Liquid biopsy by NGS: differential presence of exons (DPE) in cell-free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer.

Susana Olmedillas-López,Ramón Peiró-Pastor,Begoña Aguado,Dolores C García-Olmo,Mariano García-Arranz,Damián García-Olmo

doi:10.1002/cam4.1399

Abstract

Next‐generation sequencing (NGS) has been proposed as a suitable tool for liquid biopsy in colorectal cancer (CRC), although most studies to date have focused almost exclusively on sequencing of panels of potential clinically actionable genes. We evaluated the clinical value of whole‐exome sequencing (WES) of cell‐free DNA (cfDNA) circulating in plasma, with the goal of identifying differential clinical profiles in patients with CRC. To this end, we applied an original concept, “differential presence of exons” (DPE). We determined differences in levels of 379 exons in plasma cfDNA and used DPE analysis to cluster and classify patients with disseminated and localized disease. The resultant bioinformatics analysis pipeline allowed us to design a predictive DPE algorithm in a small subset of patients that could not be initially classified based on the selection criteria. This DPE suggests that these nucleic acids could be actively released by both tumor and nontumor cells as a means of intercellular communication and might thus play a role in the process of malignant transformation. DPE is a new technique for the study of plasma cfDNA by WES that might have predictive and prognostic value in patients with CRC.

Highlights

The analysis of circulating cell-free DNA is the most promising noninvasive alternative to conventional serial tissue biopsy for the analysis of the molecular features of tumors [1]
Circulating cell-free DNA (cfDNA) was successfully extracted from all plasma samples, obtaining a variable concentration of DNA ranging from 13.76 to 1602.90 pg/μL
We identified a set of exons whose differential presence in plasma allowed us to distinguish between groups M and N

Summary

Introduction

The analysis of circulating cell-free DNA (cfDNA) is the most promising noninvasive alternative to conventional serial tissue biopsy for the analysis of the molecular features of tumors [1]. Several studies demonstrated that elevated cfDNA levels in plasma, together with a heterogeneous pattern of hotspot. S. Olmedillas-L ópez et al. Differential Presence of Exons in CRC mutation status (including the KRAS, NRAS, BRAF, and EGFR genes, among others), provide a strong predictor of clinical prognostic value [3,4,5,6]. CfDNA was used in a recent study to reflect tumor molecular dynamics in the drug response of metastatic patients with CRC, tracking the evolution of resistance mutations in KRAS pathway genes at different time points over the course of anti-EGFR therapy [2]

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