Immune Repertoire Analysis
Immune repertoire analysis is the study of the set of T-cell receptors (TCRs) and B-cell receptors (BCRs) in an individual. This analysis provides insights into the state of the adaptive immune system and can be used to understand immune responses to diseases, vaccinations, and therapies. High-throughput sequencing has enabled deep analysis of immune repertoires, revealing millions of receptor sequences that help in diagnostics, treatment development, and monitoring.
📄️ How to Import Data
Platforma allows you to analyze immune repertoire data, explore T- and B-cell clonotypes, run differential analysis, and create publication-ready visuals—all without writing code. Before diving into clonotyping, clustering, or visualization, every project begins with one essential step: importing your data.
📄️ TCR/BCR Clonotyping
Clonotyping is a key step in VDJ analysis, especially when starting from raw sequencing data. This guide explains how to perform clonotyping analysis with the MiXCR Clonotyping Block.
📄️ Importing Preprocessed Data
While Platforma is powerful at processing raw sequencing data, you might already have clonotype tables generated from other tools like MiXCR, ImmunoSEQ, Cell Ranger or a custom formatted table. Platforma makes it easy to import this pre-processed data, allowing you to jump directly to downstream analysis and visualization.
📄️ How to create a custom reference library
Analyzing immune repertoire data from non-model organisms presents a unique challenge: the absence of built-in germline gene reference libraries. Accurate V(D)J gene alignment is crucial for clonotyping, but standard tools often only support common species like humans and mice.
📄️ Diversity and Clonality
The immune repertoire represents the complete collection of T-cell receptors (TCRs) and B-cell receptors (BCRs) in an individual. The diversity of this repertoire is a critical indicator of the immune system's health and its capacity to respond to a wide array of antigens. A diverse repertoire is generally associated with a robust immune system, while reduced diversity can indicate an ongoing immune response, immunodeficiency, or certain diseases.
📄️ Gene Usage
The immune repertoire, comprised of a vast array of T-cell and B-cell receptors (TCRs and BCRs), is generated through a process of V(D)J recombination. During this process, different V (Variable), D (Diversity, for heavy chains), and J (Joining) gene segments are randomly selected and joined together, creating a unique receptor sequence. However, this selection is not always purely random; certain gene segments may be preferentially used, a phenomenon known as "gene usage bias."
📄️ Rarefaction
When analyzing immune repertoires, a key goal is to compare the number of unique clonotypes—the clonal richness—across different samples. However, a common challenge is that samples are often sequenced to different depths. A sample with more sequencing reads will, by chance alone, likely reveal more unique clonotypes, making a direct comparison of richness misleading. This is like comparing the variety of colored candies in a small bag versus a large jar; the jar will almost certainly have more colors simply because it contains more candies.
📄 ️ Clone Tracking
Tracking individual clones over time is crucial for understanding how the immune system responds to stimuli like vaccinations, infections, or therapies. This longitudinal analysis, often called clone tracking, allows researchers to monitor the expansion, contraction, and persistence of specific immune cell populations. By tracking these dynamics, we can identify which clonotypes are driving an immune response, assess the durability of that response, and uncover potential biomarkers for disease or treatment efficacy.