Email updates

Keep up to date with the latest news and content from BMC Bioinformatics and BioMed Central.

Open Access Highly Accessed Software

Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform

Josh Eckels1, Cory Nathe1, Elizabeth K Nelson1*, Sara G Shoemaker2, Elizabeth Van Nostrand1, Nicole L Yates34, Vicki C Ashley35, Linda J Harris2, Mark Bollenbeck2, Youyi Fong6, Georgia D Tomaras3478 and Britt Piehler1

Author Affiliations

1 LabKey Software, Seattle, WA, USA

2 Statistical Center for HIV/AIDS Research & Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA

3 Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA

4 Department of Medicine, Duke University Medical Center, Durham, NC, USA

5 Department of Surgery, Duke University Medical Center, Durham, NC, USA

6 Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

7 Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA

8 Department of Immunology, Duke University Medical Center, Durham, NC, USA

For all author emails, please log on.

BMC Bioinformatics 2013, 14:145  doi:10.1186/1471-2105-14-145

Published: 30 April 2013

Abstract

Background

Immunoassays that employ multiplexed bead arrays produce high information content per sample. Such assays are now frequently used to evaluate humoral responses in clinical trials. Integrated software is needed for the analysis, quality control, and secure sharing of the high volume of data produced by such multiplexed assays. Software that facilitates data exchange and provides flexibility to perform customized analyses (including multiple curve fits and visualizations of assay performance over time) could increase scientists’ capacity to use these immunoassays to evaluate human clinical trials.

Results

The HIV Vaccine Trials Network and the Statistical Center for HIV/AIDS Research and Prevention collaborated with LabKey Software to enhance the open source LabKey Server platform to facilitate workflows for multiplexed bead assays. This system now supports the management, analysis, quality control, and secure sharing of data from multiplexed immunoassays that leverage Luminex xMAP® technology. These assays may be custom or kit-based. Newly added features enable labs to: (i) import run data from spreadsheets output by Bio-Plex Manager™ software; (ii) customize data processing, curve fits, and algorithms through scripts written in common languages, such as R; (iii) select script-defined calculation options through a graphical user interface; (iv) collect custom metadata for each titration, analyte, run and batch of runs; (v) calculate dose–response curves for titrations; (vi) interpolate unknown concentrations from curves for titrated standards; (vii) flag run data for exclusion from analysis; (viii) track quality control metrics across runs using Levey-Jennings plots; and (ix) automatically flag outliers based on expected values. Existing system features allow researchers to analyze, integrate, visualize, export and securely share their data, as well as to construct custom user interfaces and workflows.

Conclusions

Unlike other tools tailored for Luminex immunoassays, LabKey Server allows labs to customize their Luminex analyses using scripting while still presenting users with a single, graphical interface for processing and analyzing data. The LabKey Server system also stands out among Luminex tools for enabling smooth, secure transfer of data, quality control information, and analyses between collaborators. LabKey Server and its Luminex features are freely available as open source software at http://www.labkey.com webcite under the Apache 2.0 license.