Benchmark of Open-Access Star-Allele Callers to Accurately Assess Haplotypes and Phenotypes in Pharmacogenetic Studies

Systematic comparison of open-access callers (PyPGx, ursaPGx, PharmCAT, Aldy) for pharmacogenetic star-allele and phenotype calling

A French study (IGBMC/Brest) presents a rigorous benchmark of four open-access star-allele callers — PyPGx, ursaPGx, PharmCAT, and Aldy — on large public clinical cohorts covering several major pharmacogenes (CYP2D6, CYP2C19, DPYD, TPMT, CYP3A5). Performance varies significantly by gene and data type (WGS, WES, array), with pharmacogene-specific guidance. This benchmark provides laboratories wishing to implement PGx with a practical tool-selection guide.

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This benchmark from a French team (Genin/Herzig, IGBMC Strasbourg + Brest) is a directly applicable contribution for clinical genomics laboratories implementing a PGx program. Gene- and data-type-specific guidance is the practical strength. Notably, no single caller dominates across all genes — the choice remains contextual based on the laboratory's priority gene.