Leptomeningeal Disease Diagnosed Using CSF Cell-Free DNA

Leptomeningeal disease is typically diagnosed via identification of malignant cells in cerebrospinal fluid (CSF), most commonly obtained via lumbar puncture or ventriculoperitoneal (VP) shunt access. CSF cytological analysis. The currently most reliable diagnostic method, has a sensitivity of approximately only 75% and is known to produce persistently negative results in approximately 10% of patients.

A large team of Neuro-oncologists at the Massachusetts General Hospital (Boston, MA, USA) and their colleagues conducted a diagnostic study to assess 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. This study consisted of two patient populations: 22 patients with cytologically confirmed LMD without parenchymal tumors abutting their CSF and eight patients with parenchymal brain metastases with no evidence of LMD.

Cell-free DNA was isolated from blood plasma and CSF using a QIASymphony instrument with the QIASymphony DSP Circulating DNA Kit (Qiagen, Hilden, Germany). A subset of libraries was prepared with unique molecular identifier adapters (Integrated DNA Technologies, Coralville, IA, USA). Prepared libraries were sequenced on HiSeq X, HiSeq 2500, or HiSeq 4000 instruments (Illumina, San Diego, CA, USA) to a targeted mean depth of 0.1X. Samples were aligned to hg19 using bwa-mem, version 0.7.7-r441.

The scientists reported that 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 cytological analysis as having LMD with no parenchymal tumor abutting CSF, cfDNA findings were accurate in the assessment of LMD in 45 samples, whereas cytological analysis was accurate in only 36 samples. Of 43 LMD-positive samples, CSF cfDNA analysis was sensitive to LMD in 40 samples and cytological analysis was sensitive to LMD in 31 samples, a significant difference. For three patients with parenchymal brain metastases abutting the CSF and no suspicion of LMD, cytological findings were negative for LMD in all three patients, whereas cfDNA findings were positive in all three patients.

Priscilla K. Brastianos, MD, Assistant Professor of Medicine and a co-senior author of the study, said, “If we are able to confidently diagnose LMD using cell-free DNA earlier and with fewer invasive procedures, then we can institute treatment sooner and enroll patients in clinical trials for new LMD treatments. The ultimate hope is that we can improve patient survival with earlier diagnosis and treatment for this deadly disease.”

The authors concluded that the diagnostic study found improved sensitivity and accuracy of cfDNA CSF testing versus cytological assessment for diagnosing LMD with the exception of parenchymal tumors abutting CSF, suggesting improved ability to diagnosis LMD. The study was published on August 9, 2021 in the journal JAMA Network Open.

Related Links:
Massachusetts General Hospital
Qiagen
Integrated DNA Technologies
Illumina