Comparative studies of genetic and phenotypic associations for 2,168 plasma proteins measured by two affinity-based platforms in 4,000 Chinese adults

Proteomics offers unique insights into human biology and drug development, but few studies have directly compared the utility of different proteomics platforms. We measured 2,168 plasma proteins in 3,976 Chinese adults using both OLINK and SomaScan platforms and compared their genetic determinants and associations with traits and disease risk. For 1,694 proteins with one-to-one matched reagents, there was a modest between platform correlation (median rho=0.20). OLINK-proteins had fewer trans- pQTLs (766 vs 812 proteins) but more cis- pQTLs (725 vs 565) than SomaScan-proteins, including 342 with colocalising cis -pQTLs. Moreover, 1,095 OLINK- and 963 SomaScan-proteins showed significant associations with BMI, while 279 and 165 proteins were significantly associated with IHD, respectively. Addition of these IHD-associated proteins to conventional risk factors yielded NRIs for IHD of 15.3% and 17.1% for OLINK and SomaScan respectively. The results demonstrate the complementarity of different proteomic platforms and should inform assay selection in future population and clinical studies.