cfDNA sequencing as a cutting-edge technology to identify pathogenic germline variants from 8353 patients with advanced tumors at the Gustave Roussy Institute.

Abstract

3061 Background: Large cfDNA panels used for somatic profiling can incidentally reveal pathogenic variants of potential germline origin, with implications for patient management and hereditary cancer risk assessment. Methods: Between December 18 th , 2020 and July 22 nd , 2025, a weekly molecular tumor board reviewed cfDNA sequencing data from 8353 patients with advanced solid tumors treated at Gustave Roussy using the FoundationOne Liquid CDx panel, within the prospective STING trial (NCT04932525). We evaluated the yield, clinical relevance, and confirmatory outcomes of an MTB-governed workflow to flag putative germline pathogenic variants (PGPVs) from routine cfDNA profiling in advanced cancers. Across the 324 covered genes, we selected a list of 31 known hereditary cancer genes and 7 emerging candidates. Patients without prior germline confirmation were referred for genetic counseling and confirmatory testing on an independent sample. Turnaround times were compared with the conventional germline pathway. Results: Among 8,353 patients (mean age 62 years), 445 (5.3%) carried 471 PGPVs, including 23 patients with more than 2 variants. The most frequently implicated genes were BRCA2 (n=101), MUTYH (n=81) and BRCA1 (n=62). Overall, 54.6% of PGPVs were incidental findings (257/471); among incidental findings, 51.0% were clinically actionable (131/257), corresponding to 27.8% of all PGPVs (131/471). Germline status was confirmed in 172 patients (86 known prior to cfDNA profiling and 86 confirmed following cfDNA-guided referrals, including 60 incidental findings of which 52 were actionable; 14 variants (11 patients) were not confirmed and 6 were pending. For variants first flagged through cfDNA, the mean interval from liquid biopsy prescription to confirmatory germline report was 2 months, compared with 6 months through the conventional pathway. In evaluable paired cases, cfDNA showed high diagnostic performance for identifying germline findings (sensitivity 98.3%, specificity 97.4%). Conclusions: In an advanced pan-cancer real-world cohort, an MTB-governed cfDNA workflow identified PGPVs in 5% of patients, with over half representing incidental findings and 28% of all PGPVs being actionable. cfDNA profiling can accelerate referral and confirmation of hereditary cancer risk when coupled with expert interpretation and confirmatory germline testing, while acknowledging limitations for certain alterations.