Pre-analytical delay as a dominant confounder in blood RNA-seq: Rapid ex vivo gene expression changes in EDTA blood

Abstract

Although the impact of delayed processing on gene expression in EDTA blood has been well documented using targeted assays and microarray platforms, the emergence of next-generation RNA sequencing (RNA-seq) has not yet been leveraged to systematically compare these effects against stabilized whole blood collection systems. Notably, no study has performed a time course RNA-seq analysis with human bulk RNA of matched EDTA and PAXgene blood RNA samples drawn from the same subjects. EDTA is still widely used for gene expression analysis studies. Yet, the genome-wide dynamics by which EDTA blood transcriptomes deviate from a stabilized reference over time remain poorly defined. This represents an important methodological gap, given the increasing reliance on RNA-seq for biomarker discovery, clinical transcriptomics and diagnostics.