Extended Data Fig. 7: Replication of pQTLs between platforms.
From: Large-scale plasma proteomics comparisons through genetics and disease associations
a, b: Replication of sentinel cis (a) and trans (b) pQTLs detected using Olink Explore (UK biobank) in normalized SomaScan v4 (Iceland) data. For each pQTL, the plot shows the effect (in units of SD) in SomaScan v4 (y-axis) vs the effect in Olink Explore (x-axis). The assays were matched on the UniProt ID of their targeted protein. Each point is colored based on the Spearman correlation between measured protein levels using normalized SomaScan v4 and Olink Explore. The green lines show values where the effect is equal based on SomaScan v4 and Olink Explore, while the blue lines show a linear regression estimate with shaded 95% pointwise confidence intervals. c: Replication of sentinel cis pQTLs detected using Olink Explore (UK Biobank) in normalized SomaScan v4 (Iceland) data, stratified on whether the cis pQTL is in high LD with PAV (red) or not (blue). For each pQTL, the plot shows the effect (in units of SD) in SomaScan v4 (y-axis)) vs the effect in Olink Explore (x-axis). Each point is colored based on whether or not the associated variant has a protein-altering variant in high LD (r2 > 0.80). The green line shows values where the effect is equal based on SomaScan v4 and Olink Explore, while the blue and red lines show linear regression estimates with shaded 95% pointwise confidence intervals for each group (PAV in high LD; No PAV in high LD). d, e: Replication of sentinel cis (d) and trans (e) pQTL associations detected using normalized SomaScan v4 (Iceland) in Olink Explore (UK biobank) data. For each pQTL association, the plot shows the effect (in units of SD) in SomaScan v4 (x-axis) vs the effect in Olink Explore (y-axis). Each point is colored based on the Spearman correlation between measured protein levels using SomaScan v4 and Olink Explore. The green lines show values where the effect is equal based on SomaScan v4 and Olink Explore, while the blue lines show a linear regression estimate with shaded 95% pointwise confidence intervals. f: Replication of sentinel cis pQTL associations detected using normalized SomaScan v4 (Iceland) in Olink Explore (UK biobank) data, stratified on whether the cis pQTL is in high LD with PAV (blue) or not (red). For each pQTL association, the plot shows the effect (in units of SD) in SomaScan v4 (x-axis) vs the effect in Olink Explore (y-axis). Each point is colored based on whether or not the associated variant has a protein-altering variant in high LD (r2 > 0.80). The green line shows values where the effect is equal based on SomaScan v4 and Olink Explore, while the blue and red lines show linear regression estimates with shaded 95% pointwise confidence intervals for each group (PAV in high LD; No PAV in high LD).
