Turn adaptive repertoire data into actionable immune insights with Intellimune™
Move beyond one-dimensional V(D)J sequencing data and harness the full power of the adaptome.
Adaptive immune receptor repertoire (AIRR) sequencing generates rich and expansive datasets, but capturing actionable biological and clinical insights requires extensive computational expertise. Common analysis pipelines often stop at sequence mapping and rudimentary diversity metrics, leaving critical information such as rare clonotypes, clonal evolution, and antigen-driven selection hidden.
Intellimune™ is designed to bridge the gap between immune repertoire data and repertoire intelligence. Built by immunology and computational experts, our service combines proven bioinformatics workflows with advanced visualization and expert interpretation to transform standard sequencing data into clear, reproducible, and decision-ready insights. Whether you are exploring immune diversity, tracking clonal dynamics in clinical studies, or identifying biomarkers of response and toxicity, Intellimune enables you to:
- Detect and quantify rare, disease-relevant clonotypes
- Compare immune repertoires across samples, timepoints, and cohorts
- Visualize immune dynamics with intuitive, publication-ready outputs
- Translate complex AIRR data into actionable biological conclusions
From single-cell clonal discovery to patient immune repertoire response, Intellimune transforms AIRR sequencing data into clear insights that accelerate biomarker discovery, therapeutic development, and clinical decision-making.
Understand the structure and diversity of the immune repertoire with Intellimune Core
Included in all studies is Intellimune Core, our reproducible data analysis workflow that provides the following easy-to-interpret outputs:
- CDR1, CDR2, and CDR3 identification and quantification
- Clonotype frequency mapping and V–J usage analysis
- Diversity metrics: D50, Shannon entropy, and Diversity Index (DI)
- Low-resolution treemap visualizations for rapid interpretation
- Downloadable processed datasets for downstream analysis
- Single-cell paired chain visualization via iPair Analyzer with read depth, chain usage, and clonotype identification
Intellimune Core provides foundational repertoire characterization across TCR and BCR datasets, and it is best for first-time users conducting initial exploratory studies. Keep browsing to explore Inellimune Plus and Pro workflows for comprehensive data analysis and insight generation.
Expand your repertoire analysis with Intellimune Plus or Pro
Intellimune scales with your needs helping you move faster from data to discovery. Click on the cards below to see how Intellimune Plus or Pro provide comprehensive repertoire insight generation, fast.
Intellimune Plus
High-resolution metrics and visualizations:
Generate high-confidence, insights with deeper characterization of immune diversity and clonality.
Intellimune Pro
Advanced clonal dynamics and cohort-level insights:
Uncover deep biological signals — including immune evolution, therapeutic response, and biomarker candidates — across patients and timepoints.
Discover a dedicated partner for hypothesis-driven custom immune response investigations
For translational research questions and clinical applications, Intellimune Discovery provides fully customized, expert-guided analysis tailored to your study goals. From identifying response and resistance mechanisms to tracking pathogenic clones, we collaborate with you to design, analyze, and interpret AIRR datasets in a translational and clinically relevant context. Common applications for Intellimune Discovery include:
- Antigen specificity prediction and modeling
- Clonotype convergence and public clone identification
- Longitudinal immune tracking and response modeling
- Integrated cohort and multi-parameter analysis
- Custom visualizations and data storytelling
Accelerate decision-making with tailored insights aligned to your translational and clinical development objectives. Click below to learn more about our Intellimune Discovery service.
Interpret every insight with confidence
Intellimune provides a comprehensive suite of metrics and visualizations designed to capture immune diversity, clonality, and functional dynamics. See below examples of key outputs across analysis services.
Treemap Visualizations
Treemaps shows the frequency and distribution of unique clonotypes. Each shape represents a clone, with size proportional to its abundance enabling rapid identification of clonal expansion.
With multi-chain treemaps you can visualize all seven receptor chains simultaneously, revealing relative expression and immune architecture across the full adaptome.
