Extended Data Fig. 2: Validation of ASM-QTL influences in oxBS-seq data.
From: The correlation between CpG methylation and gene expression is driven by sequence variants
ASM-QTLs validated using oxBS in independent DNA samples derived from whole blood of forty-five individuals. Note, these forty-five individuals were not included in the larger cohort of 7,179 nanopore sequenced individuals. The effect size of each ASM-QTL on the 5-mCpG haplotype rates of MDSs in oxBS sequenced individuals, y-axis, are plotted against the effect size of the same ASM-QTLs on 5-mCpG haplotype rates of the corresponding MDS in nanopore sequenced samples, x-axis. We binned the validation tests according to the number of haplotypes (n) that were available for validation testing in oxBS individuals as indicated on the top of each figure. A least squares regression line, where the effect sizes in the oxBS validation cohort are used as the outcome and those in nanopore sequenced cohort as the predictor, is shown in each figure, blue colour, along with a diagonal line of identity, red colour, as we expect the regression coefficient to be equal to one (and an intercept of zero) if the effect sizes are identical in the oxBS and nanopore sequenced individuals. The regression coefficients and their 95% confidence intervals are shown at the top left-hand corner of each figure. Note that as the number of informative haplotypes (n) in the oxBS validation cohort increases, the regression coefficient approaches that of a diagonal line indicating that the effect sizes become more similar as the number of haplotypes available for testing (n) in the oxBS cohort increases.
