Experiment Overview

Repository ID: FR-FCM-ZYQT Experiment name: CNTRP Study_Multi-centre validation of flow cytometry-based biomarkers MIFlowCyt score: 30.00%
Primary researcher: Mehrnoush Malek PI/manager: CAN-ASC Ivison Uploaded by: Mehrnoush Malek
Experiment dates: 2018-10-01 - Dataset uploaded: Oct 2018 Last updated: Nov 2018
Keywords: [automated gating] [Immunophenotyping] [multi-site study] [standardized flow cytometry] [Blood-based biomarkers] Manuscripts:
BC Children's Hospital Research Institute, Dep. of Surgery, UBC, Vancouver, British Columbia (Canada)
Purpose: This study introduces a pipeline for the acquisition and analyses of standardized immunophenotyping data which can be used on group level comparisons for the discovery and validation of biomarkers using human blood or PBMCs. Detailed information about this study can be found in Ivison, Malek et al., 2018 (submitted).
Conclusion: Higher CVs (>30%) were seen with some rare subpopulations or ones defined by dim or heterogeneously expressed antigens. Generally populations <2.5% of PBMCs were more difficult to gate reproducibly. Populations expressing CD62L and/or CD45RA had very poor reproducibility due to site-specific changes in detectability of these antigens post-thaw. Flow-density based automated gating is suitable for high throughput analyses of blood. The presented pipelines are able to handle data from both healthy and post HSCT samples, as well as data obtained from a separate study or on a differently configured flow cytometer.
Comments: Each sample is linked to information about type (blood vs. PBMCs), patient vs. controls, site and cytometer; this linkage is shown in 'Metadata for Flow Repository uploads'. More data about the panels, gating, samples and experiments can be found in Ivison, Malek et al., 2018 (submitted).
Funding: Canadian National Transplant Research Program/ Canadian Institute of Health Research.
Quality control: • On-site training of key labs by Beckman-Coulter application scientists • Use of pre-formatted staining reagents. • Clinical level cytometer QC (FlowCheck-Pro and FlowSet-Pro) • Multiple staining of the same samples • Multiple analyses of the same data (3 different manual operators, automated
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