Single-chain treemap
Multi-chain treemap
Clonal Dynamics
This report shows the expanding and contracting of clones found for TRB for one individual after COVID vaccination using edgeR, with adjusted p-values and fold change for each clone.
B cell Analysis and
Somatic Hypermutation Analysis
Report that shows isotype (C-gene) usage of IgM, IgD, IgG, IgE, IgA, and isotype-related metrics, e.g., Class switch recombination (CSR) index and percentage of mutated and unmutated naïve IgD/IgM sequences will be derived from isotype mapping data. The Somatic hypermutations (SHM) score for each unique sequence in a repertoire will be calculated by measuring the percentage of mismatches (mutations) between a data sequence and its V reference. The mean of all sequences in a sample represents a repertoire’s SHM rate.
Diversity Metrics
This report provides a wide range of diversity analysis and metrics to capture the distribution of clonotypes of a sample and global changes in immune response, such as:
- D50 convergence*: Percentage of clones that make up the top 50% of the total reads or RNA expression. There is a direct relationship between D50 and diversity, with the most diverse library calculation being 50 and less diverse as 0.
- Shannon index*: Is a diversity index that incorporates the number of unique clones and their abundance. Shannon is more sensitive to the overall number of clonotypes than D50, particularly lower frequency clonotypes.
- Pielou's evenness: The Pielou index is a normalized Shannon index that describes the evenness of a TCR repertoire.
- Gini index: The Gini index measures equality of distribution and is positively correlated with T cell clonality.
- Inverse Simpson index: Is a measure of the effective number of types in a dataset. It's used to measure the diversity of unique T-cells and B-cells.
These various metrics increase confidence that the diversity is being appropriately measured, and differences may reflect nuances concerning the repertoire that would be masked otherwise.
Antigen Specificity Analysis
New computational models allow for Ag-specific prediction of individual TCRs within repertoire datasets, particularly when training data specific to peptides is generated for a subset of patient samples.
Cohort Analysis for Gene Usage and Sequence Sharing
During exploratory analysis, observe differences between groups of samples by comparing the statistical relationship of pre-calculated data points to answer hypothesis-driven questions.
See how Intellimune reveals hidden immune insights
Intellimune transforms complex AIRR datasets into intuitive visualizations that make immune dynamics immediately clear. From clonal expansion patterns to isotype switching and lineage evolution, these outputs help you identify meaningful biological signals that drive discovery and clinical progress.
Adapted from Atriedo et. al, various diversity indices were used alongside bubble plots to depict the repertoires of RA patients versus healthy controls and post TNFα inhibition therapy.
Adapted from Li et. al, SMH%s and CSR were used to distinguish PBMC and skin lesions BCR repertoires in patients with Systemic Lupus Erythematosus (SLE) and Isolate discoid LE (IDLE). Furthermore, network plots of the related clonotypes colored by isotype were compared in the skin lesions of both IDL and SLE.
Adapted from Li et al., and Atreido et al., On the left a multi-chain tree plot is shown. Each quadrant corresponds to a specific adaptive immune receptor chain as shown on the diagram. Each shape represents a clone, with size proportional to its abundance. On the right, specific clones can be tracked across dilutions.
Our commitment to quality
iRepertoire’s Quality Management System adheres to GCLP standards, ensuring its innovative products and services are of the highest quality and meet or exceed customer requirements and expectations.
Our commitment includes:
- Subject Matter Expert review, from library preparation through data QC, to ensure high quality results
- A data QC pipeline to analyze the conversion of raw reads to mapped and condensed reads, which includes quality flagging
- Batch sharing analysis for flow cells to identify potential sample mis-labeling and/or cross-contamination to guarantee reliable results
- Inclusion of negative and positive control library preparations (in replicate) alongside sample batches
- Stringent QC parameters on critical reagents utilized in processing
Our commitment to Continual Quality Improvement (CQI) includes continuous staff training, state-of-the-art equipment, and rigidly maintained systems. These measures effectively and efficiently control product supply and project completion in a timely, accurate, coherent, relevant, and professional manner.