Human CD4+ T-cell transcriptome in early arthritis

An exploration of the peripheral blood CD4+ T-cell transcriptome of early arthritis clinic attendees, seeking novel diagnostic tools and pathophysiological insights. Ex-vivo CD4+ T-cell RNA was obtained following first early arthritis clinic attendance from 173 patients. Four diagnostic categories were confirmed at median 28 months follow-up. Outcome categories are ACPA- RA (A; n=31), ACPA+ RA (B; n=41), Non-RA Inflammatory arthritis (C; n=56), and Non-RA/Non-Inflammatory arthritis (D; n=45). In order to derive and validate a diagnostic gene signature, samples were split into Training set (where patients could be diagnosed at presentation; n=111) and validation set of undifferentiated arthritis (UA; n=62) patients, in whom diagnosis could only be confirmed after the follow-up period. Arrays were processed in two phases (phases 1 and 2). Phase 1 was split into 4 labelling batches, Phase 2 was split into 2 labelling batches. Batch effects were controlled for using this information using the empirical Bayes approach of Johnson et al. (2007). The supplementary file 'GSE20098_non-normalized.txt' contains non-normalized data for Samples GSM502124-GSM502280 and GSM506251-GSM506266.