Performance of exome sequencing for pharmacogenomics

We present the potential false-negative rate of exome sequencing for the detection of pharmacogenomic variants.

Depth of coverage of 1928 pharmacogenomically relevant variant positions was ascertained from 62 exome-sequenced samples.

Approximately 14% of the 1928 variant locations examined had inadequate depth of coverage (<20x). 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.

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.