Fig. 1

Polyclonal allelic expression assay to detect the effects of regulatory variants. a Assay schematic. Inducible Cas9 HEK293T cells undergo homologous recombination after transfection with the gRNA and ssDNA template in order to introduce the alternative allele to the cells. HeLa cells without inducible Cas9 were transfected with a Cas9 plasmid. Editing is followed by targeted sequencing of gDNA and mRNA to detect the ratio of alt/ref alleles in the polyclonal population of cells. b Table with the number of each type of control and putative regulatory variant edited with the assay in HEK293T cells. c Homologous recombination rate versus standard deviation for variants replicated 2–3 times with assay in HEK293T cells. The vertical line shows the 0.4% HDR cutoff which was used to filter variants for subsequent analysis. d Scatter plot showing the reproducibility of the effect size detected by the polyclonal allelic expression assay for two replicate experiments editing the same variants in HEK293T cells