Integrated digital error suppression for improved detection of circulating tumor DNA.
Integrated digital error suppression for improved detection of circulating tumor DNA.
复制标题
DOI：
10.1038/nbt.3520
复制
发表时间：
2016-05
影响因子：
46.9
通讯作者：
Alizadeh AA
中科院分区：
文献类型：
--
作者：
Newman AM;Lovejoy AF;Klass DM;Kurtz DM;Chabon JJ;Scherer F;Stehr H;Liu CL;Bratman SV;Say C;Zhou L;Carter JN;West RB;Sledge GW;Shrager JB;Loo BW Jr;Neal JW;Wakelee HA;Diehn M;Alizadeh AA
循环肿瘤DNA（ctDNA）的高通量测序有望促进个性化癌症治疗。然而，血液中少量的无细胞DNA（cfDNA）和测序伪影目前限制了分析灵敏度。为了克服这些限制，我们介绍了一种集成数字误差抑制（iDES）的方法。我们的方法将高度定型背景伪影的计算机消除与用于cfDNA分子的有效回收的分子条形码化策略相结合。单独地，这两种方法各自将通过深度测序（CAPP-Seq）进行的癌症个性化分析的灵敏度提高约3倍，并且当组合时协同产生约15倍的改进。因此，iDES增强的CAPP-Seq有助于在数百种酶中进行非侵入性变异检测。应用于临床非小细胞肺癌（NSCLC）样本，我们的方法能够以92%的灵敏度和96%的特异性对EGFR激酶结构域突变进行无活检分析，并检测到ctDNA低至105个cfDNA分子中的4个。我们预计iDES将有助于研究和临床环境中ctDNA的非侵入性基因分型和检测。
High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by ~3 fold, and synergize when combined to yield ~15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to clinical non-small cell lung cancer (NSCLC) samples, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and 96% specificity and detection of ctDNA down to 4 in 105 cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.