使用纳米孔测序仪进行长读长全基因组测序及癌症基因组中结构变异的检测。

Long-Read Whole-Genome Sequencing Using a Nanopore Sequencer and Detection of Structural Variants in Cancer Genomes.

机构信息

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.

出版信息

Methods Mol Biol. 2023;2632:177-189. doi: 10.1007/978-1-0716-2996-3_13.

DOI:10.1007/978-1-0716-2996-3_13

PMID:36781729

Abstract

Long-read sequencing technologies enable us to precisely identify structural variants (SVs), which would be occasionally associated with various types of diseases, including cancers. In this section, we introduce experimental and computational procedures for conducting long-read whole-genome sequencing (WGS) of cancer genomes from fresh frozen tissues/cells. We also demonstrate the analysis of SVs in cancer genomes using long-read WGS data from lung cancer cell lines by several representative computational tools, such as cuteSV and Sniffles2, as examples.

摘要

长读测序技术使我们能够精确地识别结构变异（SV），这些变异偶尔与各种类型的疾病有关，包括癌症。在本节中，我们介绍了从新鲜冷冻组织/细胞中进行癌症基因组长读全基因组测序（WGS）的实验和计算程序。我们还展示了使用来自肺癌细胞系的长读 WGS 数据，通过几个代表性的计算工具（如 cuteSV 和 Sniffles2）分析癌症基因组中的 SV 的示例。