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National Institute of Environmental Health Sciences

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Publication Detail

Title: Comparison of Proteomic Assessment Methods in Multiple Cohort Studies.

Authors: Raffield, Laura M; Dang, Hong; Pratte, Katherine A; Jacobson, Sean; Gillenwater, Lucas A; Ampleford, Elizabeth; Barjaktarevic, Igor; Basta, Patricia; Clish, Clary B; Comellas, Alejandro P; Cornell, Elaine; Curtis, Jeffrey L; Doerschuk, Claire; Durda, Peter; Emson, Claire; Freeman, Christine M; Guo, Xiuqing; Hastie, Annette T; Hawkins, Gregory A; Herrera, Julio; Johnson, W Craig; Labaki, Wassim W; Liu, Yongmei; Masters, Brett; Miller, Michael; Ortega, Victor E; Papanicolaou, George; Peters, Stephen; Taylor, Kent D; Rich, Stephen S; Rotter, Jerome I; Auer, Paul; Reiner, Alex P; Tracy, Russell P; Ngo, Debby; Gerszten, Robert E; O'Neal, Wanda K; Bowler, Russell P; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium

Published In Proteomics, (2020 Jun)

Abstract: Novel proteomics platforms, such as the aptamer-based SOMAscan platform, can quantify large numbers of proteins efficiently and cost-effectively and are rapidly growing in popularity. However, comparisons to conventional immunoassays remain underexplored, leaving investigators unsure when cross-assay comparisons are appropriate. The correlation of results from immunoassays with relative protein quantification is explored by SOMAscan. For 63 proteins assessed in two chronic obstructive pulmonary disease (COPD) cohorts, subpopulations and intermediate outcome measures in COPD Study (SPIROMICS), and COPDGene, using myriad rules based medicine multiplex immunoassays and SOMAscan, Spearman correlation coefficients range from -0.13 to 0.97, with a median correlation coefficient of ≈0.5 and consistent results across cohorts. A similar range is observed for immunoassays in the population-based Multi-Ethnic Study of Atherosclerosis and for other assays in COPDGene and SPIROMICS. Comparisons of relative quantification from the antibody-based Olink platform and SOMAscan in a small cohort of myocardial infarction patients also show a wide correlation range. Finally, cis pQTL data, mass spectrometry aptamer confirmation, and other publicly available data are integrated to assess relationships with observed correlations. Correlation between proteomics assays shows a wide range and should be carefully considered when comparing and meta-analyzing proteomics data across assays and studies.

PubMed ID: 32386347 Exiting the NIEHS site

MeSH Terms: Adult; Aged; Aged, 80 and over; Cohort Studies; Female; Humans; Immunoassay/methods; Male; Middle Aged; Myocardial Infarction/blood; Myocardial Infarction/metabolism*; Proteome/metabolism*; Proteomics/methods*; Pulmonary Disease, Chronic Obstructive/blood; Pulmonary Disease, Chronic Obstructive/metabolism*; Smokers/statistics & numerical data*

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