Clinical experience of cerebrospinal fluid-based liquid biopsy demonstrates superiority of cell free DNA over cell pellet genomic DNA for molecular profiling.

Cell free DNA (cfDNA) from cerebrospinal fluid (CSF) offers unique opportunities for genomic profiling of tumors involving the central nervous system (CNS) but remains uncommonly used in clinical practice. We describe our clinical experience using cfDNA from CSF for routine molecular testing using MSK IMPACTTM (targeting 468 cancer-related genes). In all, 148 cfDNA samples were assessed, comparing results of cfDNA vs gDNA (genomic DNA from cell pellets [CP]) derived from the same CSF sample and the primary tumor. Of these, 71.6% (106/148) were successfully sequenced. Somatic alterations (mutations and fusions), were observed in 70.8% (75/106) of the samples; 97.3% (73/75) comprised variants confirming CNS involvement by a previously diagnosed tumor, 14.7% (11/75) had additional variants consistent with a therapy-related resistance mechanism and 2.7% (2/75) had variants that independently diagnosed a new primary. Among samples with paired cfDNA and gDNA sequencing results, cfDNA was more frequently positive for at least one mutation (43.6% [55/126] vs 19.8% [25/126]) and harbored 1.6X more mutations (6.94 vs 4.65, p=0.005) with higher mean variant allele fractions (41.1% vs. 13.0%, p<0.0001). Among mutation positive cfDNAs, the corresponding gDNA was frequently negative (44.6%, 25/55) or failed sequencing (17.8%, 9/55). Routine molecular profiling of cfDNA is superior to gDNA from CSF, facilitating the capture of mutations at high VAF even in the context of a negative cytology.