Standardization of pleural effusion-based tumor mutation burden (TMB) estimation using capture-based targeted sequencing

BACKGROUND: Tumor mutation burden (TMB) has received considerable attention as a potential predictive biomarker for response to anticancer treatment with immune checkpoint inhibitors (ICIs), and has been increasingly incorporated into clinical practice. Currently, TMB is often determined with tissue biopsies using whole-exome sequencing (WES) or panel-based targeted sequencing. Meanwhile, liquid biopsies such as blood are actively investigated as alternative media, although there is currently no report of the performance of targeted sequencing in assessing TMB using pleural effusion (PE) specimens. METHODS: Thirty-two patients diagnosed with advanced non-small cell lung cancer (NSCLC) with associated PE were prospectively enrolled (NCT 03546452). Cell-free DNA (cfDNA) from the supernatant of PE was subjected to both WES and capture-based targeted sequencing using various commercially-available panels. RESULTS: All five panels assessed in this study demonstrated a good correlation with WES-derived TMB, with correlation coefficients ranging from 0.68–0.81. Two- and three-tier classification systems built on the TMB estimates achieved respective concordance rates of 74% and 63% between classifications based on WES- and panel-derived TMB levels. CONCLUSIONS: This study provides real-world evidence that all panels assessed in this study can be used for TMB evaluation based on PE samples. We also demonstrated that PE can serve as an alternative medium for TMB evaluation. To the best of our knowledge, this is the first study evaluating the potential of PE samples for TMB estimation, thereby providing a basis for establishing future standard protocols.