Comparative studies of 2168 plasma proteins measured by two affinity-based platforms in 4000 Chinese adults

Baihan Wang, Alfred Pozarickij, Mohsen Mazidi, Neil Wright, Pang Yao, Saredo Said, Andri Iona, Christiana Kartsonaki, Hannah Fry, Kuang Lin, Yiping Chen, Huaidong Du, Daniel Avery, Dan Schmidt-Valle, Canqing Yu, Dianjianyi Sun, Jun Lv, Michael Hill, Liming Li, Derrick A. Bennett, Rory Collins, Robin G. Walters, Robert Clarke, Iona Y. Millwood () and Zhengming Chen ()
Additional contact information
Baihan Wang: University of Oxford
Alfred Pozarickij: University of Oxford
Mohsen Mazidi: University of Oxford
Neil Wright: University of Oxford
Pang Yao: University of Oxford
Saredo Said: University of Oxford
Andri Iona: University of Oxford
Christiana Kartsonaki: University of Oxford
Hannah Fry: University of Oxford
Kuang Lin: University of Oxford
Yiping Chen: University of Oxford
Huaidong Du: University of Oxford
Daniel Avery: University of Oxford
Dan Schmidt-Valle: University of Oxford
Canqing Yu: Peking University
Dianjianyi Sun: Peking University
Jun Lv: Peking University
Michael Hill: University of Oxford
Liming Li: Peking University
Derrick A. Bennett: University of Oxford
Rory Collins: University of Oxford
Robin G. Walters: University of Oxford
Robert Clarke: University of Oxford
Iona Y. Millwood: University of Oxford
Zhengming Chen: University of Oxford

Nature Communications, 2025, vol. 16, issue 1, 1-13

Abstract: Abstract Proteomics offers unique insights into human biology and drug development, but few studies have directly compared the utility of different proteomics platforms. We measured plasma levels of 2168 proteins in 3976 Chinese adults using both Olink Explore and SomaScan platforms. The correlation of protein levels between platforms was modest (median rho = 0.29), with protein abundance and data quality parameters being key factors influencing correlation. For 1694 proteins with one-to-one matched reagents, 765 Olink and 513 SomaScan proteins had cis-pQTLs, including 400 with colocalising cis-pQTLs. Moreover, 1096 Olink and 1429 SomaScan proteins were associated with BMI, while 279 and 154 proteins were associated with risk of ischaemic heart disease, respectively. Addition of Olink and SomaScan proteins to conventional risk factors for ischaemic heart disease improved C-statistics from 0.845 to 0.862 (NRI: 12.2%) and 0.863 (NRI: 16.4%), respectively. These results demonstrate the utility of these platforms and could inform the design and interpretation of future studies.

Date: 2025
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DOI: 10.1038/s41467-025-56935-2

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