Detection of Leptomeningeal Disease Using Cell-Free DNA From Cerebrospinal Fluid

Abstract

Importance: Leptomeningeal disease (LMD) is a devastating complication of cancer that is frequently underdiagnosed owing to the low sensitivity of cerebrospinal fluid (CSF) cytologic assessment, the current benchmark diagnostic method. Improving diagnostic sensitivity may lead to improved treatment decisions.

Objective: To assess whether cell-free DNA (cfDNA) analysis of CSF may be used to diagnose LMD more accurately than cytologic analysis.

Design, setting, and participants: This diagnostic study conducted in a neuro-oncology clinic at 2 large, tertiary medical centers assessed the use of genomic sequencing of CSF samples obtained from 30 patients with suspected or confirmed LMD from 2015 through 2018 to identify tumor-derived cfDNA. From the same CSF samples, cytologic analyses were conducted, and the results of the 2 tests were compared. This study consisted of 2 patient populations: 22 patients with cytologically confirmed LMD without parenchymal tumors abutting their CSF and 8 patients with parenchymal brain metastases with no evidence of LMD. Patients were considered positive for the presence of LMD if previous CSF cytologic analysis was positive for malignant cells. The analysis was conducted from 2015 to 2018.

Main outcomes and measures: The primary outcome was the diagnostic accuracy of cfDNA analysis, defined as the number of tests that resulted in correct diagnoses out of the total number of tests assayed. Hypotheses were formed before data collection.

Results: In total, 30 patients (23 women [77%]; median age, 51 years [range, 28-81 years]), primarily presenting with metastatic solid malignant neoplasms, participated in this study. For 48 follow-up samples from patients previously diagnosed via cytologic analysis as having LMD with no parenchymal tumor abutting CSF, cfDNA findings were accurate in the assessment of LMD in 45 samples (94%; 95% CI, 83%-99%), whereas cytologic analysis was accurate in 36 samples (75%; 95% CI, 60%-86%), a significant difference (P = .02). Of 43 LMD-positive samples, CSF cfDNA analysis was sensitive to LMD in 40 samples (93%; 95% CI, 81%-99%), and cytologic analysis was sensitive to LMD in 31 samples (72%; 95% CI, 56%-85%), a significant difference (P = .02). For 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 findings were positive in all 3 patients.

Conclusions and relevance: This diagnostic study found improved sensitivity and accuracy of cfDNA CSF testing vs cytologic assessment for diagnosing LMD with the exception of parenchymal tumors abutting CSF, suggesting improved ability to diagnosis LMD. Consideration of incorporating CSF cfDNA analysis into clinical care is warranted.

Conflict of interest statement

Conflict of Interest Disclosures: Dr Cahill reported receiving personal fees from Boston Pharmaceuticals, the Department of Defense, Eli Lilly and Company, GlaxoSmithKline, Merck & Co, and the National Institutes of Health outside the submitted work. Dr Adalsteinsson reported receiving personal fees from Bertis Inc and AGCT GmbH outside the submitted work and having a patent pending for methods for genome characterization. Dr Sullivan reported receiving grants from Amgen and Merck & Co and receiving personal fees from Array Biopharma, Asana Biosciences, AstraZeneca, Bristol-Myers Squibb, Compugen, Eisai Co, Iovance Biotherapeutics, Merck & Co, OncoSec, Pfizer, Novartis, and Replimune outside the submitted work. Dr Brastianos reported receiving grants to Massachusetts General Hospital from Bristol Myers Squibb, Eli Lilly and Company, Merck & Co, and Mirati; receiving grants from the Breast Cancer Research Foundation, Damon Runyon Cancer Research Foundation, Mirati, and the National Institutes of Health during the conduct of the study; and receiving personal fees from Angiochem, Dantari, ElevateBio, Eli Lilly and Company, Genentech-Roche, Merck & Co, Pfizer, SK Life Sciences, Tesaro, and Voyager Therapeutics outside the submitted work. No other disclosures were reported.

Figures

Figure 1.. Cerebrospinal Fluid (CSF) Collection and Analysis

A, Samples were collected by lumbar puncture or ventriculoperitoneal shunt access. Collected CSF samples were fractionated and analyzed via cytology and ultra–low-pass, whole-genome sequencing of cell-free DNA (cfDNA). B, Cytologic and CSF cfDNA analyses results were collected in 48 samples from patients with cytologically confirmed leptomeningeal disease (LMD) without parenchymal tumors (PTs) that abutted the CSF (PTACSF). Cytologic and CSF cfDNA analyses disagree for assessment of LMD in 11 samples, with the CSF cfDNA finding correct in 10 samples. The 1 sample for which cytologic analysis better assessed LMD than CSF cfDNA analysis was for a patient (ie, patient CSF-089) with acute myeloid leukemia, the only such patient in the cohort. Patients shown were those previously diagnosed as having LMD by using cytologic evidence, which comprised 43 of 48 total samples. C, Inferred cancer fraction is not significantly different for all patients with LMD vs those with PTACSF, and both populations showed significantly higher inferred cancer fractions than patients with PTs that did not abut the CSF. D, Concentrations of CSF cfDNA were not significantly different among patients with LMD, PTACSF, or PT. DFCI indicates Dana-Farber Cancer Institute; +, positive for LMD; and −, negative for LMD. aPatient CSF-089.

Figure 2.. Spine and Brain Gadolinium Contrast–Enhanced, T1-Weighted Magnetic Resonance Imaging Scans (T1 + C) for Patient CSF-088

Days indicate time since the original image was obtained on day 0; LMD, leptomeningeal disease; and cfDNA, cell-free DNA.

Figure 3.. Biomarkers for Disease Status Assessment

cfDNA indicates cell-free DNA.