Journal article
Comparison of Proteomic Assessment Methods in Multiple Cohort Studies
Proteomics (Weinheim), Vol.20(12), e1900278
06/01/2020
DOI: 10.1002/pmic.201900278
PMCID: PMC7425176
PMID: 32386347
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. We explored the correlation of results from immunoassays with relative protein quantification 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 (RBM) multiplex immunoassays and SOMAscan, Spearman correlation coefficients ranged from −0.13 to 0.97, with a median correlation coefficient of ~0.5 and consistent results across cohorts. A similar range was observed for immunoassays in the population based Multi-Ethnic Study of Atherosclerosis (MESA) 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 showed a wide correlation range. Finally, we integrated
cis
pQTL data, mass spectrometry aptamer confirmation, and other publicly available data 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.
Details
- Title: Subtitle
- Comparison of Proteomic Assessment Methods in Multiple Cohort Studies
- Creators
- Laura M. Raffield - University of North Carolina at Chapel HillHong Dang - University of North Carolina at Chapel HillKatherine A. Pratte - National Jewish HealthSean Jacobson - National Jewish HealthLucas Gillenwater - National Jewish HealthElizabeth Ampleford - Wake Forest UniversityIgor Barjaktarevic - University of California, Los AngelesPatricia Basta - University of North Carolina at Chapel HillClary B. Clish - Broad InstituteAlejandro P. Comellas - University of IowaElaine Cornell - University of VermontJeffrey L. Curtis - University of MichiganClaire Doerschuk - University of North Carolina at Chapel HillPeter Durda - University of VermontClaire EmsonChristine Freeman - University of MichiganXiuqing Guo - The Lundquist InstituteAnnette T. Hastie - Wake Forest UniversityGregory A. Hawkins - Wake Forest UniversityJulio Herrera - ProterixBio (United States)W. Craig Johnson - University of WashingtonWassim W. Labaki - University of MichiganYongmei Liu - Wake Forest UniversityBrett Masters - ProterixBio (United States)Michael Miller - ProterixBio (United States)Victor E. Ortega - Wake Forest UniversityGeorge Papanicolaou - National Heart Lung and Blood InstituteStephen Peters - Wake Forest UniversityKent D. Taylor - The Lundquist InstituteStephen S. Rich - University of VirginiaJerome I. Rotter - The Lundquist InstitutePaul Auer - University of Wisconsin–MilwaukeeAlex P. Reiner - Fred Hutch Cancer CenterRussell P. Tracy - University of VermontDebby Ngo - Beth Israel Deaconess Medical CenterRobert E. Gerszten - Beth Israel Deaconess Medical CenterWanda Kay O’NealRussell P. Bowler - National Jewish HealthNHLBI Trans-Omics Precision Medicine (TOPMed) Consortium
- Resource Type
- Journal article
- Publication Details
- Proteomics (Weinheim), Vol.20(12), e1900278
- DOI
- 10.1002/pmic.201900278
- PMID
- 32386347
- PMCID
- PMC7425176
- NLM abbreviation
- Proteomics
- ISSN
- 1615-9853
- eISSN
- 1615-9861
- Grant note
- DOI: 10.13039/100000738, name: U.S. Department of Veterans Affairs, award: Merit Review I01 CX000911; DOI: 10.13039/100000050, name: National Heart, Lung, and Blood Institute, award: R01 HL132947, T32 HL007749, T32 HL129982
- Language
- English
- Date published
- 06/01/2020
- Academic Unit
- Pulmonary, Critical Care, and Occupational Medicine; Psychiatry; ICTS; Internal Medicine
- Record Identifier
- 9984359560902771
Metrics
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