Lennon Niall J, Adalsteinsson Viktor A, Gabriel Stacey B
Broad Institute of MIT & Harvard, Cambridge, MA, 02142, USA.
Genome Med. 2016 Oct 26;8(1):112. doi: 10.1186/s13073-016-0370-4.
Technological, methodological, and analytical advances continue to improve the resolution of our view into the cancer genome, even as we discover ways to carry out analyses at greater distances from the primary tumor sites. These advances are finally making the integration of cancer genomic profiling into clinical practice feasible. Formalin fixation and paraffin embedding, which has long been the default pathological biopsy medium, is now being supplemented with liquid biopsy as a means to profile the cancer genomes of patients. At each stage of the genomic data generation process-sample collection, preservation, storage, extraction, library construction, sequencing, and variant calling-there are variables that impact the sensitivity and specificity of the analytical result and the clinical utility of the test. These variables include sample degradation, low yields of nucleic acid, and low variant allele fractions (proportions of assayed molecules carrying variant allele(s)). We review here the most common pre-analytical and analytical factors relating to routine cancer patient genome profiling, some solutions to common challenges, and the major sample preparation and sequencing technology choices available today.
技术、方法和分析方面的进展不断提高我们对癌症基因组的观察分辨率，即便我们发现了在远离原发肿瘤部位进行分析的方法。这些进展终于使癌症基因组分析纳入临床实践变得可行。长期以来一直作为默认病理活检介质的福尔马林固定和石蜡包埋，现在正被液体活检作为一种分析患者癌症基因组的手段所补充。在基因组数据生成过程的每个阶段——样本采集、保存、存储、提取、文库构建、测序和变异检测——都存在影响分析结果的敏感性和特异性以及检测临床效用的变量。这些变量包括样本降解、核酸产量低和变异等位基因比例低（携带变异等位基因的检测分子比例）。我们在此回顾与常规癌症患者基因组分析相关的最常见的分析前和分析因素、一些常见挑战的解决方案以及当今可用的主要样本制备和测序技术选择。
