Skip to content

Cell-Free DNA Analysis Outperforms Cytology for Diagnosing Leptomeningeal Disease

Key findings

  • This proof-of-principle study compared two methods for diagnosing leptomeningeal disease (LMD): cytologic analysis of cerebrospinal fluid (CSF), the standard procedure, and sequencing of cell-free DNA (cfDNA) derived from CSF
  • 43 samples came from patients who had participated in an LMD clinical trial and eight came from patients who had LMD ruled out as part of another study; three of the latter patients had a parenchymal tumor that abutted the CSF
  • The three samples from LMD-negative patients with a parenchymal tumor that abutted the CSF were falsely positive for LMD on cfDNA analysis
  • On analysis of the 48 other samples, the specificities of the two diagnostic methods were the same (100%), and the accuracy and sensitivity of cfDNA analysis were significantly superior
  • These findings suggest laboratories should consider incorporating CSF cfDNA analysis into LMD diagnostic workflows, except for patients who have a parenchymal tumor that abuts the CSF

Leptomeningeal disease (LMD) is a complication of solid and hematologic cancers that causes multiple neurologic symptoms and can progress rapidly, causing death within four to six weeks if not identified and treated. Cytologic analysis of cerebrospinal fluid (CSF) is currently the most reliable diagnostic method but has a sensitivity of only about 75%.

In a proof-of-principle study, researchers from the Massachusetts General Hospital Cancer Center showed sequencing of CSF-derived cell-free DNA (cfDNA) is superior to cytologic CSF analysis for diagnosing LMD. Michael D. White, MD, formerly a fellow in the Center for Neuro-Oncology, Priscilla K. Brastianos, MD, an attending neuro-oncologist there, and colleagues report in JAMA Network Open.


The team analyzed 51 CSF samples from 30 patients:

  • 22 patients (43 samples) who had participated in a clinical trial of pembrolizumab for LMD
  • Eight patients with brain metastases (eight samples) who had undergone CSF cytologic analysis to rule out LMD as part of another study; three of these LMD-negative patients had a parenchymal tumor that abutted the CSF (PTACSF)

Patients With PTACSF

In the three samples from the LMD-negative control subjects with PTACSF, cfDNA analysis was positive for the presence of LMD. These patients were removed from further investigation.

Patients Without PTACSF

In analyses of the remaining 48 samples, CSF cfDNA analysis was superior to CSF cytology in assessing LMD:

  • Accuracy—94% for cfDNA vs. 75% for cytology (P=0.01)
  • Sensitivity—93% vs. 72% (P=0.02)
  • Specificity—100% and 100%
  • Positive predictive value—100% and 100%
  • Negative predictive value—63% vs. 29%

cfDNA analysis also provided information that might be useful in predicting response to treatment or disease progression.


Laboratories should consider incorporating CSF cfDNA analysis into LMD diagnostic workflows. CSF cfDNA is stable after extraction and does not require immediate processing.

The exception is that traditional diagnostic methods, including cytology and neuroimaging, are preferable for patients with PTACSF.

Learn more about the Mass General Cancer Center

Refer a patient to the Mass General Cancer Center

Related topics


Investigators at Massachusetts General Hospital are encouraged by the results of the first prospective clinical trial of an immune checkpoint inhibitor specifically for patients with leptomeningeal dissemination of solid tumors.


The first large-scale genomic characterization of lung adenocarcinoma brain metastases has detected several novel, potentially clinically informative mutations in known cancer genes.