Automated Pharmacogenomic Reports for Clinical Genome Sequencing

Clinical laboratories offering genome sequencing have the opportunity to return pharmacogenomic findings to patients, providing the added benefit of preemptive testing that could help inform medi-cation selection or dosing throughout the lifespan. Implementation of pharmacogenomic reporting must address several challenges, including inherent limitations in short-read genome sequencing methods, gene and variant selection, standardization of genotype and phenotype nomenclature, and choice of guidelines and drugs to report. An automated pipeline, lmPGX, was developed as an end-to -end solution that produces two versions of a pharmacogenomic report, presenting either Clinical Pharmacogenetics Implementation Consortium or US Food and Drug Administration guidelines for 12 genes. The pipeline was validated for performance using reference samples and pharmacogenetic data from the Genetic Testing Reference Materials Coordination Program. To determine performance and limitations, lmPGX was compared with three additional publicly available pharmacogenomic pipelines. The lmPGX pipeline offers clinical laboratories an opportunity for seamless integration of pharmaco-genomic results with genome reporting.

Automated summary

Clinical laboratories offering genome sequencing can provide pharmacogenomic findings to patients, which can help inform medication selection and dosing throughout the lifespan. The lmPGX pipeline offers a solution for seamlessly integrating pharmacogenomic results with genome reporting, addressing various challenges in reporting.