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tooluniverse-hla-immunogenomics
HLA gene-family analysis and MHC-peptide binding for transplant compatibility, vaccine epitope coverage, and cancer immunotherapy. Uses IMGT (HLA polymorphism), IEDB (epitope-MHC binding), UniProt (annotation), DGIdb (druggability). Use for HLA typing/imputation review, vaccine HLA coverage, and immunotherapy prediction biomarkers (HLA-LOH, neoantigen presentation).
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# HLA & Immunogenomics Analysis
Pipeline for exploring HLA gene families, MHC-peptide binding, epitope associations, and their clinical implications in transplantation, vaccine development, and cancer immunotherapy. Bridges immunogenetic databases (IMGT, IEDB) with functional annotation (UniProt) and druggability data (DGIdb).
## Reasoning Strategy
HLA analysis is fundamentally about peptide presentation: the polymorphism of HLA molecules determines which peptides are displayed to T cells, which in turn governs disease susceptibility, transplant rejection, drug hypersensitivity, and vaccine immunogenicity. HLA type affects disease susceptibility for autoimmune conditions (HLA-B27 and ankylosing spondylitis), transplant rejection (HLA mismatch drives alloresponse), drug hypersensitivity (abacavir causes severe hypersensitivity reactions only in HLA-B*57:01 carriers), and vaccine design (epitopes must be presented by the recipient's HLA alleles to elicit a T-cell response). Class I and Class II HLA molecules have fundamentally different binding grooves, peptide lengths, and T-cell partners — never conflate them. The absence of an epitope from IEDB means it has not been tested, not that it cannot bind.
**LOOK UP DON'T GUESS**: Never assume an allele's binding properties or population frequency — query IEDB for experimental binding data and IMGT for allele annotation. Do not guess which HLA alleles are common in a population; look up published frequency data via PubMed.
**Guiding principles**:
1. **HLA nomenclature precision** -- HLA allele names follow strict conventions (e.g., HLA-A*02:01); get the resolution level right
2. **MHC class awareness** -- Class I (A, B, C) and Class II (DR, DQ, DP) have different binding properties and clinical roles
3. **Species context** -- most queries target human HLA, but MHC exists across vertebrates; confirm species early