Tsang Hsinyi, Addepalli KanakaDurga, Davis Sean R
Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Gaithersburg, MD, United States.
Attain, LLC, McLean, VA, United States.
Front Oncol. 2017 Sep 19;7:214. doi: 10.3389/fonc.2017.00214. eCollection 2017.
Precision genomic oncology-applying high throughput sequencing (HTS) at the point-of-care to inform clinical decisions-is a developing precision medicine paradigm that is seeing increasing adoption. Simultaneously, new developments in targeted agents and immunotherapy, when informed by rich genomic characterization, offer potential benefit to a growing subset of patients. Multiple previous studies have commented on methods for identifying both germline and somatic variants. However, interpreting individual variants remains a significant challenge, relying in large part on the integration of observed variants with biological knowledge. A number of data and software resources have been developed to assist in interpreting observed variants, determining their potential clinical actionability, and augmenting them with ancillary information that can inform clinical decisions and even generate new hypotheses for exploration in the laboratory. Here, we review available variant catalogs, variant and functional annotation software and tools, and databases of clinically actionable variants that can be used in an approach with research samples or incorporated into a data platform for interpreting and formally reporting clinical results.
精准基因组肿瘤学——在临床护理点应用高通量测序（HTS）以指导临床决策——是一种正在逐渐被广泛采用的精准医学模式。同时，在丰富的基因组特征指导下，靶向药物和免疫疗法的新进展为越来越多的患者带来了潜在益处。此前已有多项研究对识别种系和体细胞变异的方法进行了评论。然而，解释单个变异仍然是一项重大挑战，这在很大程度上依赖于将观察到的变异与生物学知识相结合。已经开发了许多数据和软件资源来协助解释观察到的变异，确定其潜在的临床可操作性，并通过辅助信息对其进行补充，这些辅助信息可为临床决策提供依据，甚至为实验室探索产生新的假设。在此，我们综述了可用的变异目录、变异和功能注释软件及工具，以及可用于研究样本或纳入数据平台以解释和正式报告临床结果的临床可操作变异数据库。
