Transcriptome analyses of whole blood samples from normal healthy control subjects and patients with Parkinson’s disease (PD) have the potential to uncover biological pathways disrupted by disease processes. Detectable changes in the transcriptome of a readily accessible biofluid, such as blood, have the potential to be valuable biomarkers. Moreover, integration of transcriptomic data with genomic whole-genome sequencing data has the potential to give insight to variants of unknown significance and previously identified genetic loci. In this study, we report transcriptome profiling of whole blood from 4,756 samples longitudinally collected from over 1,570 individuals who also have whole genome DNA sequence, as part of Michael J. Fox Foundation’s Parkinson’s Progression Markers Initiative (PPMI) cohort. Sequencing performed by HudsonAlpha demonstrated a plate to plate variability of <1% across this large cohort.