Background: Tumor mutational burden (TMB) is an emerging genomic biomarker in cancer that has been associated with improved response to immune checkpoint inhibitors (ICIs) in adult cancers. It was described that variability in TMB assessment is introduced by different laboratory techniques and various settings of bioinformatic pipelines. In pediatric oncology, no study has been published describing this variability so far. Methods: In our study, we performed whole exome sequencing (WES, both germline and somatic) and calculated TMB in 106 patients with high-risk/recurrent pediatric solid tumors of 28 distinct cancer types. Subsequently, we used WES data for TMB calculation using an in silico approach simulating two The Food and Drug Administration (FDA)-approved/authorized comprehensive genomic panels for cancer. Results: We describe a strong correlation between WES-based and panel-based TMBs; however, we show that this high correlation is significantly affected by inclusion of only a few hypermutated cases. In the series of nine cases, we determined TMB in two sequentially collected tumor tissue specimens and observed an increase in TMB along with tumor progression. Furthermore, we evaluated the extent to which potential ICI indication could be affected by variability in techniques and bioinformatic pipelines used for TMB assessment. We confirmed that this technological variability could significantly affect ICI indication in pediatric cancer patients; however, this significance decreases with the increasing cut-off values. Conclusions: For the first time in pediatric oncology, we assessed the reliability of TMB estimation across multiple pediatric cancer types using real-life WES and in silico analysis of two major targeted gene panels and confirmed a significant technological variability to be introduced by different laboratory techniques and various settings of bioinformatic pipelines.

中文翻译：

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通过真实全外显子组测序和靶向基因组的计算机模拟评估小儿肿瘤中的肿瘤突变负担：方法的选择如何影响临床决策？

背景：肿瘤突变负荷 (TMB) 是一种新兴的癌症基因组生物标志物，与成人癌症中对免疫检查点抑制剂 (ICI) 的反应改善有关。据描述，TMB 评估的可变性是由不同的实验室技术和生物信息学管道的各种设置引入的。在儿科肿瘤学中，迄今为止还没有发表任何描述这种变异性的研究。方法：在我们的研究中，我们对 106 名患有 28 种不同癌症类型的高风险/复发性儿童实体瘤患者进行了全外显子组测序（WES，生殖系和体细胞）并计算了 TMB。随后，我们使用 WES 数据进行 TMB 计算，使用计算机方法模拟两个美国食品和药物管理局 (FDA) 批准/授权的癌症综合基因组面板。结果：我们描述了基于 WES 和基于面板的 TMB 之间的强相关性；然而，我们表明这种高度相关性受到仅包含少数超突变病例的显着影响。在九个病例系列中，我们在两个连续收集的肿瘤组织标本中测定了 TMB，并观察到 ​​TMB 随着肿瘤进展而增加。此外，我们评估了潜在 ICI 适应症可能受用于 TMB 评估的技术和生物信息学管道的可变性影响的程度。我们证实，这种技术变异可能会显着影响儿科癌症患者的 ICI 适应症；然而，这种显着性随着截止值的增加而降低。结论：首次在儿科肿瘤学中，