Low-input CSF cfDNA shallow whole-genome sequencing for CNV-based diagnosis and monitoring of leptomeningeal metastasis in lung cancer

Leptomeningeal metastasis (LM) is a life-threatening complication of lung cancer for which magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) cytology may miss disease and provide limited molecular guidance. Because the low cfDNA input typical of CSF constrains deep sequencing and mutation-focused approaches may underrepresent the copy-number-rich genomic architecture of CNS metastases, we developed a low-input shallow whole-genome sequencing approach to quantify genome-wide copy-number changes from trace CSF cfDNA. In 57 patients with lung cancer and CNS metastases (28 with LM and 29 with brain metastasis only), CSF showed stronger tumor-DNA signals and a higher burden of genome amplification than matched plasma (54 pairs), despite lower cfDNA concentrations. Among samples with detectable tumor DNA, genome amplification proportion (GAP), defined as the fraction of the genome showing amplification, identified LM with 86% sensitivity and no false positives observed in this cohort, and showed performance comparable to cytology as a complementary quantitative readout. Copy-number profiling further highlighted chromosomal regions and focal gene amplifications enriched within LM, supporting a CNV-enriched molecular state in the CSF compartment. Serial CSF sampling also captured treatment-associated molecular shifts, including progressive TYMS amplification during intrathecal pemetrexed in an exploratory case. Together, these findings support low-input CSF sequencing as a practical molecular approach to complement LM diagnosis and longitudinal monitoring in lung cancer and provide a rationale for prospective validation in independent multi-center cohorts.