CEI: A Clonal Expansion Identifier for T-cell receptor clones following SARS-CoV-2 vaccination.

Yunbei Pan¹, Christian Hofmann², Barbara Banbury³, Harsh Patel³, Stephanie A Bien³, Tom Chou⁴, Otto O Yang²

¹Department of Computational Medicine, UCLA, 621 Charles E. Young Drive S., Los Angeles, 90095-1766, CA, USA.

²Depts. of Medicine and Microbiology, Immunology, and Molecular Genetics, UCLA, 615 Charles E. Young Drive S., Los Angeles, 90095, CA, USA.

³Adaptive Biotechnologies, 1165 Eastlake Ave E, Seattle, 98109, WA, USA.

⁴Department of Computational Medicine, UCLA, 621 Charles E. Young Drive S., Los Angeles, 90095-1766, CA, USA; Department of Mathematics, UCLA, 520 Portola Plaza, MS 6363, Los Angeles, 90095-1555, CA, USA. Electronic address: tomchou@ucla.edu.

PubMed DOI

Abstract

Each T cell typically carries a specific T-cell receptor (TCR) that determines its specificity against an epitope presented by the HLA complex on a target cell. Antigenic challenge triggers the expansion of reactive cells within a diverse pool of T cells with randomly generated receptors, a process that results in epitope-driven shifts of TCR frequencies over time. Here, we analyze the effects of…

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