powerTCR: A model-based approach to comparative analysis of the clone size distribution of the T cell receptor repertoire

Hillary Koch, Dmytro Starenki, Sara J. Cooper, Richard M. Myers, Qunhua Li

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Sequencing of the T cell receptor repertoire is a powerful tool for deeper study of immune response, but the unique structure of this type of data makes its meaningful quantification challenging. We introduce a new method, the Gamma-GPD spliced threshold model, to address this difficulty. This biologically interpretable model captures the distribution of the TCR repertoire, demonstrates stability across varying sequencing depths, and permits comparative analysis across any number of sampled individuals. We apply our method to several datasets and obtain insights regarding the differentiating features in the T cell receptor repertoire among sampled individuals across conditions. We have implemented our method in the open-source R package powerTCR.

Original languageEnglish (US)
Article numbere1006571
JournalPLoS computational biology
Volume14
Issue number11
DOIs
StatePublished - Nov 2018

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

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