Tumor Mutational Burden by Whole-Genome Sequencing in Resected NSCLC of Never Smokers

Abstract

Background: Data are scarce about tumor mutational burden (TMB) as a biomarker in never smokers with non-small-cell lung cancer (NSCLC). Methods: TMB was assessed by whole-genome sequencing (WGS) and compared with in-silico reduced whole-exome sequencing (WES) and targeted commercial NGS gene panels in 92 paired tumor-normal samples from never smokers who underwent NSCLC resection with curative intent. Analyses were performed to test for association with survival after surgery and to identify the optimal prognostic TMB cutoff. Results: Tumors of never smokers with NSCLC had low TMB scores (median 1.57 mutations/megabase, range 0.13-17.94). A TMB cutoff of 1.70 mutations/megabase was associated with a 5-year overall survival of 58% in the high-TMB (42% of cases) compared to 86% in low-TMB patients (Wald p = 0.0029). TMB scores from WGS and WES were highly correlated (Spearman ρ = 0.93, p <2.2e-16). TMB scores from NGS panels demonstrated high intra-individual fluctuations and identified high-TMB patients with 65% concordance in average compared to WGS. Conclusions: In resected NSCLC of never smokers, high TMB was associated with worse prognosis. WES provided a good estimate of TMB while targeted NGS panels seem to lack adequate depth and resolution in the setting of low mutation burden. Impact: TMB is a prognostic indicator of survival in resected NSCLC from individuals who never smoked. In this setting of low mutation counts, TMB can be accurately measured by WGS or WES, but not NGS panels.

The prognostic value of TMB in early-stage non-small cell lung cancer: a systematic review and meta-analysis

“…29,55 Four studies utilized the U.S. Food and Drug Agency approved gene panel tests, namely, FoundationOne, FoundationOne CDx (F1 CDx), and MSK-IMPACT, that have shown acceptable concordance with WES in empirical and in-silico TMB assessment. 18,29,31,32,56,57 Similarly, a pooled analysis from TCGA database did not find a significant prognostic impact of TMB on LUAD (HR 1.35, 95% CI 0.89, 2.05) and LSCC (HR, 0.77, 95% CI 0.50, 1.18) survival independent of TMB assessment methods (WES, MSK-IMPACT, and FoundationOne CDx). 58 Two international consortiums, the Friends of Cancer Research and Quality Assurance Initiative Pathology validated bioinformatic algorithms, standardized panelbased TMB estimates using in-silico analysis, and assessed between-TMB panel variations in FFPE tumor specimens for multiple cancer types, thereby taking TMB one step closer to a more refined prognostic biomarker.…”

“…Subsequently, 119 articles underwent full-text screening and 10 studies finally fulfilled the inclusion criteria. [16][17][18][19][28][29][30][31][32][33] The PRISMA flowchart for the study selection process is presented in Figure 1.…”

“…Approximately 56% of the entire population were males and 43% were ever-smokers. Data were available on LUAD from six studies 17,18,28,29,31,32 and LSCC from two studies. 28,33 The sample source was reported in all except one study, 17 and most studies used Formalin-Fixed Paraffin-Embedded (FFPE) resected primary tumor specimens.…”

“…16 Two studies required the extraction of data from the survival curves. 17,30 The results from the NOS revealed that seven studies had a low risk 16,18,19,28,29,31,32 and the rest had a moderate risk of bias (Table 1 and Supplemental Table S3). Most studies provided independent and comparable cohorts, adequate ascertainment of exposure, appropriate statistical analysis, and thorough experimental results.…”

A Review of Biomarkers and Their Clinical Impact in Resected Early-Stage Non-Small-Cell Lung Cancer

“…The TIM-3 positivity/PD-1 positivity/CD8 negativity subgroup had the worst prognosis, whereas the TIM-3 negativity/PD-1 negativity/CD8 positivity subgroup had the best forecast [ 84 ]. Regarding early-stage nonsmoking patients, tumour mutation burden (TMB) was a poor prognostic indicator for OS [ 85 ]. Conversely, another study demonstrated that TMB had no prognostic value on stage I–II resected LUAD [ 86 ].…”