Cerebrospinal fluid circulating tumor DNA depicts profiling of brain metastasis in NSCLC

Abstract Brain metastasis (BM) genetically diverges from the primary tumor in non-small-cell lung cancer (NSCLC). Hence, accurately capturing clinically relevant alterations is pivotal for the delivery of targeted therapies. Circulating tumor DNA (ctDNA) sequencing has emerged as a promising liquid biopsy in the biomarker-based clinical management of recurrent and extracranial metastatic NSCLC. However, absence of simultaneous sequencing data from brain metastatic sites prevents the definitive evaluation of the efficacy of ctDNA representing genetic profiles in BM. Here, we performed parallel genomic comparisons between matched BM and primary tumor DNA, plasma ctDNA, and cerebrospinal fluid (CSF) ctDNA. The results indicated that CSF ctDNA had a greater ability than plasma ctDNA in comprehensively representing the mutational landscape of BM, with CSF ctDNA detecting all BM mutations in 83.33% of patients while plasma ctDNA was only 27.78%. Mutant allele frequency (MAF) in CSF ctDNA was highly correlated with the tumor size of BM (r = 0.95), and the mean MAF in CSF ctDNA was more abundant than that in plasma ctDNA (38.05% vs. 4.57%). MAF and tumor mutational burden (TMB) in CSF ctDNA were strongly associated with those in BM (r = 0.96 and 0.97, respectively). Of note, CSF ctDNA had significantly higher concordance with BM than plasma ctDNA (99.33% vs. 67.44%), facilitating the identification of clinically relevant mutations. Moreover, we found that plasma ctDNA has stronger profiling performance with a concordance of 93.01% in multiple brain metastases, equivalent to CSF ctDNA. Collectively, our study indicates that CSF ctDNA is superior to plasma ctDNA in accurately represent the profiling of single BM, plasma ctDNA could be an alternative liquid biopsy material to be applied in multiple brain metastatic NSCLC.