ToolUniverse Immune Repertoire Analysis

Comprehensive skill for analyzing T-cell receptor (TCR) and B-cell receptor (BCR) repertoire sequencing data to characterize adaptive immune responses, clonal expansion, and antigen specificity.

Domain Reasoning

Repertoire diversity reflects immune history. High clonality — a few clones dominating — indicates antigen-driven expansion, as seen in active infection, tumor-infiltrating lymphocytes, or chronic stimulation. Low diversity points to immunodeficiency or treatment-induced lymphopenia. Always compare observed metrics against healthy donor reference distributions before drawing conclusions; a Shannon entropy of 7 is unremarkable in a healthy adult but alarming post-chemotherapy.

LOOK UP DON'T GUESS

• Clonotype frequency thresholds, CDR3 length ranges, and convergence ratios: query IEDB or VDJdb; do not assume values from memory.
• Epitope specificities for expanded clones: search iedb_search_tcell_assays and BVBRC_search_epitopes; never infer antigen identity from CDR3 alone.
• V gene family usage biases in healthy donors: retrieve published reference data or query ImmPort; do not assume baseline distributions are uniform.
• Sequencing depth adequacy: compute rarefaction curves from the actual data; do not guess whether depth is sufficient.

Overview