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

Publication ,  Journal Article
Eckels, J; Nathe, C; Nelson, EK; Shoemaker, SG; Nostrand, EV; Yates, NL; Ashley, VC; Harris, LJ; Bollenbeck, M; Fong, Y; Tomaras, GD; Piehler, B
Published in: BMC Bioinformatics
April 30, 2013

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 under the Apache 2.0 license.

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Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

April 30, 2013

Volume

14

Start / End Page

145

Location

England

Related Subject Headings

  • Software
  • Quality Control
  • Immunoassay
  • Humans
  • HIV-1
  • Cooperative Behavior
  • Computer Security
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences
 

Citation

APA
Chicago
ICMJE
MLA
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Eckels, J., Nathe, C., Nelson, E. K., Shoemaker, S. G., Nostrand, E. V., Yates, N. L., … Piehler, B. (2013). Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics, 14, 145. https://doi.org/10.1186/1471-2105-14-145
Eckels, Josh, Cory Nathe, Elizabeth K. Nelson, Sara G. Shoemaker, Elizabeth Van Nostrand, Nicole L. Yates, Vicki C. Ashley, et al. “Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.BMC Bioinformatics 14 (April 30, 2013): 145. https://doi.org/10.1186/1471-2105-14-145.
Eckels J, Nathe C, Nelson EK, Shoemaker SG, Nostrand EV, Yates NL, et al. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics. 2013 Apr 30;14:145.
Eckels, Josh, et al. “Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform.BMC Bioinformatics, vol. 14, Apr. 2013, p. 145. Pubmed, doi:10.1186/1471-2105-14-145.
Eckels J, Nathe C, Nelson EK, Shoemaker SG, Nostrand EV, Yates NL, Ashley VC, Harris LJ, Bollenbeck M, Fong Y, Tomaras GD, Piehler B. Quality control, analysis and secure sharing of Luminex® immunoassay data using the open source LabKey Server platform. BMC Bioinformatics. 2013 Apr 30;14:145.
Journal cover image

Published In

BMC Bioinformatics

DOI

EISSN

1471-2105

Publication Date

April 30, 2013

Volume

14

Start / End Page

145

Location

England

Related Subject Headings

  • Software
  • Quality Control
  • Immunoassay
  • Humans
  • HIV-1
  • Cooperative Behavior
  • Computer Security
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences