The labs of Jennifer Adair and Hans-Peter Kiem at the Fred Hutchinson Cancer Research Center use LabKey Server SDMS software to speed efforts in the development of stem cell gene therapy for a wide range of diseases, from HIV/AIDS to cancers.
LabKey Server-based assay tools free lab members to focus on data interpretation instead of manual processing, help them look quickly across results collected from multiple experiments over time, and enable them to scale up analysis as fast as sequencing throughput.
They use LabKey Server’s assay infrastructure to automate manual workflows and provide rich, real-time reporting. Instead of painstakingly stitching together a multiplicity of spreadsheets to answer questions about their data, lab staff can see results right away. Transformation scripts pre-process data during import, so quality control statistics are available immediately through a web-based interface. If results require normalization, adjustments can be made in bulk, with changes tracked. Once data and metadata are in the system, lab members can view real-time reports written in R that summarize and visualize results, or use LabKey Server’s graphical tools to further sort, filter, combine, and chart results.
The teams employ an Ion Torrent sequencer, so each run generates tens of thousands of data rows. These results must not only be processed for analysis, but also stored for potential reuse. LabKey Server provides both a back-end repository for archiving results and tools for looking across multiple runs, enabling comparison of results over time or across experiments. LabKey Software hosts the Kiem Lab instance of LabKey Server, so storage capacity and version upgrades are handled transparently.
The Adair and Kiem labs have used LabKey Server to develop ground-breaking approaches to gene therapy and chemotherapy, such as a treatment for glioblastoma that has already extended survival for a small number of cancer patients from months to years. LabKey Server helps the team pursue projects that range from identifying genes that protect stem cells from chemotherapy to investigating safer viral vectors for gene therapy.
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