Genomics of Circulating Tumor Cells

Comprehensive analyses of cancer genomes in clinical settings promise to inform prognoses and guide the deployment of precise cancer treatments. A major barrier, however, is the inaccessibility of adequate metastatic tissue for accurate genomic analysis in prostate and other cancers. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming multiple technical hurdles. Here, we report an integrated process to isolate, qualify, and sequence whole exomes of CTCs with high fidelity, using a census-based sequencing strategy. Power calculations suggest that mapping of over 99.995% of the territory accessible in bulk exome sequencing is possible in CTCs. We validated our sequencing process in two prostate cancer patients including one for whom we compared CTC-derived mutations to mutations found in a lymph node metastasis and nine cores of the primary tumor. 51 of 73 CTC mutations (70%) were observed in matched tissue. Moreover, we identified 10 early trunk mutations and 56 metastatic trunk mutations in the non-CTC tumor samples and found 90% and 73% of these, respectively, in CTC exomes. This study establishes a foundation for CTC genomics in the clinic.]]>临床场景下对癌症基因组的全面分析，有望为预后判断提供依据，并指导精准癌症治疗方案的部署。然而，前列腺癌及其他癌症中难以获取足够的转移组织以开展精准基因组分析，这是主要障碍。循环肿瘤细胞（circulating tumor cells, CTCs）表征是潜在解决方案，但需攻克多项技术难关。本研究报道了一种基于普查型测序策略的整合流程，可高保真地分离、质控并对循环肿瘤细胞的全外显子组进行测序。功效分析（power calculations）显示，在循环肿瘤细胞中可实现覆盖批量外显子组测序（bulk exome sequencing）99.995%以上的可检测区域。我们在两名前列腺癌患者中验证了该测序流程，其中一例患者的循环肿瘤细胞衍生突变可与淋巴结转移灶及原发肿瘤的9个活检芯的突变进行比对。73个循环肿瘤细胞突变中有51个（70%）在匹配的组织样本中被检出。此外，我们在非循环肿瘤细胞的肿瘤样本中鉴定出10个早期主干突变与56个转移主干突变，其中分别有90%与73%可在循环肿瘤细胞外显子组中被检测到。本研究为临床场景下的循环肿瘤细胞基因组学奠定了基础。