PDF(Pubmed)
Abstract：
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic techniques are applied to detect such aberrations, but they are limited in resolution and do not cover features smaller than several hundred kilobases. Optical genome mapping and nanopore sequencing are attractive technologies that bridge this resolution gap and offer enhanced performance for cytogenetic applications. These methods profile native, individual DNA molecules, thus capturing epigenetic information. We applied both techniques to characterize a clear cell renal cell carcinoma (ccRCC) tumor\'s structural and copy number landscape, highlighting the relative strengths of each method in the context of variant size and average read length. Additionally, we assessed their utility for methylome and hydroxymethylome profiling, emphasizing differences in epigenetic analysis applicability.
摘要：
癌症发生通常涉及癌症基因组结构的重大改变，标记为难以用短读取测序捕获的大的结构和拷贝数变异(SV和CNV)。传统上,细胞遗传学技术被用来检测这种异常，但是它们的分辨率有限，不包括小于几百千碱基的功能。光学基因组作图和纳米孔测序是有吸引力的技术，可以弥合这种分辨率差距，并为细胞遗传学应用提供增强的性能。这些方法描述原生，单个DNA分子，从而捕获表观遗传信息。我们应用这两种技术来表征透明细胞肾细胞癌（ccRCC）肿瘤的结构和拷贝数景观，在变体大小和平均读取长度的上下文中突出显示每种方法的相对强度。此外,我们评估了它们在甲基化和羟甲基化方面的效用，强调表观遗传分析适用性的差异。
