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 (<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.

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.

Keywords: exome sequencing; pharmacogenomics; warfarin.

Figure 1. Coverage of pharmacogenomic variants by the exome capture kits

(A) A pie chart showing the genomic distribution of the 1928 PGx variants examined. (B) For each of the four exome capture kits, the ratio of variants targeted versus those not targeted. (C) Of those variants not targeted by the exome capture kits, the distribution of their genomic locations is shown. PGx: Pharmacogenomics; UTR: Untranslated Regions.

Figure 2. Box plots showing coverage of pharmacogenomic variants by exome sequencing

The boxes represent the 25th to 75th quartiles with the median value indicated by the black line for all 62 samples; the whiskers are 1 standard deviation from the interquartile values and the circles represent outliers. (A) Plotted are the distributions of coverage for the variants broken down by genomic region of each variant. Each graph represents all 62 samples and the number of variants at each genomic location is indicated. The y-axis is the percent of variant positions with less than 20x depth of coverage. (B) The depth of coverage for the three variants used for therapeutic dosing of warfarin. The x-axis is the depth of coverage for each of the three variants. The dashed red line indicates a 20x coverage threshold used. UTR: Untranslated Regions.