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COMPASS identifies T-cell subsets correlated with clinical outcomes.

Publication ,  Journal Article
Lin, L; Finak, G; Ushey, K; Seshadri, C; Hawn, TR; Frahm, N; Scriba, TJ; Mahomed, H; Hanekom, W; Bart, P-A; Pantaleo, G; Tomaras, GD; Kim, JH ...
Published in: Nat Biotechnol
June 2015

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.

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Published In

Nat Biotechnol

DOI

EISSN

1546-1696

Publication Date

June 2015

Volume

33

Issue

6

Start / End Page

610 / 616

Location

United States

Related Subject Headings

  • Treatment Outcome
  • T-Lymphocyte Subsets
  • Single-Cell Analysis
  • Male
  • Immunoglobulin A
  • Immunity, Cellular
  • Humans
  • Healthy Volunteers
  • HIV-1
  • HIV Infections
 

Citation

APA
Chicago
ICMJE
MLA
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Lin, L., Finak, G., Ushey, K., Seshadri, C., Hawn, T. R., Frahm, N., … Gottardo, R. (2015). COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol, 33(6), 610–616. https://doi.org/10.1038/nbt.3187
Lin, Lin, Greg Finak, Kevin Ushey, Chetan Seshadri, Thomas R. Hawn, Nicole Frahm, Thomas J. Scriba, et al. “COMPASS identifies T-cell subsets correlated with clinical outcomes.Nat Biotechnol 33, no. 6 (June 2015): 610–16. https://doi.org/10.1038/nbt.3187.
Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, et al. COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol. 2015 Jun;33(6):610–6.
Lin, Lin, et al. “COMPASS identifies T-cell subsets correlated with clinical outcomes.Nat Biotechnol, vol. 33, no. 6, June 2015, pp. 610–16. Pubmed, doi:10.1038/nbt.3187.
Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart P-A, Pantaleo G, Tomaras GD, Rerks-Ngarm S, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Michael NL, Kim JH, Robb ML, O’Connell RJ, Karasavvas N, Gilbert P, C De Rosa S, McElrath MJ, Gottardo R. COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol. 2015 Jun;33(6):610–616.

Published In

Nat Biotechnol

DOI

EISSN

1546-1696

Publication Date

June 2015

Volume

33

Issue

6

Start / End Page

610 / 616

Location

United States

Related Subject Headings

  • Treatment Outcome
  • T-Lymphocyte Subsets
  • Single-Cell Analysis
  • Male
  • Immunoglobulin A
  • Immunity, Cellular
  • Humans
  • Healthy Volunteers
  • HIV-1
  • HIV Infections