Clinical actionability enhanced through deep targeted sequencing of solid tumors.
Clinical actionability enhanced through deep targeted sequencing of solid tumors.
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通过对实体瘤的深层测序增强了临床可行性。
DOI：
10.1373/clinchem.2014.231100
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发表时间：
2015-03
影响因子：
9.3
通讯作者：
Eterovic AK
中科院分区：
文献类型：
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作者：
Chen K;Meric-Bernstam F;Zhao H;Zhang Q;Ezzeddine N;Tang LY;Qi Y;Mao Y;Chen T;Chong Z;Zhou W;Zheng X;Johnson A;Aldape KD;Routbort MJ;Luthra R;Kopetz S;Davies MA;de Groot J;Moulder S;Vinod R;Farhangfar CJ;Shaw KM;Mendelsohn J;Mills GB;Eterovic AK
靶向癌症治疗的进一步发展需要对临床肿瘤样本中肿瘤细胞亚群中存在的体细胞突变进行全面深入的分析。然而，目前尚不清楚这种肿瘤内异质性存在的程度，以及它是否会影响临床决策。为了解决这一挑战，我们建立了一个深度靶向测序平台，以识别肿瘤样本中潜在的可操作DNA改变。通过捕获和测序201个癌症相关基因的所有外显子，我们分析了来自11个疾病位点的515个FFPE肿瘤样本和匹配的种系（475例患者）。报告了突变、索引和拷贝数数据。我们获得了1000倍的平均测序深度，并在分析的样本中鉴定出4794个非同义突变，其中15.2%的等位基因频率低于10%。这些低水平突变大多发生在已知的致癌热点，可能是功能性的。鉴定低水平突变改善了118例（24.84%）患者可操作基因突变的鉴定，其中47例（9.8%）患者不可操作基因突变。此外，获得超高深度也保证了FFPE样本的低错误发现率（小于2.2%）。我们的结果与市售的符合clia的热点面板一样准确，但允许在可操作基因中检测更多的突变。我们的研究揭示了获取和利用高深度分析临床肿瘤样本的重要性，并为癌症护理机构实施常规测序提供了一个非常有用的平台。
Further advances of targeted cancer therapy require comprehensive in-depth profiling of somatic mutations that are present in subpopulations of tumor cells in a clinical tumor sample. However, it is unclear to what extent such intra-tumor heterogeneity is present and whether it may affect clinical decision making. To unravel this challenge, we established a deep targeted sequencing platform to identify potentially actionable DNA alterations in tumor samples. We assayed 515 FFPE tumor samples and matched germline (475 patients) from 11 disease sites by capturing and sequencing all the exons in 201 cancer related genes. Mutations, indels and copy number data were reported. We obtained a 1000-fold average sequencing depth and identified 4794 non-synonymous mutations in the samples analyzed, which 15.2% were present at less than 10% allele frequency. Most of these low level mutations occurred at known oncogenic hotspots and are likely functional. Identifying low level mutations improved identification of mutations in actionable genes in 118 (24.84%) patients, among which 47 (9.8%) would otherwise be unactionable. In addition, acquiring ultra-high depth also ensured a low false discovery rate (less than 2.2%) from FFPE samples. Our results were as accurate as a commercially available CLIA-compliant hotspot panel, but allowed the detection of a higher number of mutations in actionable genes. Our study revealed the critical importance of acquiring and utilizing high depth in profiling clinical tumor samples and presented a very useful platform for implementing routine sequencing in a cancer care institution.