TCRs_to_clinic

Contributors:

• Ankita Das
• Sheethal Umesh Nagalakshmi

Goals

• Monitor immunotherapy treatment (TCR clonotype over time)
• Diagnosing disease early with TCR clonality change in blood

Introduction

Methods

• FASTQ files obtained from TCR a/b/g/d sequencing
• Run this through automated pipelines available on DNAnexus and a Jupyter lab version
• Analyze Bulk TCR Takara or 5’RACE or Multiplex PCR using ClonoMap Immune Profiler and Immunearch
• Analyze TCR data using Immunarch for data visualization

Running the ClonoMap Immune Profiler pipeline on DNAnexus

Running the ClonoMap paired end pipeline with FASTQ files

Upload metedata file to go with the files and run Immunarch

Implementation

Input:

Bulk TCR Takara or 5’RACE or Multiplex PCR analysis using ClonoMap Immune Profiler and Immunearch

Paired or single end Fastq files generated from the respective chemistries for TCR a/b/g/d sequencing

TCR data analysis using Immunarch

Path for single or list of repertoire files.

Package installation

Automated pipelines are available on DNAnexus. Jupyter lab version is available to institute on any other environment. Immunarch package can be installed following instruction s here: https://immunarch.com/

Running the ClonoMap Immune Profiler pipeline on DNAnexus

Output:

TSV of clones Immunearch generated Pdf reports that can be downloaded. TCR data visualization graphs from Immunarch can be downloaded.

Number of clones and distributions of clones

Relative abundance of clonotypes

Clonotype tracking

Diversity analysis

References:

ImmunoMind Team. (2019). immunarch: An R Package for Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires. Zenodo. http://doi.org/10.5281/zenodo.3367200

Samir, J., Rizzetto, S., Gupta, M. et al. Exploring and analysing single cell multi-omics data with VDJView. BMC Med Genomics 13, 29 (2020). https://doi.org/10.1186/s12920-020-0696-z