Detection of aneuploidy in cerebrospinal fluid from patients with breast cancer can improve diagnosis of leptomeningeal metastases.

Purpose Detection of leptomeningeal metastasis (LM) is hampered by limited sensitivities of currently used techniques: MRI and cytology of cerebrospinal fluid (CSF). Detection of cell-free tumor DNA (ctDNA) in CSF has been proposed as a tumor specific candidate to detect LM at an earlier stage. The aim of this study was to investigate mutation and aneuploidy status in CSF-derived cfDNA of breast cancer patients with a clinical suspicion of LM. Methods Cell-free DNA was isolated from stored remnant CSF and analyzed by targeted next generation sequencing (NGS) (n=30) and the modified Fast Aneuploidy Screening Test-Sequencing System (mFAST-SeqS) (n=121). The latter method employs selective amplification of long interspaced nuclear elements (LINE-1)-sequences which are present throughout the genome and allows for fast and cheap detection of aneuploidy. We compared these results with the gold standard to diagnose LM: cytology. Results LM was cytology-proven in 13 of 121 patients. Low DNA yields resulted in insufficient molecular coverage of NGS for the majority of samples (success rate 8/30). The mFAST-SeqS method, successful in 112/121 (93%) samples, detected genome-wide aneuploidy in 24 patients. Ten of these patients had cytology-proven LM, 8 additional patients were either concurrently diagnosed with CNS metastases by radiological means or developed these soon after the LP. The remaining 6 cases were suspected of LM but could not be confirmed by cytology or imaging. Aneuploidy was associated with development of LM and significantly worse overall survival. Conclusions Aneuploidy in CSF-derived cfDNA may provide a promising biomarker to improve timely detection of LM.