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Cytometry A. 2018 Dec 20. doi: 10.1002/cyto.a.23664. [Epub ahead of print]

Implementation and Validation of an Automated Flow Cytometry Analysis Pipeline for Human Immune Profiling.

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Earle A. Chiles Research Institute, Providence Portland Medical Center, Portland, Oregon.
Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia.
Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia.


Automated reagent preparation, sample processing, and data acquisition have increased the rate at which flow cytometry data can be generated. Furthermore, advances in technology and flow cytometry instrumentation continually increase the complexity and dimensionality of this data. Together, this leads to increased pressure on manual data analysis, which has inherent limitations including subjectivity of the analyst and the length of time needed for data processing. These issues can create bottlenecks in the data processing workflow and potentially compromise data quality. To address these issues, as well as the challenges associated with manual gating in a high-volume human immune profiling laboratory, we sought to implement an automated analysis pipeline. In this report, we discuss considerations for selecting an automated analysis method, the process of implementing an automated pipeline, and detail our successful incorporation of an automated gating strategy with flowDensity into our analysis workflow. This validated pipeline augments our laboratory's ability to provide rapid high-throughput immune profiling for patients participating in cancer immunotherapy clinical trials.


T cells; automated analysis; automated gating; cancer; flowDensity; immune profiling; immunotherapy


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