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Measuring TCR-pMHC Binding In Situ using a FRET-based Microscopy Assay

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Published on: October 30, 2015

Flexible Distance-Based TCR Analysis in Python with tcrdist3.

Koshlan Mayer-Blackwell¹, Andrew Fiore-Gartland¹, Paul G Thomas²

¹Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|September 10, 2022

Summary

This summary is machine-generated.

This study introduces tcrdist3, a Python package for analyzing T cell receptor (TCR) sequences. It helps identify antigen-specific TCRs and understand immune responses by analyzing sequence similarities and network features.

Keywords:

Bioinformatics Distance-based learning Epitope-specificity Python T cell receptors TCR

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Streamlined Single Cell TCR Isolation and Generation of Retroviral Vectors for In Vitro and In Vivo Expression of Human TCRs

Published on: September 10, 2017

Area of Science:

Immunology
Bioinformatics
Computational Biology

Background:

T cell receptor (TCR) sequencing is crucial for studying adaptive immunity.
Antigen-specific TCRs often share sequence motifs, indicating functional relationships.

Purpose of the Study:

To introduce tcrdist3, a novel Python package for distance-based TCR analysis.
To demonstrate tcrdist3's utility in identifying antigen-specific TCRs and analyzing immune repertoires.

Main Methods:

Utilizing sequence similarity networks, gene-usage plots, and CDR3 logos for TCR analysis.
Employing the TCRjoin feature for querying TCR sequences against large datasets.
Leveraging the TCRdist metric for neighbor enrichment testing to identify antigenically selected TCRs.

Main Results:

Demonstrated identification of TCR sequence features associated with antigen specificity.
Showcased flexible querying of TCR sequences against bulk repertoires.
Illustrated identification of candidate polyclonal TCRs under antigenic selection.

Conclusions:

tcrdist3 offers a flexible and powerful framework for distance-based TCR analysis.
The package facilitates the identification of antigen-specific TCRs and the study of immune responses.
tcrdist3 enhances the analysis of TCR repertoire data for immunological research.