O006

Thursday, November 13th, 2025 17:40 – 17:50
Speaker Francesca Gaino

Genome wide Copy Number Alterations in ctDNA as Novel Biomarker in Head and Neck Squamous Cell Cancer (IDENTIFY Trial)

Background
New strategies to stratify the risk of Head and Neck Squamous Cell Cancer (HNSCC) beside clinical stage and HPV, as well to follow patients (pts) after treatments (Tx) are strongly awaited. Liquid biopsy is a promising, minimally invasive alternative to tissue biopsy for cancer diagnosis and monitoring. Aim of this study is to explore the potential of Genome wide Copy Number Alterations (CNA) in circulating tumor DNA (ctDNA), described as a tumor fraction (TF) of cell free DNA (cfDNA), in defining prognosis of HNSCC patients and for early identification of recurrence.
Methods
Pts with stage I-IV HNSCC before curative treatment were enrolled and underwent blood collections at baseline (T0) and during follow up (FU) at 3, 6, 12 and 18 months. cfDNA was isolated and purified from plasma, and shallow Whole Genome Sequencing was performed to identify regions of CNA. Subsequently, the % of ctDNA over total cfDNA (defined as TF) was obtained. Descriptive statistics and correlation analyses were performed in order to explore associations between ctDNA and clinical characteristics. We herein report the results of the baseline analysis of the first enrolled pts.
Results
Among enrolled pts between March 2021 and April 2025, 53 T0 blood samples were analysed. Two failures occurred, resulting in a failure rate of 3.8% with our technique. 51 pts (11 females) were included in the analyses. Median age was 63 years (39-85). HPV+ pts were 11 (21.6%). Stage distribution was as follows: I in 3 pts, II in 5 pts, III in 20 pts, IV in 23 pts. 32 pts underwent surgery + adjuvant Tx, and 19 pts (chemo)radiotherapy. Median FU was 26 months (1-43). 19 pts relapsed (37.3%) with a median time to relapse of 28 months. Median T0 TF was 5.3 (1.6-47.8) in the whole sample and 10.7 (3.9-37.8) in HPV+ pts. Analysis showed no correlation between TF at T0 and sex, age, smoking status, overall stage, and N stage. A non-significant trend toward higher T0 TF was observed in HPV+ pts (p=0.08). Pts who relapsed showed significantly higher TF values at T0 (p=0.05).
Discussion
Our technique proved to be feasible with a low failure rate. Baseline TF correlated with relapse in our pts. Further analyses are warranted to explore dynamic variations of TF during FU.