Cell-free DNA analysis of cerebrospinal fluid associated with improved diagnostic accuracy and sensitivity for the detection of leptomeningeal disease

1. Improved diagnostic accuracy and sensitivity were found with cerebrospinal fluid-derived cell-free DNA analysis for the diagnosis of leptomeningeal disease compared to cytologic assessment, the current diagnostic standard.

2. Cerebrospinal fluid-derived cell-free DNA analysis was able to diagnose leptomeningeal disease in patients with persistently negative findings on cytologic analysis, a known phenomenon in current diagnostic tests.

Evidence Rating Level: 2 (Good)

Study Rundown: Cytologic evaluation using cerebrospinal fluid (CSF) is the current standard method for diagnosing leptomeningeal disease (LMD), a serious complication of cancer. However, this invasive diagnostic test has low sensitivity resulting in chronic underdiagnosis of LMD in patients with cancer. Thus, studies investigating new diagnostic methods focused on improving sensitivity are important for early disease detection and improved clinical decision-making. This retrospective diagnostic study sought to establish proof-of-principle LMD diagnosis via genomic sequencing of CSF-derived cell-free DNA (cfDNA) and compared its accuracy with conventional cytologic analysis. The main endpoint was diagnostic accuracy of cfDNA analysis, defined as the number of test samples that resulted in correct concordant diagnoses out of the total number of tests assayed. Among 43 CSF samples from 22 LMD-positive patients confirmed via cytologic assessment who did not have parenchymal tumors abutting their CSF, tumor-derived cfDNA was detected in 40 (93%) of the CSF samples, compared to 31 (72%) positive samples for malignant neoplasm as determined by cytologic analysis. These findings demonstrated improved diagnostic accuracy and sensitivity of CSF-derived cfDNA analysis for the diagnosis of LMD compared to CSF cytologic assessment, the current diagnostic standard. Furthermore, CSF cfDNA analysis was able to diagnose LMD in patients with persistently negative findings on cytologic analysis, a known phenomenon in current diagnostic tests. Further follow-up studies with prospective design and randomization are needed to concurrently compare CSF cfDNA analysis with cytologic assessment to clarify the utility of CSF cfDNA analysis as a diagnostic test and marker of treatment response, with the goal of its inclusion into diagnostic guidelines and treatment algorithms. A limitation of this study was the low sensitivity achieved through low-pass genomic sequencing in malignant neoplasms with near-diploid genomes. To mitigate this inadequacy, deeper sequencing via the detection of somatic nucleotide variations should be used as a method for detecting LMD.

Click to read the study in JAMA Network Open

Relevant Reading: The diagnostic accuracy of magnetic resonance imaging and cerebrospinal fluid cytology in leptomeningeal metastasis

In-Depth [retrospective diagnostic study]: This retrospective diagnostic study included 30 patients (23 women [77%]; median age, 51 years [range, 28-81 years]) primarily presenting with metastatic solid malignant neoplasms from neuro-oncology clinic at 2 large, tertiary medical centers between 2015 to 2018. Patients with suspected or confirmed LMD were evaluated via genomic sequencing of CSF samples to identify tumor derived cfDNA and compare the results against cytologic analyses. Patients were separated into 2 cohorts for analysis including 22 patients with cytologically confirmed LMD without parenchymal tumors abutting their CSF and 8 patients with parenchymal brain metastases with no evidence of LMD. The presence of malignant cells on past CSF cytologic analysis was used to define patients positive for LMD. cfDNA results were accurate in the diagnosis of LMD in 45/48 follow-up samples (94%; 95%CI, 83%-99%) from patients previously diagnosed with LMD with no parenchymal tumor abutting CSF compared to 36/48 samples (75%; 95%CI, 60%-86%) via cytologic analysis, a significant difference (P = .02). Furthermore, CSF cfDNA analysis was sensitive to LMD in 40/43 LMD-positive samples (93%; 95%CI, 81%-99%) compared to 31/43 samples (72%; 95%CI, 56%-85%) via cytologic analysis, a significant difference (P = .02). Lastly, in 3 patients with parenchymal brain metastases abutting the CSF and no suspicion of LMD, cytologic findings were negative for LMD in all 3 patients, whereas cfDNA analysis produced discordant results with all 3 patients positive for LMD.

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