TMB is a clinically relevant biomarker associated with response to immune checkpoint inhibitors in patients with NSCLC. Tumor TMB (tTMB) can be assessed by next-generation sequencing (NGS) gene panels; however, obtaining sufficient tumor tissue can be challenging, and NGS methods have been developed for TMB assessment from blood (bTMB). We compared bTMB values using 3 commercial NGS assays that differ in gene number, depth of coverage, and variant allele cutoff.
bTMB was assessed in 25 commercial NSCLC plasma samples with 3 NGS assays, and values were compared by Spearman’s correlation. For assay A, < 500 genes were sequenced to a depth of < 1000x. Assays B and C each comprised > 500 genes, sequenced to a depth of ∼ 1500x. To determine concordance between bTMB and tTMB we assessed 86 commercial NSCLC matched plasma and tumor samples using bTMB assays A and C and a clinically validated tTMB gene panel assay, and performed subgroup analysis by disease stage.
bTMB in stage I–III NSCLC samples assessed by assays B and C showed greater correlation (r = 0.78) than by assays A and B (r = 0.59) and A and C (r = 0.53). Across 86 matched samples, tTMB and bTMB concordance was lower for assay A (r = 0.24) than assay C (r = 0.51) and was higher among stage IV NSCLC samples (A, r = 0.38; C, r = 0.72) than stage I–III (A, r = 0.24; C, r = 0.40). Using clinically relevant cutoffs, high bTMB was observed in 5/30 patients with assay A (range: 10.5–21.1), and 19/30 patients with assay C (range: 12.4–67.6); high tTMB ranged from 10.0 to 36.6.
In patients with NSCLC, bTMB was concordant (r > 0.5) between 3 NGS assays. Concordance between bTMB and tTMB varied and was improved for bTMB assays with increased coverage and sequencing depth, and in patients with higher stage metastatic disease. Assay parameters impact accurate and reproducible TMB assessment, with lower coverage and sequencing depth, and differing variant allele cutoff, risking false-negative results that may affect outcomes in response to immune checkpoint inhibitor therapy. These data underscore the need for demonstrating clinical utility of bTMB assays and for assessment of bridging analytical performance between assays.
Amrita Dervan, PhD, and Jay Rathi, MA, of Spark Medica Inc, funded by BristolMyers Squibb.
Bristol-Myers Squibb.
Bristol-Myers Squibb.
J. Baden: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb; Shareholder/Stockholder/Stock options: Johnson & Johnson. H. Chang: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb. D.M. Greenawalt: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb. S. Kirov: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb. S. Pant: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb. A. Seminara: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb. S. Srinivasan: Shareholder / Stockholder / Stock options, Full/Part-time employment: Bristol-Myers Squibb. G. Green: Shareholder/Stockholder/Stock options, Full/Part-time employment: Bristol-Myers Squibb.