Correlations Within and Between Highly Multiplexed Proteomic Assays of Human Plasma
Mary R. Rooney, Jingsha Chen, Christie M. Ballantyne, Ron C. Hoogeveen, Eric Boerwinkle, Bing Yu, Keenan A. Walker, Pascal Schlosser, Elizabeth Selvin, Nilanjan Chatterjee, David Couper, Morgan E. Grams, Josef Coresh
Abstract
INTRODUCTION: The number of assays on proteomic platforms has grown rapidly. The leading platforms, SomaScan and Olink, have strengths and limitations. Comparisons of precision on the latest platforms-SomaScan 11k and Olink Explore HT-have not yet been established. METHODS: Among 102 participants in the Atherosclerosis Risk in Communities Study (mean age 74 years, 53% women, 47% Black), we used split plasma samples to measure platform precision. CV and Spearman correlations were calculated for each assay. Cross-platform agreement was assessed for overlapping proteins. RESULTS: SomaScan 11k demonstrated a median correlation of 0.85 for the 10 778 assays and a median CV of 6.8%, similar precision to earlier versions. The 5420 assays on Olink Explore HT exhibited a median correlation of 0.65 and median CV of 35.7%, which was higher than observed in its predecessors (e.g., 19.8% for Olink Explore 3072). Precision of Olink assays was inversely correlated with the percentage of samples above the limit of detection (LOD) (r = -0.77). Upon replacing Olink values below the LOD with values half the LOD, the median correlation for Olink assays measured in duplicate increased to 0.79; the median CV decreased to 13.3%. The distribution of between-platform correlations for the 4443 overlapping proteins had peaks at r approximately 0 and at r approximately 0.8. One-tenth of the protein pairs had cross-platform correlations r ≥ 0.8. CONCLUSIONS: Precision of these 2 proteomics platforms in human plasma has diverged as the coverage has increased. These results highlight the need for careful consideration in platform selection based on specific research requirements.