Genomic Copy Number Variation Profiling of Pleural Effusion cfDNA via LP-WGS for Precision Diagnosis and Prognostic Stratification in Lung Adenocarcinoma-associated Malignant Pleural Effusion running title: cfDNA CNV for LUAD-MPE Diagnosis and Prognosis

<title>Abstract</title> <p> Background Lung adenocarcinoma (LUAD)-associated malignant pleural effusion (MPE) is an advanced disease hallmark with a median survival of 3–12 months. Current diagnostic strategies suffer from critical limitations: cytological examination has inadequate sensitivity, invasive biopsy is poorly tolerated by some patients, and traditional biomarkers such as carcinoembryonic antigen (CEA) lack sufficient accuracy. Additionally, validated prognostic biomarkers for clinical risk stratification of MPE remain scarce, creating an urgent need for noninvasive, high-sensitivity tools for diagnosis and prognosis. Methods A prospective cohort of 41 patients with pleural effusion (30 with confirmed LUAD-associated MPE and 11 benign controls) was included. Copy number variation (CNV) profiling was performed using low-pass whole-genome sequencing (LP-WGS). Diagnostic performance was assessed through ROC curves, and the results were compared with the CEA level. Correlations between genomic features and clinicopathological variables were evaluated using Spearman’s correlation coefficient, and survival analysis was conducted using the Kaplan–Meier method with the log-rank test. Results CNVs were detected in 96.7% of MPE patients compared with only 9.1% of patients with benign effusions ( <italic>P</italic>  &lt; 0.001). A CNV-based diagnostic model achieved an area under the curve (AUC) of 0.939, outperforming CEA testing, with 96.7% sensitivity and 90.9% specificity. The tumor fraction and genome-wide |Z score| were strongly correlated with the cytological tumor cell proportion ( <italic>R</italic>  = 0.67–0.70; <italic>P</italic>  &lt; 0.0001). Poorly differentiated tumors exhibited significantly greater genomic instability ( <italic>P</italic>  = 0.032), and specific alterations, including 18p amplification and 8p, 9q, and 19q deletions, were associated with shorter overall survival ( <italic>P</italic>  &lt; 0.05). Conclusions LP-WGS-based CNV analysis of pleural effusion cfDNA is a cost-effective, noninvasive tool for distinguishing MPE from benign effusions and predicting prognosis. It can serve as a complementary test to cytology and CEA, especially for patients unable to undergo invasive biopsy, facilitating early diagnosis and personalized management of advanced LUAD-associated MPE. </p>