Low-Coverage WGS-Based CIN Scoring Enables Cost-Effective Molecular Stratification and Prognostic Risk Assessment in Laryngeal Squamous Cell Carcinoma

Objective: To explore the feasibility of chromosomal instability (CIN) as a biomarker for molecular subtyping of laryngeal squamous cell carcinoma (LSCC) and to evaluate its correlation with clinical prognosis. Methods: This study included 38 patients with LSCC. Formalin-fixed paraffin-embedded (FFPE) tumor tissue samples were collected for low-coverage whole genome sequencing (LC-WGS, ~1×). A customized bioinformatics workflow, the ultra-sensitive chromosomal aneuploidy detector (UCAD), was employed to analyze genome-wide copy number variations (CNVs). The CIN score was calculated based on the product of chromosome arm length and Z-score, with a threshold of 178, dividing patients into high-CIN (n=28, 73.7%) and low-CIN (n=10, 26.3%) groups. Correlations between CIN and clinicopathological features, including tumor differentiation, tumor type, recurrence, and progression-free survival (PFS), were analyzed using chi-square tests, Log-rank tests, and Cox regression. Results: All 38 samples passed quality control. The cohort comprised exclusively male patients with a mean age of 63.8 years. 81.6%t had a smoking history (median: 30 pack-years), and 28.9% had a drinking history (median: 32.5 pack-years). 7 patients (18.4%) were well-differentiated; 31 (81.6%) were poorly or moderately differentiated. CIN was elevated in 28 patients (76.7%) and low in 10 (26.3%). Genomic analysis revealed recurrent arm-level alterations: losses at 1p, 3p, 4q, 5q, 9p, 13q, 16q, 17p, 18q; gains at 1q, 3q, 5p, 7p, 8q, 17q, 20q. Key amplified genes included TERT (5p15.33) as well as PIK3CA and SOX2 (3q26.3). CIN-low tumors were predominantly located in the glottic region (P=0.033) and well-differentiated (P=0.005). CIN-high tumors correlated with advanced anatomical sites (transglottic/hypopharyngeal), poor differentiation, death (P=0.043), and shorter overall srvival （OS）(median OS: <51 months vs NR; P=0.032)，and showed a marginally significant relationship with progression-free survival (PFS) (median PFS: <66 months vs NR; P=0.051). High CIN may warrant attention as a potential prognostic factor. Conclusion: CIN, quantified by LC-WGS, enables robust molecular stratification of LSCC. Low-CIN tumors exhibit glottic origin, high differentiation, and favorable prognosis; high-CIN tumors are associated with transglottic/hypopharyngeal location, poor differentiation, and poor survival. CIN is an independent prognostic biomarker and provides a cost-effective tool for mutation-poor tumors.