To demonstrate the utility of this assay, mirSNPs predicted to alter miRNA regulation of 17 pharmacogenes were selected for functional testing from the RNA-seq dataset described earlier. These variants were functionally tested using the PASSPORT-seq assay in HeLa, HepG2, HEK293, and HepaRG (hepatic cells that retain characteristics of primary human hepatocytes) cells. Out of the 111 genetic variants tested, the effect of 33 variants were statistically significant in at least one cell line, including 6, 13, 12, and 27 in HeLa, HepG2, HEK293, and HepaRG cells, respectively (Figure 5 and Supplementary Table 4). The effects of several mirSNPs were shown to be cell line-specific. Only four mirSNPs had significant effects in all the four cell lines (Figure 6). The effect of a genetic variant (rs12979270), located in the 3′ UTR of the pharmacogene- CYP2B6, was shown to be statistically significant in HepaRG cells. A recent study shows that this variant, could explain part of the interindividual variability seen in the activity of this critical pharmacogene (Burgess et al., 2017). These results demonstrate the potential of this assay to identify clinically relevant functional genetic variants.
