1. 3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database
- Author
-
Yiming Lu, Gangqiao Zhou, Jie Ping, Cheng Quan, and Hao Lu
- Subjects
Adult ,RNA, Untranslated ,AcademicSubjects/SCI00010 ,Computational biology ,Biology ,Polymorphism, Single Nucleotide ,Structural variation ,Annotation ,Fetus ,Databases, Genetic ,Genetics ,Humans ,Database Issue ,Cell Lineage ,Annotation database ,Transposase ,Internet ,Genome, Human ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,Molecular Sequence Annotation ,Human cell ,Chromatin ,Single Molecule Imaging ,Eukaryotic Cells ,Human fetal ,Single-Cell Analysis ,Software - Abstract
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/.
- Published
- 2021