Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration.
Serial Next-Generation Sequencing of Circulating Cell-Free DNA Evaluating Tumor Clone Response To Molecularly Targeted Drug Administration.
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DOI：
10.1158/1078-0432.ccr-15-0584
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发表时间：
2015-10-15
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影响因子：
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通讯作者：
de Bono JS
中科院分区：
文献类型：
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作者：
Frenel JS;Carreira S;Goodall J;Roda D;Perez-Lopez R;Tunariu N;Riisnaes R;Miranda S;Figueiredo I;Nava-Rodrigues D;Smith A;Leux C;Garcia-Murillas I;Ferraldeschi R;Lorente D;Mateo J;Ong M;Yap TA;Banerji U;Gasi Tandefelt D;Turner N;Attard G;de Bono JS
我们评估了cfDNA的下一代测序（NGS）是否可用于患者选择，并作为参与靶向药物早期临床试验的晚期癌症患者的肿瘤克隆反应生物标志物。每月采集至少完成2个研究性靶向治疗疗程的已知肿瘤突变患者的血浆样本，直至疾病进展。在Ion Torrent PGM平台上依次进行NGS。从39名患有各种肿瘤类型的患者中提取cfDNA。给予的治疗靶向PI 3 K-AKT-mTOR通路（n=28）或MEK（n=7）。总共对159份血浆样品进行了测序，在整个实验中实现的平均测序覆盖率为1，685 X。在试验开始时（C1 D1），39例患者中有23例（59%）在cfDNA中至少鉴定出一种突变（平均值2，范围1-5）。TP 53、PIK 3CA和KRAS是鉴定的前3个突变基因，分别具有16个（39%）、9个（22%）和8个（17%）不同的突变。在这23名患者中，13名接受了与其肿瘤特征相匹配的靶向药物。对于在C1 D1时具有cfDNA突变的23名患者，在靶向药物治疗期间监测连续血浆样品中的突变等位基因频率（AF）证明了潜在的治疗相关克隆应答。具有多个突变的cfDNA样品的纵向监测表明存在表现不一致的单独克隆。根据RECIST标准，cfDNA突变水平的分子变化与至疾病进展的时间相关。cfDNA的靶向NGS具有监测靶向疗法的递送的潜在临床效用。
We evaluated whether next generation sequencing (NGS) of cfDNA could be used for patient selection and as a tumor clone response biomarker in patients with advanced cancers participating in early phase clinical trials of targeted drugs. Plasma samples from patients with known tumor mutations who completed at least 2 courses of investigational targeted therapy were collected monthly, until disease progression. NGS was performed sequentially on the Ion Torrent PGM platform. cfDNA was extracted from 39 patients with various tumor types. Treatments administered targeted mailnly the PI3K-AKT-mTOR pathway (n=28) or MEK (n=7). Overall 159 plasma samples were sequenced with a mean sequencing coverage achieved of 1,685X across experiments. At trial initiation (C1D1), 23 of 39 (59%) patients had at least one mutation identified in cfDNA (mean 2, range 1-5). TP53, PIK3CA and KRAS were the top 3 mutated genes identified, with 16 (39%), 9 (22%) and 8 (17%) different mutations, respectively. Out of these 23 patients, 13 received a targeted drug matching their tumor profile. For the 23 patients with cfDNA mutation at C1D1, the monitoring of mutation allele frequency (AF) in consecutive plasma samples during treatment with targeted drugs demonstrated potential treatment associated clonal responses. Longitudinal monitoring of cfDNA samples with multiple mutations indicated the presence of separate clones behaving discordantly. Molecular changes at cfDNA mutation level were associated with time to disease progression by RECIST criteria. Targeted NGS of cfDNA has potential clinical utility to monitor the delivery of targeted therapies.