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

ABSTRACT: Sequencing of the T cell receptor (TCR) 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.

SUBMITTER: Koch H

PROVIDER: S-EPMC6287877 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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

Koch Hillary H Starenki Dmytro D Cooper Sara J SJ Myers Richard M RM Li Qunhua Q

PLoS computational biology 20181128 11

Sequencing of the T cell receptor (TCR) 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 sample ...[more]

PMID: 30485278

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