Burden of tumor mutations, neoepitopes, and other variants are dubious predictors of cancer immunotherapy response and overall survival

Background Tumor mutational burden (TMB, the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as a result. However, TMB harbors intrinsic variability across cancer types, and its assessment and interpretation are poorly standardized. Methods Using a standardized approach, we quantify the robustness of TMB as a metric and its potential as a predictor of immunotherapy response and survival among a diverse cohort of cancer patients. We also explore the additive predictive potential of RNA-derived variants and neoepitope burden, incorporating several novel metrics of immunogenic potential. Results We find that TMB is a partial predictor of immunotherapy response in melanoma and non-small cell lung cancer, but not renal cell carcinoma. We find that TMB is predictive of overall survival in melanoma patients receiving immunotherapy, but not in an immunotherapy-naive population. We also find that it is an unstable metric with potentially problematic repercussions for clinical cohort classification. We finally note minimal additional predictive benefit to assessing neoepitope burden or its bulk derivatives, including RNA-derived sources of neoepitopes. Conclusions We find sufficient cause to suggest that the predictive clinical value of TMB should not be overstated or oversimplified. While it is readily quantified, TMB is at best a limited surrogate biomarker of immunotherapy response. The data do not support isolated use of TMB in renal cell carcinoma. * αCTLA4 : Anti-cytotoxic T-lymphocyte-associated protein 4 αPD1 : Anti-programmed cell death protein 1 AUC : Area Under the Curve COAD : Colon Adenocarcinoma GATK : Genome Analysis Toolkit GTEx : Genotype Tissue Expression HLA : Human Leukocyte Antigen Indel : Insertion or deletion KIRC : Kidney Renal Clear Cell Carcinoma kma : Keep Me Around LUAD : Lung Adenocarcinoma LUSC : Lung Squamous Cell Carcinoma MHC : Major Histocompatiblity Complex MMR : Mismatch Repair NSCLC : Non Small Cell Lung Cancer PRAD : Prostate Adenocarcinoma RCC : Renal Cell Carcinoma RI : Retained intron RNA-seq : RNA sequencing ROC : Receiver Operating Characteristic SKCM : Skin Cutaneous Melanoma SRA : Sequence Read Archive TCGA : The Cancer Genome Atlas THCA : Thyroid carcinoma TMB : Tumor Mutational Burden TPM : Transcripts Per Million TVB : Tumor Variant Burden UCEC : Uterine Corpus Endometrial Carcinoma VCF : Variant Call Format WES : Whole Exome Sequencing