Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2026
License: CC BY
Data sources: ZENODO
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Dataset . 2026
License: CC BY
Data sources: ZENODO
ZENODO
Dataset . 2026
License: CC BY
Data sources: Datacite
addClaim

AgenticGenomics: pharmacogenomics benchmark dataset for "Trustworthy agentic genomics through versioned skill libraries"

Authors: Corpas, Manuel; Iacoangeli, Alfredo; Bourdenx, Mathieu; Skene, Nathan; Aldraimli, Mahmoud; Fatumo, Segun; Guio, Heinner;

AgenticGenomics: pharmacogenomics benchmark dataset for "Trustworthy agentic genomics through versioned skill libraries"

Abstract

AgenticGenomics benchmark dataset. Controlled three-arm comparison of nine frontier large language models on pharmacogenomic interpretation: Claude Opus 4, Claude Sonnet 4, GPT-5.2, GPT-4.1, o3, o4-mini, Gemini 2.5 Flash, DeepSeek V3 and Mistral Large 2, evaluated on 110 CPIC Level A cases across three population contexts (European, admixed Latin American, East African) under three conditions (free-prompted; retrieval-augmented from the CPIC guideline corpus; constrained by a versioned SKILL.md-format specification executed as a contract), three replicates per cell, 26,730 evaluations. The archive contains raw model responses, baseline and clinical-equivalence rescorer outputs, the locked merged three-arm dataset (26,730 rows), the forward and reverse adversarial scrambled-specification experiments, the (gene, drug)-keyed chunking control, the drug-recommendation regression classification, and figure-input tables. Records are scored on phenotype identification (A1), drug recommendation (A2) and lethal-class safety action (A3). All data derive from public CPIC Level A guidelines and PharmGKB annotations; genotypes are synthetic canonical cases; no patient data and no new sequencing data are included. Analysis code: https://github.com/manuelcorpas/24-AGENTIC-PGX-BENCHMARK (commit dc2c849e). Companion to the Perspective "Agentic Genomics: From Pipeline Automation to Autonomous Validation" (under review at Cell Genomics). Version 1.1.0 adds the three-population real-genome validation arm: agent interpretation of star-allele diplotypes called by a single deterministic caller (PyPGx, GRCh37) from a European family (Corpas family), the Peruvian Genome Project (Latin American) and the Uganda Genome Resource (East African, controlled access; no genotypes redistributed). Adds the aggregate per-population result table, the cross-population figure, and a complete snapshot of the analysis repository at commit a6a8e9d. No individual-level genotypes are included.

Keywords

pharmacogenomics, clinical decision support, agentic genomics, CPIC, benchmark, retrieval-augmented generation, precision medicine, large language models, reproducibility, skill libraries

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average