LabKey Server NAb: A tool for analyzing, visualizing and sharing results from neutralizing antibody assays

Abstract

BackgroundMultiple types of assays allow sensitive detection of virus-specific neutralizing antibodies. For example, the extent of antibody neutralization of HIV-1, SIV and SHIV can be measured in the TZM-bl cell line through the degree of luciferase reporter gene expression after infection. In the past, neutralization curves and titers for this standard assay have been calculated using an Excel macro. Updating all instances of such a macro with new techniques can be unwieldy and introduce non-uniformity across multi-lab teams. Using Excel also poses challenges in centrally storing, sharing and associating raw data files and results.ResultsWe present LabKey Server's NAb tool for organizing, analyzing and securely sharing data, files and results for neutralizing antibody (NAb) assays, including the luciferase-based TZM-bl NAb assay. The customizable tool supports high-throughput experiments and includes a graphical plate template designer, allowing researchers to quickly adapt calculations to new plate layouts. The tool calculates the percent neutralization for each serum dilution based on luminescence measurements, fits a range of neutralization curves to titration results and uses these curves to estimate the neutralizing antibody titers for benchmark dilutions. Results, curve visualizations and raw data files are stored in a database and shared through a secure, web-based interface. NAb results can be integrated with other data sources based on sample identifiers. It is simple to make results public after publication by updating folder security settings.ConclusionsStandardized tools for analyzing, archiving and sharing assay results can improve the reproducibility, comparability and reliability of results obtained across many labs. LabKey Server and its NAb tool are freely available as open source software at http://www.labkey.com under the Apache 2.0 license. Many members of the HIV research community can also access the LabKey Server NAb tool without installing the software by using the Atlas Science Portal (https://atlas.scharp.org). Atlas is an installation of LabKey Server.

Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1

“…All inhibitory values were calculated using a formally validated Excel-based macro or web-based neutralizing antibodies tool (Piehler et al, 2011) that utilizes average virus and cell control RLU values as well as replicate test well RLU values to calculate the neutralizing antibody titer as a function of the reduction of luciferase reporter gene expression. All means, standard deviations, and R 2 values were calculated using Microsoft Excel formulas.…”

Optimization and validation of a neutralizing antibody assay for HIV-1 in A3R5 cells

“…All IC50/ID50 values were calculated using a formally validated Excel-based macro or web-based neutralizing antibody (Nab) tool (Piehler et al, 2011), both of which utilize average virus and cell control RLU values as well as duplicate test well RLU values to calculate the neutralizing antibody titer as a function of the reduction of luciferase reporter gene expression. Statistical analyses were performed using SAS Version 9.2.…”

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

“…After a lab has completed quality control for a set of runs, a lab data manager copies finalized data into a shared, study-type project. A study-type project serves as an integration and analysis hub for many types of related data for a study (e.g., specimen information, study participant demographics and results from other assays) [47,59]. Collaborators with appropriate permissions can use the server’s web portal to view and analyze this data.…”

“…These include: a fine-grained security model; auditing; options for exporting data in a variety of formats; file upload and sharing; and client APIs (application programming interfaces) for building custom interfaces and workflows using a variety of common languages (e.g., JavaScript, Java, Python, R, etc.) [47,48,59]. …”