A new study shows variant allele frequency measured from CSF may support diagnosis and monitoring in leptomeningeal disease.
Leptomeningeal disease (LMD) remains one of the most challenging diagnoses in neuro-oncology. MRI returns normal or inconclusive results in 20-30% of confirmed cases, and CSF cytology can miss roughly one in three patients at initial testing.
A new peer-reviewed study published in Diagnostics suggests that a standard lumbar puncture may help address this diagnostic gap. By measuring variant allele frequency (VAF) in tumour-derived DNA from CSF using the Summit liquid biopsy assay (Belay Diagnostics), clinicians gain specific, quantitative signals to support diagnosis and monitor treatment response over time.
The study analysed 118 CSF specimens from patients with a provisional diagnosis of metastatic CNS cancer, spanning breast, lung, and other primary malignancies. Summit identified clinically significant variants in all 118 specimens across 22 of the 32 genes on the panel, including TP53, EGFR, KRAS, and PIK3CA.
A VAF threshold of 5% emerged as a potentially meaningful marker for LMD. Of patients with confirmed LMD, 69% had VAFs above that threshold, while most patients with parenchymal metastases or unconfirmed LMD had VAFs below 5%. In cases where imaging and cytology were inconclusive, an elevated VAF prompted further investigation that ultimately led to confirmed LMD diagnoses. In 10 additional cases initially categorised as parenchymal metastases or suspected LMD, VAFs above 5% were later associated with confirmed LMD on clinical or pathological follow-up.
For patients in treatment, serial CSF testing with Summit showed that VAF changes tracked clinical outcomes. Half of patients (7 of 14) with repeat testing showed decreasing or absent VAF following treatment, correlating with clinical improvement. In one patient, a rising VAF likely corresponded with disease progression. In three cases, a new variant appeared on repeat testing, suggesting clonal evolution or spatial heterogeneity within the leptomeningeal space, a finding that indicates serial CSF liquid biopsy may capture how tumour genomics evolve over time.
"This study illustrates how liquid biopsy with the Belay assay represents a paradigm shift in neuro-oncology. This technology allows for the continuous monitoring of a tumour’s molecular evolution, enabling physicians to detect clonal evolution and possibly treatment resistance ahead of radiographic progression, closing the gap between biological change and clinical intervention," said Nancy Ann O Bush MD PhD, Clinical Director, Division of Neuro-Oncology, Department of Neurological Surgery and Neurology, University of California, San Francisco.
This work provides the foundation for prospective validation in larger, tumour-specific cohorts.
- Udhane V, Larson A, Adams JN, et al. Variant Allelic Frequency to Track Therapy Response and Evaluate Leptomeningeal Disease in Metastatic Central Nervous System Cancers. Diagnostics (Basel). 2026 Mar 13;16(6):851. doi:10.3390/diagnostics16060851