New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States.
New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States.
Semin Cancer Biol. 2022 Sep;84:23-31. doi: 10.1016/j.semcancer.2021.07.003. Epub 2021 Jul 10.
Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
全基因组测序或与全转录组测序联合应用已开始用于分析临床肿瘤样本，以改善诊断、提供风险分层并选择针对患者的治疗方法。与目前主要集中在少数基因逐个测试或靶向面板的基因组检测策略相比，全基因组和转录组测序 (WGTS) 提供了新的机会，可以识别和报告具有诊断、预后和/或预测影响的潜在更多数量的可操作改变。这些改变包括点突变、插入缺失、拷贝数异常和结构变异，但也包括种系变异、融合基因、非编码改变和突变特征。然而，这些综合测试伴随着许多挑战，包括这些方法检测到的序列改变的程度和多样性，以及解释这些改变的复杂性和有限的现有标准化。我们描述了 WGTS 解释的挑战和全面基因组测试的机会。
