Abstract 3093: Quantifying the confounders of panel-based tumor mutational burden (TMB) measurement

Abstract

Abstract Retrospective data including subgroup analyses in clinical studies have sparked strong interest in developing tumor mutational burden (TMB) as a predictive biomarker for immune checkpoint blockade. While individual factors interfering with panel sequencing based measurement of TMB (psTMB) have been discussed in recent studies, an integrative study quantifying, comparing and combining all potential confounders is still missing. We separated different potential confounders of psTMB measurement including “panel size”, “germline mutation filtering”, “biological variance” and “technical variance” and developed a specific error model for each of these factors. Published experimental psTMB data were fitted to the error models to quantify the contribution of each of the confounders. The total psTMB variance was obtained as sum over the different variance contributions. Using a typical large panel (size 1 to 1.5 Mbp) total errors of 57%, 42%, 34% and 28% were observed for tumors with psTMB of 5, 10, 20 and 40 muts/Mbp. Even for large panels, the stochastic error connected to the panel size represented the largest of all contributions to the total psTMB variance, especially for tumors with TMB up to 20 muts/Mbp. Other sources of psTMB variability could be kept under control, but rigorous quality control, best practice laboratory workflows and optimized bioinformatics pipelines are essential. We developed an integrated framework for the analysis of psTMB variability and provide a set of recommendations for implementation of psTMB as a laboratory developed test. Our approach highlights the stochastic portion of psTMB variability. The stochastic error connected inherently with psTMB could in part explain the suboptimal performance of the biomarker in some of the recent lung cancer studies. Citation Format: Jan Budczies, Daniel Kazdal, Michael Allgäuer, Petros Christopoulos, Eugen Rempel, Nicole Pfarr, Wilko Weichert, Stefan Fröhling, Michael Thomas, Solange Peters, Volker Endris, Peter Schirmacher, Albrecht Stenzinger. Quantifying the confounders of panel-based tumor mutational burden (TMB) measurement [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3093.