Publication: COMPASS identifies T-cell subsets correlated with clinical outcomes
Issued Date
2015-06-11
Resource Type
ISSN
15461696
10870156
10870156
DOI
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2-s2.0-84930945915
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Mahidol University
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SCOPUS
Bibliographic Citation
Nature Biotechnology. Vol.33, No.6 (2015), 610-616
Suggested Citation
Lin Lin, Greg Finak, Kevin Ushey, Chetan Seshadri, Thomas R. Hawn, Nicole Frahm, Thomas J. Scriba, Hassan Mahomed, Willem Hanekom, Pierre Alexandre Bart, Giuseppe Pantaleo, Georgia D. Tomaras, Supachai Rerks-Ngarm, Jaranit Kaewkungwal, Sorachai Nitayaphan, Punnee Pitisuttithum, Nelson L. Michael, Jerome H. Kim, Merlin L. Robb, Robert J. O'Connell, Nicos Karasavvas, Peter Gilbert, Stephen C. De Rosa, M. Juliana McElrath, Raphael Gottardo COMPASS identifies T-cell subsets correlated with clinical outcomes. Nature Biotechnology. Vol.33, No.6 (2015), 610-616. doi:10.1038/nbt.3187 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/35437
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Title
COMPASS identifies T-cell subsets correlated with clinical outcomes
Author(s)
Lin Lin
Greg Finak
Kevin Ushey
Chetan Seshadri
Thomas R. Hawn
Nicole Frahm
Thomas J. Scriba
Hassan Mahomed
Willem Hanekom
Pierre Alexandre Bart
Giuseppe Pantaleo
Georgia D. Tomaras
Supachai Rerks-Ngarm
Jaranit Kaewkungwal
Sorachai Nitayaphan
Punnee Pitisuttithum
Nelson L. Michael
Jerome H. Kim
Merlin L. Robb
Robert J. O'Connell
Nicos Karasavvas
Peter Gilbert
Stephen C. De Rosa
M. Juliana McElrath
Raphael Gottardo
Greg Finak
Kevin Ushey
Chetan Seshadri
Thomas R. Hawn
Nicole Frahm
Thomas J. Scriba
Hassan Mahomed
Willem Hanekom
Pierre Alexandre Bart
Giuseppe Pantaleo
Georgia D. Tomaras
Supachai Rerks-Ngarm
Jaranit Kaewkungwal
Sorachai Nitayaphan
Punnee Pitisuttithum
Nelson L. Michael
Jerome H. Kim
Merlin L. Robb
Robert J. O'Connell
Nicos Karasavvas
Peter Gilbert
Stephen C. De Rosa
M. Juliana McElrath
Raphael Gottardo
Other Contributor(s)
Fred Hutchinson Cancer Research Center
University of Washington, Seattle
South African Tuberculosis Vaccine Initiative
Centre Hospitalier Universitaire Vaudois
Duke University Medical Center
Thailand Ministry of Public Health
Mahidol University
Armed Forces Research Institute of Medical Sciences, Thailand
Walter Reed Army Institute of Research
HJF
University of Washington, Seattle
South African Tuberculosis Vaccine Initiative
Centre Hospitalier Universitaire Vaudois
Duke University Medical Center
Thailand Ministry of Public Health
Mahidol University
Armed Forces Research Institute of Medical Sciences, Thailand
Walter Reed Army Institute of Research
HJF
Abstract
© 2015 Nature America, Inc. All rights reserved. Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software.