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

Author

Listed:
  • 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
    Peking University Center for Public Health and Epidemic Preparedness and Response
    Ministry of Education)

  • Dianjianyi Sun

    (Peking University
    Peking University Center for Public Health and Epidemic Preparedness and Response
    Ministry of Education)

  • Jun Lv

    (Peking University
    Peking University Center for Public Health and Epidemic Preparedness and Response
    Ministry of Education)

  • Michael Hill

    (University of Oxford)

  • Liming Li

    (Peking University
    Peking University Center for Public Health and Epidemic Preparedness and Response
    Ministry of Education)

  • 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)

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.

Suggested Citation

  • 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 Sc, 2025. "Comparative studies of 2168 plasma proteins measured by two affinity-based platforms in 4000 Chinese adults," Nature Communications, Nature, vol. 16(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56935-2
    DOI: 10.1038/s41467-025-56935-2
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    References listed on IDEAS

    as
    1. Kursa, Miron B. & Rudnicki, Witold R., 2010. "Feature Selection with the Boruta Package," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 36(i11).
    2. Pei-Kuan Cong & Wei-Yang Bai & Jin-Chen Li & Meng-Yuan Yang & Saber Khederzadeh & Si-Rui Gai & Nan Li & Yu-Heng Liu & Shi-Hui Yu & Wei-Wei Zhao & Jun-Quan Liu & Yi Sun & Xiao-Wei Zhu & Pian-Pian Zhao , 2022. "Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    3. Grimur Hjorleifsson Eldjarn & Egil Ferkingstad & Sigrun H. Lund & Hannes Helgason & Olafur Th. Magnusson & Kristbjorg Gunnarsdottir & Thorunn A. Olafsdottir & Bjarni V. Halldorsson & Pall I. Olason & , 2023. "Large-scale plasma proteomics comparisons through genetics and disease associations," Nature, Nature, vol. 622(7982), pages 348-358, October.
    4. Yu Xu & Scott C. Ritchie & Yujian Liang & Paul R. H. J. Timmers & Maik Pietzner & Loïc Lannelongue & Samuel A. Lambert & Usman A. Tahir & Sebastian May-Wilson & Carles Foguet & Åsa Johansson & Praveen, 2023. "An atlas of genetic scores to predict multi-omic traits," Nature, Nature, vol. 616(7955), pages 123-131, April.
    5. Benjamin B. Sun & Joshua Chiou & Matthew Traylor & Christian Benner & Yi-Hsiang Hsu & Tom G. Richardson & Praveen Surendran & Anubha Mahajan & Chloe Robins & Steven G. Vasquez-Grinnell & Liping Hou & , 2023. "Plasma proteomic associations with genetics and health in the UK Biobank," Nature, Nature, vol. 622(7982), pages 329-338, October.
    Full references (including those not matched with items on IDEAS)

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