Aim: This study provides clinicians and researchers with an informed choice between current commercially available targeted sequencing panels and exome sequencing panels in the context of pan-cancer pharmacogenetics. Materials & methods: Nine contemporary commercially available targeted pan-cancer panels and the xGen Exome Research Panel v2 were investigated to determine to what extent they cover the pharmacogenetic variant-drug interactions in five available cancer knowledgebases, and the driver mutations and fusion genes in the Cancer Genome Atlas. Results: xGen Exome Research Panel v2 and TrueSight Oncology 500 target 71.0 and 68.9% of the pharmacogenetic interactions in the available knowledgebases; and 93.7 and 86.0% of the driver mutations in the Cancer Genome Atlas, respectively. All other studied panels target lower percentages. Conclusion: Exome sequencing outperforms pan-cancer targeted sequencing panels in terms of covered cancer pharmacogenetic variant-drug interactions and pharmacogenetic cancer variants.
Keywords: TCGA; exome sequencing; pan-cancer; pharmacogenetic knowledgebase; targeted sequencing.