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arXiv · 2509.04939

The SChISM study: Cell-free DNA size profiles as predictors of progression in advanced carcinoma treated with immune-checkpoint inhibitors

Linh Nguyen Phuong·Frederic Fina·Laurent Greillier·Pascale Tomasini·Jean-Laurent Deville·Romain Zakrasjek·Lucie Della-Negra·Audrey Boutonnet·Frédéric Ginot·Jean-Charles Garcia·Sébastien Benzekry·Sébastien Salas
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Abstract

Background: Many advanced cancer patients experience progression under immune-checkpoint inhibitors (ICIs). Circulating cell-free DNA (cfDNA) size profiles offer a promising noninvasive multi-cancer approach to monitor and predict immunotherapy response. Methods: In the SChISM (Size CfDNA Immunotherapy Signature Monitoring) study (NCT05083494), pre-treatment plasmatic cfDNA size profiles from 126 ICI-treated advanced carcinomas were quantified using the BIABooster device. Fragmentomederived variables (concentration, peaks' position, and fragment size ranges) at baseline were analyzed for associations with early progression (EP, progression at first imaging) and progression-free survival (PFS), using logistic and Cox regression models. Bootstrap analysis validated robustness. Additional analyses were performed in homogeneous subpopulations: first-line lung cancer patients (n = 60) and head-andneck patients treated with Nivolumab (n = 25). Results: Higher cfDNA concentration and high quantities of short fragments (111-240 base pairs (bp)) were associated with poor response, unlike long fragments (> 300 bp). The proportion of fragments longer than 1650 bp demonstrated highest discriminatory power (AUC = 0.73, C-index = 0.69). It was significantly associated with non-EP (odds ratio = 0.39 [95% CI: 0.25-0.62]) and longer PFS (hazard ratio: 0.54 [95% CI: 0.42-0.68]). These associations remained significant when adjusted for confounders (age, sex, Eastern Cooperative Oncology Group performance status, tumor type, and neutrophil-to-lymphocyte ratio) and across both subpopulations. Bootstrap analysis confirmed robustness with mean accuracy of 70.1 $\pm$ 4.17% and positive predictive value of 55.6 $\pm$ 7.37%, in test sets. Conclusion: cfDNA size profiles significantly predicted ICI response and anticipate relapse, outperforming the routinely used marker programmed death-ligand 1 immunohistochemistry and reflecting enhanced immune system activation. Trial registration: (NCT05083494), date of registration: 2021-10-19.

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Linh Nguyen Phuong, Frederic Fina, Laurent Greillier, Pascale Tomasini, Jean-Laurent Deville, Romain Zakrasjek, Lucie Della-Negra, Audrey Boutonnet, Frédéric Ginot, Jean-Charles Garcia, Sébastien Benzekry, Sébastien Salas. 2025-09-05. The SChISM study: Cell-free DNA size profiles as predictors of progression in advanced carcinoma treated with immune-checkpoint inhibitors. https://arxiv.org/abs/2509.04939

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