domains / families / science / neoantigen-pipeline

neoantigen-pipeline

separate

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) + expression/readcount annotation, proximal-variant phasing, pVACseq MHC-I/II binding, CCF/clonality, and immunogenicity/quality ranking. Use when recognizing that binding is single-digit PPV and the critical steps are downstream (full-resolution HLA + LOH gating, proximal-variant phasing, clonality from purity+CN not raw VAF, expression), sequencing normalize+annotate -> phase -> HLA -> binding -> quality in the defensible order, dropping candidates on LOH-lost alleles, supplying --phased-proximal-variants-vcf so the mutant peptide is real, or ranking WITHIN patient rather than a fixed IC50 threshold. Hands mechanism to the immunoinformatics component skills; not a re-teach of any single step.

When to use

• neoantigen discovery from somatic variants
• ranked vaccine candidates
• HLA typing with LOH gating
• VEP annotation with Wildtype and Frameshift plugins
• proximal-variant phasing
• pVACseq MHC-I/II binding prediction
• CCF/clonality assessment
• immunogenicity and quality ranking

When not to use

• re-teaching any single step
• using fixed IC50 thresholds across patients
• relying on raw VAF for clonality
• ignoring LOH-lost alleles
• skipping proximal-variant phasing

Skill page

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