Molecular profiling of tumor derived cell free DNA (cfDNA) is gaining ground as a prognostic and predictive biomarker. However to what extent cfDNA reflects the full metastatic landscape as currently determined by tumor tissue analysis remains controversial. Though technically challenging, whole exome sequencing (WES) of cfDNA enables thorough evaluation of somatic alterations. Here, we review the feasibility of WES of cfDNA and determine the sensitivity of WES-detected single nucleotide variants (SNVs) in cfDNA on individual patient data level using paired tumor tissue as reference (sharedSNVsAlltissueSNVs×100%). The pooled sensitivity was 50% (95% credible interval (CI): 29-72%). The tissue mutant allele frequency (MAF) of variants exclusively identified in tissue was significantly lower (12.5%, range: 0.5-18%) than the tissue MAF of variants identified in both tissue and cfDNA (23.9%, range: 17-38%), p = 0.004. The overall agreement (sharedSNVsAllSNVs×100%)between SNVs in cfDNA and tumor tissue was 31% (95% CI: 15-49%). The number of detected SNVs was positively correlated with circulating tumor DNA (ctDNA) fraction (p = 0.016). A sub analysis of samples with ctDNA fractions ≥ 25% improved the sensitivity to 69% (95% CI: 46-89%) and agreement to 46% (95% CI: 36-59%), suggesting that WES is mainly feasible for patients with high ctDNA fractions. Pre- and post-analytical procedures were highly variable between studies rendering comparisons problematic. In conclusion, various aspects of WES of cfDNA are largely in its investigative phase, standardization of methodologies is highly needed to bring this promising technique to its clinical potential.

中文翻译：

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无细胞DNA的整个外显子组测序-系统评价和贝叶斯个体患者数据荟萃分析。

肿瘤衍生的无细胞DNA（cfDNA）的分子谱分析作为一种预后和预测性生物标记物正在获得发展。但是，cfDNA在多大程度上反映了目前由肿瘤组织分析确定的完整转移情况仍然存在争议。尽管在技术上具有挑战性，但cfDNA的全外显子组测序（WES）能够全面评估体细胞变化。在这里，我们回顾了cfDNA的WES可行性，并使用配对的肿瘤组织作为参考（共享SNVsAlltissueSNVs×100％），确定了cfDNA中WES检测到的cfDNA中单核苷酸变体（SNV）在各个患者数据水平上的敏感性。合并的敏感性为50％（95％可信区间（CI）：29-72％）。仅在组织中鉴定出的变体的组织突变等位基因频率（MAF）明显较低（12.5％，范围：0。比在组织和cfDNA中均鉴定出的变异体的组织MAF高5-18％（23.9％，范围：17-38％），p = 0.004。cfDNA中的SNV与肿瘤组织之间的总体一致性（共享SNVsAllSNV x 100％）为31％（95％CI：15-49％）。检测到的SNV数量与循环肿瘤DNA（ctDNA）分数呈正相关（p = 0.016）。对ctDNA分数≥25％的样品进行亚分析可将灵敏度提高到69％（95％CI：46-89％），并将一致性提高到46％（95％CI：36-59％），这表明WES主要适用于ctDNA分数高的患者。在研究之间，分析前和分析后的程序差异很大，使得比较存在问题。总之，cfDNA的WES的各个方面都处于研究阶段，为使这一有希望的技术发挥其临床潜力，高度需要方法学的标准化。