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

Abstract

BackgroundImmunoassays 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.ResultsThe 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.ConclusionsUnlike 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 under the Apache 2.0 license.

ELISA in the multiplex era: Potentials and pitfalls

“…Accordingly, generating a robust set of quality controls for clinical diagnostics applicable to different assays/platforms presents a significant technical challenge and currently quantitative comparison of samples between different platforms is markedly inconsistent. Currently, ascertaining quality control over several assay cycles laboriously involves calculating representative metrics for each standard curve per cycle, plotting the attained metrics and expected ranges on Levey–Jennings charts to define outliers, excluding data from analysis based on quality metrics and identifying trends that require further investigation . A lack of robust multivariate quality control algorithms and data rejection criteria for multiplexed immunoassays is also problematic.…”

Eight practices for data management to enable team data science

“…2). BLIS is a customized instance of the open-source LabKey [6][7][8][9][10], an application developed to integrate, analyze, and share biomedical research data, including flow cytometry, proteomics, Luminex, ELISpot, ELISA, Nab, rt-PCR, other plate-based assay data, as well as specimen inventory and clinical subject data (Fig. 2).…”

“…To effectively use data science techniques to resolve these translational questions requires innovation in the organization and management of these data. For over a decade the informatics team of the University of Rochester Clinical and Translational Science Institute's Research Data Integration and Analytics group has been developing comprehensive data management workflows for laboratory assays, specimen inventories, and study-specific data using the open-source LabKey platform [6][7][8][9][10]. Early funding for this effort came from several NIAID grants that recognized the need to develop a system to manage and integrate high-throughput genomics and related data from human subjects.…”

Validation of a Triplex Pharmacokinetic Assay for Simultaneous Quantitation of HIV-1 Broadly Neutralizing Antibodies PGT121, PGDM1400, and VRC07-523-LS

“…Quality control (QC) acceptance criteria for Triplex PK assay include but are not limited to: 1) FI-Bkgd readout must have a percentage of coefficient of variation (%CV) between replicates < 20% for each dilution in the titration series and < 15% for a sample that is assayed at a single dilution when fluorescence- background (FI-Bkgd)>100, 2) Three out of five spiked controls must have a recovery between 70 -130% of their input concentration, and 3) the positive control antibody titer, defined as the half maximal effective concentration (EC50) from a five parameter logistic curve fit (5PL) and the highest FI-Bkgd in the positive control standard curve must be within three standard deviations of the historical mean as tracked with Levey-Jennings charts [Portal, Labkey, Seattle, WA ( 25 )]. Guide sets for Levey-Jennings charts that enable tracking of positive controls to historical data were established from >10 standardized assays.…”