Tumor mutation burden derived from small next generation sequencing targeted gene panel as an initial screening...

With the increasing use of immune checkpoint inhibitors, tumor mutation burden (TMB) assessment is now routinely included in reports generated from targeted sequencing with large gene panels; however, not all patients require comprehensive profiling with large panels. Our study aims to explore the feasibility of using a small 56-gene panel as a screening method for TMB prediction.

TMB from 406 non-small cell lung cancer (NSCLC) patients was estimated using a large 520-gene panel simulated with the prospective TMB status for the small panel. This information was then used to determine the optimal cut-off. An independent cohort of 30 NSCLC patients was sequenced with both panels to confirm the cut-off value.

By comparing sensitivity, specificity, and positive predictive value (PPV), the cut-off was set up as 10 mutations/megabase, yielding 81.4% specificity, 83.6% sensitivity, and 62.4% PPV. Further validation with an independent cohort sequenced with both panels using the same cut-off achieved 95.7% sensitivity, 71.4% specificity and 91.7% PPV. The decreasing trend of sensitivity with the increasing trend of both specificity and PPV with a concomitant increase in the cut-off for the small panel suggests that TMB is overestimated but highly unlikely to yield false-positive results. Hence, patients with low TMB (<10) can be reliably stratified from patients with high TMB (≥10).

The small panel, more cost-effective, can be used as a screening method to screen for patients with low TMB, while patients with TMB ≥10 are recommended for further validation with a larger panel.