Case Study 1: Automating Analysis of Clinical Trial Data
We recently analyzed a large dataset from a clinical trial of anti-IgE (omalizumab), which examined whether combination therapy with omalizumab and allergen immunotherapy for ragweed reduced seasonal allergic rhinitis compared with immunotherapy alone. The four-arm, randomized, double-blind, placebo-controlled study had nine time points, eight panels examining immune cell activation and one negative control panel—producing 10,991 flow cytometry standard (FCS) data files.
Manual organization, analysis, and report generation with these FCS files would produce a large bottleneck, slowing the progress of trial reporting and publication. However, with three key tools described in this article—group organization, templates, and command line—FlowJo provided an automation solution, addressing the bottleneck with a scalable solution that can:
- Organize samples and batch analyze
- Maintain consistent analysis for repeated SOP
- Reduce downtime caused by manual analysis and report generation
- Increase lab capability for high-throughput and high-content assays
Groups Organize Samples and Enable Batch Analysis
An intuitive user interface facilitates rapid setup of an analysis strategy, including statistics, hierarchical cellular subsetting through “gating” (boundaries which isolate events), and batch application to related samples using a patented groups structure. Data organization and management is a critical component in any data-analysis strategy, and groups organize related samples in a database-like structure, add metadata, apply analysis, and provide the underlying organization for batched reports.
Templates Execute Consistent Analysis for Repeated SOP
FlowJo has the ability to generate workspace templates, which saves sample organization, analysis strategy, and report output options without the flow cytometry data (FCS) files. Thus, when data is placed into a template, samples are organized into groups, analyses executed, reports generated, and analysis workspaces created and saved for review.
Command Line Reduces Time from Collection to Reports
The final piece of the automation puzzle comes through the ability to launch FlowJo without a user interface or human intervention. With a few lines of text, command line on Mac, PC, or LINUX is used to point FlowJo to the files to be analyzed, perform auto-compensation (signal processing), calculate gates and statistics, and produce output files such as batch spreadsheet and graph reports (Figure 1).