Plasma shallow whole-genome sequencing profiling in patients with

RAS
WT

metastatic colorectal cancer (mCRC) undergoing first-line anti-EGFR therapy.
Authors: Martelli Valentino , Vidal Barrull Joana , Fernández-Rodríguez Concepción , Gibert Joan , Moreno Ana , Louhamane Aya , Linares-Aceituno Jenniffer , Garcia-Alfonso Pilar , Paez David , Alonso Vicente , Gomez Espana Maria Auxiliadora , Santos Cristina , Durán Gema , Elez Elena , Bellosillo Paricio Beatriz , Tabernero Josep , Salazar Ramon , Aranda Enrique , Toledo Rodrigo A , Montagut Clara O. 
Published: January 2025

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Background:
Acquired resistance (AR) to first-line (1L) chemotherapy (CT) + anti-EGFR inhibitors is a major challenge in the management of

RAS
WT

mCRC patients (pts). While AR in later lines has been explained with point mutations in the
EGFR
pathway, its real mechanisms in 1L remain poorly understood. Tumor molecular biology can be dynamically studied through circulating tumor DNA (ctDNA) analysis, a real-time, non-invasive approach to detect AR. In this context, we conducted the multicenter prospective PLATFORM-B study, which enrolled 100

RAS
WT

mCRC pts receiving 1L CT + cetuximab across 15 Spanish Medical Oncology Departments, alongside 30

RAS
MUT

pts (control) treated with 1L CT + bevacizumab. Peripheral blood samples have been collected at baseline (BL), week 8, and disease progression (PD). Next-generation sequencing analysis (Ion S5 system) of ctDNA at PD revealed AR mutations in only 10% of pts, suggesting that alterations in the EGFR pathway may only partially explain AR in 1L. Therefore, we conducted shallow whole-genome sequencing (shWGS) to further characterize genomic profiles possibly related with novel mechanisms of AR.
Methods:
Baseline and PD samples with sufficient remaining plasma were considered for this analysis. shWGS was performed with a coverage ranging 0.5X to 2.0X and analyzed using ichorCNA pipeline to evaluate various genomic characteristics such as copy number alterations (CNA), tumor fraction (TF), subclonal fraction (SF), and ploidy. Molecular results were correlated to clinical-pathological features and outcomes.
Results:
Overall, 35 mCRC pts (27

RAS
WT

and 8

RAS
MUT

) were included in the study. At BL (
N
= 26), median TF (mTF) was 0.19, median ploidy 2, median SC fraction 0.5, median SC genome fraction 0.21, and median subclonal CNA fraction 0.41. At PD (
N
= 33), mTF was 0.08, median ploidy 2, median SC fraction 0.5, median SC genome fraction 0.17, and median subclonal CNA fraction 0.38. Of all the features analyzed, only the TF showed potential prognostic value. At BL, pts with TF levels above the median had poorer overall survival (OS) compared to those with lower levels, approaching statistical significance (
P
= .055). At PD, higher TF levels were statistically significantly associated with worse OS (
P
= .02). No meaningful differences between the

RAS
WT

and

RAS
MUT

groups were observed. Specific variations in CNA, TF, SF, or ploidy under treatment are being correlated to clinical data to seek for predictive value.
Conclusions:
This preliminary analysis of the PLATFORM-B using shWGS showed the prognostic value of TF. Further analyses are undergoing to better understand the molecular landscape of acquired resistance to 1L anti-EGFR-based therapy in

RAS
WT

mCRC pts.