Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in non-small cell lung cancer.
Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in non-small cell lung cancer.
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DOI：
10.5483/bmbrep.2021.54.7.045
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发表时间：
2021-07
期刊：
影响因子：
3.8
通讯作者：
Ahn MJ
中科院分区：
文献类型：
--
作者：
Park S;Lee C;Ku BM;Kim M;Park WY;Kim NKD;Ahn MJ
由于NGS（下一代测序）的快速进步，基因组改变现在被认为是影响许多癌症病例治疗决策的重要预测生物标志物。在各种预测性生物标志物中，肿瘤突变负荷 (TMB) 通过 NGS 进行了鉴定，并被认为可用于预测免疫疗法治疗的癌症病例的临床反应。在本研究中，我们直接比较了靶标测序panel、K-MASTER panel v3.0和全外显子组测序（WES）的实验室开发测试（LDT）结果，以评估TMB的一致性。作为第一步，使用已知 TMB 状态的参考材料 (n = 3) 作为探索性测试。为了验证和评估 TMB，我们使用了从非小细胞肺癌 (NSCLC) 患者手术切除组织中获取的 100 个样本。采用LDT和WES两种方法对每个样本进行TMB检测，同时提取样本中的DNA。此外，我们还评估了捕获区域的影响，这可能会导致TMB值不同；捕获区域的评估基于NGS和目标测序panel的大小。在本次试点研究中，使用重复的参考样品通过LDT和WES对TMB进行了评估； TMB结果显示出较高的一致性（R2 = 0.887）。这也反映在临床样本 (n = 100) 中，其 R2 为 0.71。编码序列比例（3.49%）和突变比例（4.8%）之间的差异表明LDT panel识别出相对较多的突变。利用LDT panel计算TMB是可行的，可用于临床。此外，必须开发一种定制的方法来计算 TMB，该方法根据癌症类型和特定的临床环境而有所不同。
Owing to rapid advancements in NGS (next generation sequen-cing), genomic alteration is now considered an essential pre-dictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was con-sidered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly com-pared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture re-gion, which might lead to different values of TMB; the evalu-ation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evalu-ated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R2 = 0.887). This was also reflected in clinical samples (n = 100), which showed R2 of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.