Targeted DNA Sequencing of Circulating Tumor Cell-Enriched Samples from Stage II/III NSCLC Patients

Targeted DNA sequencing of circulating tumor cell (CTC) enriched blood samples from stage II/III non-small cell lung cancer (NSCLC) patients prior to undergoing chemoradiation and immunotherapy treatment. The CTC samples were enriched using a label-free microfluidic platform, the Labyrinth. Following enrichment, the samples were fixed in 80% methanol or ethanol and stored at -80C or -20C, respectively. DNA was extracted from the samples using Qiagen's DNA/RNA AllPrep kit and submitted to the Univeristy of Michigan's Advanced Genomics Core (AGC) to perform targeted DNA sequencing using Illumina's TruSight Oncology (TSO) 500 assay. The TSO 500 assay consists of a 523 gene panel of specific oncogenes. Following sequecing, the pair-end fastq files were locally processed through the TSO 500 analysis pipeline (version: ruo-2.2.0.12) to produce the CombinedVariantOutput files per patient. Each file contains a list of all variants detected within the patient. For each variant, the following information is provided: gene name, chromosome, genomic position, reference call, alternative call, allele frequency, depth, p-dot notation, c-dot notation, consequence of variant, and the number of affected exons.本数据集针对拟接受放化疗联合免疫治疗的II/III期非小细胞肺癌（non-small cell lung cancer, NSCLC）患者的富集循环肿瘤细胞（circulating tumor cell, CTC）血液样本开展靶向DNA测序。研究采用无标记微流控平台Labyrinth对CTC样本进行富集。富集完成后，样本分别以80%甲醇或乙醇固定，并分别存储于-80℃或-20℃环境中。随后使用凯杰（Qiagen）的DNA/RNA AllPrep试剂盒提取样本基因组DNA，并提交至密歇根大学高级基因组学核心实验室（Advanced Genomics Core, AGC），采用Illumina的TruSight Oncology（TSO）500检测试剂盒完成靶向DNA测序。TSO 500检测试剂盒搭载包含523个特定致癌基因的基因面板。测序完成后，通过TSO 500分析流程（版本：ruo-2.2.0.12）对双端fastq文件进行本地处理，为每位患者生成CombinedVariantOutput文件。每份文件包含该患者体内检出的全部变异体列表，针对每个变异体，文件提供以下信息：基因名称、染色体编号、基因组位置、参考碱基、变异碱基、等位基因频率、测序深度、p-点突变命名、c-点突变命名、变异功能后果以及受影响外显子数量。