Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA.
Global Biometric Sciences, Bristol-Myers Squibb, Princeton, NJ, USA.
Mol Diagn Ther. 2019 Aug;23(4):507-520. doi: 10.1007/s40291-019-00408-y.
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 III clinical trial.
In the CheckMate 026 clinical trial, 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. WES and FoundationOne CDx outputs were highly correlated (Spearman's r = 0.90).
Parameter variation can impact TMB calculations, highlighting the need for standardization. Encouragingly, differences between assays could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms, and centers is achievable.
肿瘤突变负荷（TMB）已成为一种具有临床相关性的生物标志物，可能与免疫检查点抑制剂的疗效相关。TMB 测量的标准化对于实施诊断工具以指导治疗至关重要。
本研究深入评估了使用全外显子组测序（WES）对来自 III 期临床试验的福尔马林固定、石蜡包埋样本进行的生物信息学 TMB 分析。
在 CheckMate 026 临床试验中，对接受一线纳武单抗治疗或标准护理化疗的 312 名非小细胞肺癌患者（意向治疗人群的 58%）进行了 TMB 的回顾性评估。我们考察了 TMB 评估对生物信息学过滤方法的敏感性，并评估了 WES 与 FoundationOne CDx 检测得出的 TMB 数据之间的一致性。
包含同义、插入缺失、移码和无义突变（所有突变）的 TMB 评分比仅包含错义突变的评分高 3.1 倍，但两者高度相关（Spearman r=0.99）。仅包含错义突变的 CheckMate 026 样本评分与来自癌症基因组图谱的数据相似，但包含所有突变的评分通常更高。使用用于种系消除的数据库（而非匹配对照）显示 TMB 评分存在依赖种族的趋势。WES 和 FoundationOne CDx 的输出高度相关（Spearman r=0.90）。
参数变化会影响 TMB 计算，突出了标准化的必要性。令人鼓舞的是，通过经验校准可以解释检测之间的差异，这表明可以在不同的检测、平台和中心实现可靠的 TMB 评估。
