Beijing Institute of Radiation Medicine, State Key Laboratory of Proteomics, Beijing 100850, China.
Nucleic Acids Res. 2022 Jan 7;50(D1):D950-D955. doi: 10.1093/nar/gkab1008.
The rapid development of single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) technologies presents both challenges and opportunities for the annotation of noncoding variants. Here, we updated 3DSNP, a comprehensive database for human noncoding variant annotation, to expand its applications to structural variation (SV) and to implement variant annotation down to single-cell resolution. The updates of 3DSNP include (i) annotation of 108 317 SVs from a full spectrum of functions, especially their potential effects on three-dimensional chromatin structures, (ii) evaluation of the accessible chromatin peaks flanking the variants across 126 cell types/subtypes in 15 human fetal tissues and 54 cell types/subtypes in 25 human adult tissues by integrating scATAC-seq data and (iii) expansion of Hi-C data to 49 human cell types. In summary, this version is a significant and comprehensive improvement over the previous version. The 3DSNP v2.0 database is freely available at https://omic.tech/3dsnpv2/.
单分子长读测序（LRS）和转座酶可及染色质测序（scATAC-seq）技术的快速发展，为非编码变异的注释带来了挑战和机遇。在这里，我们更新了 3DSNP，这是一个用于人类非编码变异注释的综合性数据库，以扩展其在结构变异（SV）方面的应用，并实现单细胞分辨率的变异注释。3DSNP 的更新包括：（i）从全功能范围注释了 108317 个 SV，特别是它们对三维染色质结构的潜在影响，（ii）通过整合 scATAC-seq 数据，评估了变体侧翼的可及染色质峰在 15 个人类胎儿组织中的 126 种/亚型和 25 个人类成年组织中的 54 种/亚型，（iii）将 Hi-C 数据扩展到 49 个人类细胞类型。总之，这个版本相对于上一个版本有了显著和全面的改进。3DSNP v2.0 数据库可在 https://omic.tech/3dsnpv2/ 免费获取。
