Abstract
The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses’ Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours after collection, as well as those of samples collected from the same individuals 1 year apart. CVs were <20% for 99% of proteins overall and <10% for 92% of proteins in heparin samples compared to 66% for EDTA samples. We observed ICC or Spearman r (comparing immediate vs. 24-hour delayed processing) ≥0.75 for 61% of proteins, with some variation by anticoagulant (56% for heparin and 70% for EDTA) and protein class (ranging from 49% among kinases to 83% among hormones). Within-person stability over 1 year was good (ICC or Spearman r ≥ 0.4) for 91% of proteins. These results demonstrate the feasibility of SOMAscan for analyses of archived plasma samples.
Highlights
Protein levels in blood can change as a function of age, health, and environmental exposures and can provide important diagnostic, prognostic, and therapeutic information
Qiao and colleagues investigated the proteomic profile of hepatocellular carcinoma using SOMAscan and identified 68 proteins with differential expression between tumor and non-tumor tissues and 8 proteins associated with vascular invasion[13]
The blood samples used in this pilot study included plasma from 16 participants of the Nurses’ Health Study (NHS), 40 participants of the NHSII Mind Body Study (MBS), and 12 local volunteers
Summary
Protein levels in blood can change as a function of age, health, and environmental exposures and can provide important diagnostic, prognostic, and therapeutic information. High-throughput proteomics technologies have developed rapidly in recent years and have the potential for use in biomarker discovery. One such technology is an aptamer-based proteomics platform called SOMAscan (SomaLogic, Inc, Boulder, Colorado). The platform has been applied to discover biomarkers related to many other diseases including lung cancer[14], mesothelioma[15], cancer exosomes[16], Alzheimer’s disease[17], influenza[18], and latent tuberculosis infection[8] Despite its potential, this modified aptamer-based proteomics technology has yet to be applied widely to archived blood samples from population-based cohort studies. We performed secondary analyses of variations in protein levels by participants’ age, BMI, and fasting status, and compared our results with those from previous reports
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