Current challenges and best practices for cell-free long RNA biomarker discovery

The analysis of biomarkers in biological fluids, also known as liquid biopsies, is seen with great potential to diagnose complex diseases such as cancer with a high sensitivity and minimal invasiveness. Although it can target any biomolecule, most liquid biopsy studies have focused on circulating nucleic acids. Historically, studies have aimed at the detection of specific mutations on cell-free DNA (cfDNA), but recently, the study of cell-free RNA (cfRNA) has gained traction. Since 2020, a handful of cfDNA tests have been approved for therapy selection by the FDA, however, no cfRNA tests are approved to date. One of the main drawbacks in the field of RNA-based liquid biopsies is the low reproducibility of the results, often caused by technical and biological variability, a lack of standardized protocols and insufficient cohorts. In this review, we will identify the main challenges and biases introduced during the different stages of biomarker discovery in liquid biopsies with cfRNA and propose solutions to minimize them.

Automated summary

The analysis of biomarkers in biological fluids, known as liquid biopsies, has the potential to diagnose complex diseases like cancer with high sensitivity and minimal invasiveness. While liquid biopsies can target any biomolecule, most studies have focused on circulating nucleic acids. However, RNA-based liquid biopsies face challenges in terms of low reproducibility of results due to technical and biological variability, lack of standardized protocols, and insufficient cohorts. This review aims to identify these challenges and biases and propose solutions to minimize them during biomarker discovery in liquid biopsies with cfRNA.