TY - JOUR T1 - Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer JF - bioRxiv DO - 10.1101/626143 SP - 626143 AU - Han Chang AU - Ariella Sasson AU - Sujaya Srinivasan AU - Ryan Golhar AU - Danielle M. Greenawalt AU - William J. Geese AU - George Green AU - Kim Zerba AU - Stefan Kirov AU - Joseph Szustakowski Y1 - 2019/01/01 UR - http://biorxiv.org/content/early/2019/05/05/626143.abstract N2 - Tumor mutational burden (TMB) has emerged as a clinically relevant biomarker that may be associated with immune checkpoint inhibitor efficacy. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Here we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase 3 clinical trial. In CheckMate 026, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or standard-of-care chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne® CDx assay. TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can therefore impact TMB calculations, highlighting the need for standardization. Encouragingly, WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90) and differences could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms, and centers is achievable.FDAUS Food and Drug AdministrationFFPEformalin-fixed, paraffin-embeddedindelshort insertion or deletionMbmegabasesmut/Mbmutations per megabaseNGSnext-generation sequencingNSCLCnon-small cell lung cancerPD-L1programmed death ligand 1PFSprogression-free survivalSNVsingle nucleotide variationTCGAThe Cancer Genome AtlasTMBtumor mutational burdenVCFvariant call format fileWESwhole exome sequencing. ER -