover, when computational analysis was performed by using RchyOptimix, novel immunophenotypes were identified. Multicolour flow cytometry is becoming a preferential tool for immuno-monitoring and biomarker discovery in large human studies, thus requiring standardization of both experimental and analytical methods. However, available data refer to relatively small antibody cocktails and include the most common fluorochromes, thus only allowing the detection of a restricted set of markers [13,15,16]. Here, we measured for the first time 12 parameters using a LFP with and without polyclonal cell activation. Its positive performance for immunophenotyping and cytokine detection makes it a suitable alternative to CFP. LFP has the advantage of simplifying the experimental protocol, is time saving (,3 hours in each of our experiments), and allows aComputational analysis identifies novel cell populationsHig.