Hatakeyama Keiichi, Nagashima Takeshi, Urakami Kenichi, Ohshima Keiichi, Serizawa Masakuni, Ohnami Sumiko, Shimoda Yuji, Ohnami Shumpei, Maruyama Koji, Naruoka Akane, Akiyama Yasuto, Kusuhara Masatoshi, Mochizuki Tohru, Yamaguchi Ken
Medical Genetics Division, Shizuoka Cancer Center Research Institute.
Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute.
Biomed Res. 2018;39(3):159-167. doi: 10.2220/biomedres.39.159.
Tumor mutational burden (TMB) is an emerging characteristic in cancer and has been associated with microsatellite instability, defective DNA replication/repair, and response to PD-1 and PD-L1 blockade immunotherapy. When estimating TMB, targeted panel sequencing is performed using a few hundred genes; however, a comparison of TMB results obtained with this platform and with whole exome sequencing (WES) has not been performed for various cancer types. In the present study, we compared TMB results using the above two platforms in 2,908 solid tumors that were obtained from Japanese patients. For next-generation sequencing, we used fresh-frozen tissue specimens. The Ion Proton System was employed to detect somatic mutations in the coding genome and to sequence an available cancer panel that targeted 409 genes. We then selected 2,040 samples with sufficient tumor cellularity for TMB analysis. In tumors with TMB-high (TMB ≥ 20 mutations/Mb), TMB derived from WES correlated well with the estimated TMB (eTMB) based on panel sequencing, whereas TMB in the remaining tumors showed a weak correlation. In particular, eTMB was overestimated in tumors with low-frequency mutations, resulting in the accumulation of EGFR mutations not being discriminated as a feature of lung cancer with low-frequency mutations. The eTMB in tumors harboring POLE mutations and microsatellite instability was not overestimated, suggesting that panel sequencing could accurately estimate TMB in tumors with high-frequency mutations such as hypermutator tumors. These results may provide helpful information for interpreting TMB results based on clinical sequencing using a targeted gene panel.
肿瘤突变负荷（TMB）是癌症中一种新出现的特征，与微卫星不稳定性、DNA复制/修复缺陷以及对PD-1和PD-L1阻断免疫疗法的反应相关。在估计TMB时，使用几百个基因进行靶向 panel 测序；然而，尚未针对各种癌症类型对该平台与全外显子组测序（WES）获得的TMB结果进行比较。在本研究中，我们比较了使用上述两种平台在2908例来自日本患者的实体瘤中获得的TMB结果。对于下一代测序，我们使用新鲜冷冻的组织标本。使用Ion Proton系统检测编码基因组中的体细胞突变，并对靶向409个基因的可用癌症panel进行测序。然后我们选择了2040个具有足够肿瘤细胞含量的样本进行TMB分析。在TMB高（TMB≥20个突变/Mb）的肿瘤中，来自WES的TMB与基于panel测序的估计TMB（eTMB）相关性良好，而其余肿瘤中的TMB显示出弱相关性。特别是，低频突变肿瘤中的eTMB被高估，导致EGFR突变的积累未被区分为低频突变肺癌的特征。携带POLE突变和微卫星不稳定性的肿瘤中的eTMB未被高估，这表明panel测序可以准确估计高突变肿瘤等高频突变肿瘤中的TMB。这些结果可能为基于使用靶向基因panel的临床测序来解释TMB结果提供有用信息。
