Samsung Genome Institute, Samsung Medical Center, Seoul, 06351, Korea.
Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, 06351, Korea.
Nat Commun. 2017 Nov 9;8(1):1377. doi: 10.1038/s41467-017-01470-y.
Accurate detection of genomic alterations using high-throughput sequencing is an essential component of precision cancer medicine. We characterize the variant allele fractions (VAFs) of somatic single nucleotide variants and indels across 5095 clinical samples profiled using a custom panel, CancerSCAN. Our results demonstrate that a significant fraction of clinically actionable variants have low VAFs, often due to low tumor purity and treatment-induced mutations. The percentages of mutations under 5% VAF across hotspots in EGFR, KRAS, PIK3CA, and BRAF are 16%, 11%, 12%, and 10%, respectively, with 24% for EGFR T790M and 17% for PIK3CA E545. For clinical relevance, we describe two patients for whom targeted therapy achieved remission despite low VAF mutations. We also characterize the read depths necessary to achieve sensitivity and specificity comparable to current laboratory assays. These results show that capturing low VAF mutations at hotspots by sufficient sequencing coverage and carefully tuned algorithms is imperative for a clinical assay.
使用高通量测序准确检测基因组改变是精准癌症医学的重要组成部分。我们对 5095 个临床样本中的体细胞单核苷酸变异和插入缺失的变异等位基因分数 (VAF) 进行了特征描述，这些样本是使用定制面板 CancerSCAN 进行分析的。我们的结果表明，相当一部分具有临床可操作性的变异具有低 VAF，这通常是由于肿瘤纯度低和治疗诱导的突变所致。在 EGFR、KRAS、PIK3CA 和 BRAF 的热点中，VAF 低于 5%的突变百分比分别为 16%、11%、12%和 10%，EGFR T790M 为 24%，PIK3CA E545 为 17%。就临床相关性而言，我们描述了两名患者，尽管 VAF 突变低，但靶向治疗仍能缓解疾病。我们还描述了实现与当前实验室检测相当的灵敏度和特异性所需的读取深度。这些结果表明，通过足够的测序覆盖和精心调整的算法捕获热点处的低 VAF 突变对于临床检测至关重要。
