State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China.
GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China.
Nucleic Acids Res. 2024 Jan 5;52(D1):D1218-D1226. doi: 10.1093/nar/gkad845.
DNA damage and its improper repair are the major source of genomic alterations responsible for many human diseases, particularly cancer. To aid researchers in understanding the underlying mechanisms of genome instability, a number of genome-wide profiling approaches have been developed to monitor DNA damage and repair events. The rapid accumulation of published datasets underscores the critical necessity of a comprehensive database to curate sequencing data on DNA damage and repair intermediates. Here, we present DNA Damage Atlas (DDA, http://www.bioinformaticspa.com/DDA/), the first large-scale repository of DNA damage and repair information. Currently, DDA comprises 6,030 samples from 262 datasets by 59 technologies, covering 16 species, 10 types of damage and 135 treatments. Data collected in DDA was processed through a standardized workflow, including quality checks, hotspots identification and a series of feature characterization for the hotspots. Notably, DDA encompasses analyses of highly repetitive regions, ribosomal DNA and telomere. DDA offers a user-friendly interface that facilitates browsing, searching, genome browser visualization, hotspots comparison and data downloading, enabling convenient and thorough exploration for datasets of interest. In summary, DDA will stand as a valuable resource for research in genome instability and its association with diseases.
DNA 损伤及其不当修复是导致许多人类疾病（尤其是癌症）的基因组改变的主要来源。为了帮助研究人员了解基因组不稳定性的潜在机制，已经开发了许多全基因组分析方法来监测 DNA 损伤和修复事件。大量已发表数据集的快速积累突显了建立一个综合数据库来整理 DNA 损伤和修复中间体测序数据的迫切需要。在这里，我们展示了 DNA 损伤图谱 (DDA，http://www.bioinformaticspa.com/DDA/)，这是第一个大规模的 DNA 损伤和修复信息库。目前，DDA 包含来自 59 种技术的 262 个数据集的 6,030 个样本，涵盖 16 个物种、10 种损伤类型和 135 种处理方法。DDA 中收集的数据经过标准化工作流程处理，包括质量检查、热点识别和一系列热点特征描述。值得注意的是，DDA 涵盖了高度重复区域、核糖体 DNA 和端粒的分析。DDA 提供了一个用户友好的界面，便于浏览、搜索、基因组浏览器可视化、热点比较和数据下载，方便对感兴趣的数据集进行全面深入的探索。总之，DDA 将成为研究基因组不稳定性及其与疾病关联的宝贵资源。
