Performance of exome sequencing for pharmacogenomics

Abstract

Aim: We present the potential false-negative rate of exome sequencing for the detection of pharmacogenomic variants. Materials & Methods: Depth of coverage of 1928 pharmacogenomically relevant variant positions was ascertained from 62 exome-sequenced samples. Results: Approximately 14% of the 1928 variant locations examined had inadequate depth of coverage (<20×). The variants with inadequate coverage were predominantly located outside of protein-coding portions and included some clinically relevant variant positions, such as the warfarin VKORC1 variant. Conclusion: While the use of exome sequencing is becoming more prevalent in fundamental research, clinical trials and clinical use; there is a possibility of false-negative results. The possible quality issues such as false-negative rate should be considered with the use of exome sequencing.