Stability and reproducibility of proteomic profiles measured with an aptamer-based platform

Kim, Claire H.; Tworoger, Shelley S.; Stampfer, Meir J.; Dillon, Simon T.; Gu, Xuesong; Sawyer, Sherilyn; Chan, Andrew T.; Libermann, Towia A.; Eliassen, A. Heather

doi:10.1038/s41598-018-26640-w

Cited by 124 publications

(119 citation statements)

References 61 publications

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“…SOMAmer proteomic analysis. SOMAscan technology (84,85) was used to simultaneously measure 1129 proteins from each sample at SomaLogic Inc. BALF was diluted with buffer to a standard protein concentration of 20 μg/ml, and 100 μl diluted BALF was equilibrated with a SOMAmers mix (Gold 2010). The SOMAmer mixture allowed for the detection and quantitation of 1129 protein aptamers simultaneously in each sample recorded as relative florescence units (RFU).…”

Section: Methodsmentioning

confidence: 99%

A SFTPC BRICHOS mutant links epithelial ER stress and spontaneous lung fibrosis

Katzen¹,

Wagner²,

Venosa³

et al. 2019

JCI Insight

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Section: Methodsmentioning

confidence: 99%

A SFTPC BRICHOS mutant links epithelial ER stress and spontaneous lung fibrosis

Katzen¹,

Wagner²,

Venosa³

et al. 2019

JCI Insight

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“…[ 1 ] There is increasing interest in the use of novel large scale proteomics platforms to facilitate biomarker discovery for sub‐phenotyping and risk prediction in complex diseases. [ 2 ] Oligonucleotide aptamer‐based platforms, such as the SOMAscan assays marketed by SomaLogic (Boulder, CO), can be used for quantification of >1300 proteins, [ 3–6 ] with >4000 proteins assayed in recent publications. [ 7 ] Aptamers are randomly generated nucleotide sequences that bind specific antigens, mimicking the function of antibodies.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

et al. 2020

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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.

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“…In an independent study, the SomaScan assay with plasma samples has recently demonstrated a high degree of stability and reproducibility. 29 …”

Section: Methodsmentioning

confidence: 99%

Plasma Biomarkers of Reticular Pseudodrusen and the Risk of Progression to Advanced Age-Related Macular Degeneration

Lynch

Wagner

Palestine

et al. 2020

Trans. Vis. Sci. Tech.

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Purpose To determine, using an aptamer-based technology in patients with intermediate age-related macular degeneration (AMD), (1) if there is a difference in plasma levels of 4979 proteins in patients with and without reticular pseudodrusen (RPD), and (2) if plasma levels of proteins are related to time to conversion to advanced AMD. Methods Patients with intermediate AMD and RPD were identified from an AMD registry. Relative concentrations of each protein were log (base 2) transformed and compared between patients with and without RPD using linear regression. A Cox proportional hazards survival model was fit to each aptamer to quantify associations with time to conversion. A pathway analysis was conducted in converters versus non-converters using the Reactome database. Results Of the 109 intermediate AMD patients, 39 had bilateral RPD (36%). Two proteins, TCL1A and CNDP1, were lower in patients in the intermediate AMD group with RPD. Twenty-one patients converted to advanced AMD with a median time to conversion of 25.2 months (range, 2.3–48.5 months) and median follow-up time in non-converters of 26.4 months (range, 0.03–49.7 months). Several proteins (lysozyme C, TFF3, RNAS6, and SAP3) distinguished patients who converted from those who did not convert to advanced AMD. The top conversion pathways included tumor necrosis factors bind their physiological receptors, digestion and absorption, signaling by activin, and signaling by TGF-β family members. Conclusions We identified a protein signature related to RPD, as well as to conversion to advanced AMD. The pathway analysis suggests that dysfunction of critical systemic pathways may have links to conversion to advanced AMD. Translational Relevance Biomarkers identified in plasma likely reflect systemic alterations in protein expression in patients with intermediate AMD.

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Stability and reproducibility of proteomic profiles measured with an aptamer-based platform

Cited by 124 publications

References 61 publications

A SFTPC BRICHOS mutant links epithelial ER stress and spontaneous lung fibrosis

A SFTPC BRICHOS mutant links epithelial ER stress and spontaneous lung fibrosis

Comparison of Proteomic Assessment Methods in Multiple Cohort Studies

Plasma Biomarkers of Reticular Pseudodrusen and the Risk of Progression to Advanced Age-Related Macular Degeneration

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