Patients were classified as either normal or as having one of seven possible disease states (COPD, Mononucleosis, Myeloma, Psoriasis, Rheumatoid Arthritis, and Type 2 Diabetes). Patient personal record and medical history were blinded and their sample identification was randomized prior to analysis. Samples were analysed across three 96-well plates, labelled here as Plate = (plate1, plate2, plate3), for the presences of 37 analytes (April, Baff, CD163, CD30, Chitinase, gp130, IFN-a2, IFN-b, IFN-g, IL-10, IL-11, IL-12p40, IL-12p70, IL-19, IL-2, IL-20, IL-22, IL-26, IL-27, IL-28, IL-29, IL-32, IL-34, IL-35, IL-6RA, IL-8, Light, MMP-1, MMP-2, MMP-3, OCN, OPN, Pentraxin, TNFR1, TNFR2, TSLP, and Tweak). The actual number of patients associations between sample types, conditions and plates are given in
The fluorescence responses and concentrations of analytes were obtained using a Bio-Plex Pro™ Human Inflammation Panel 37-Plex assay kit with magnetic beads (171AL1001M, Bio-Rad, Hercules, California, USA) and analysed with a Luminex100 system and the accompanying Bio-Plex ManagerTM Software 6.1(Bio-Rad, Hercules, California, USA).
The concentration values and detection limits were determined from standard curves generated from each kit’s standards using the Bio-Plex Software ManagerTM weighted 5PL curve fitting procedure. To maximize the number of concentrations values available for analysis we included the Bio-Plex extrapolated values. Therefore, the definition of out-of-range here, and unless otherwise stated, refers to concentration values that cannot be obtained from the 5PL logistic curve; that is beyond extrapolation.
All statistical analysis was performed using R version 3.1.0 (2014-04-10)45 via RStudio Version 0.98.50746 . The mixed-effects modelling were done using lmer47 (link). The visualization of regression results was done using visreg44 , and the significance of interactions terms and interaction means were determined using Phia package43 . Unless otherwise stated all p-values have been multiple test corrected according to Holm’s method48 . For simulation experiments normal distributions were obtained from rnorm and skewed distribution were obtained using skew normal distribution methods, rsn, from the R package sn49 .