3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database

Area of Science:

• Genomics
• Bioinformatics
• Epigenetics

Background:

• Single-molecule long-read sequencing (LRS) and single-cell assay for transposase accessible chromatin sequencing (scATAC-seq) are advancing noncoding variant annotation.
• Existing databases face challenges in incorporating structural variations and single-cell resolution data.

Purpose of the Study:

• To update the 3DSNP database for comprehensive human noncoding variant annotation.
• To expand annotation capabilities to include structural variations (SVs) and single-cell resolution.
• To integrate diverse genomic data for enhanced variant effect prediction.

Main Methods:

• Annotation of 108,317 structural variations (SVs) and their functional impact on 3D chromatin structures.
• Integration of scATAC-seq data to evaluate chromatin accessibility across 126 fetal and 54 adult cell types/subtypes.
• Expansion of Hi-C data to 49 human cell types for improved 3D genome analysis.

Main Results:

• 3DSNP v2.0 now supports annotation for a wide range of SVs, including their effects on chromatin architecture.
• Detailed chromatin accessibility profiles for variants across numerous human tissues and cell types are available.
• The database provides a significantly improved resource for noncoding variant analysis.

Conclusions:

• 3DSNP v2.0 represents a major advancement in noncoding variant annotation, incorporating SVs and single-cell data.
• The updated database facilitates deeper understanding of variant impacts on gene regulation and 3D genome organization.
• This resource is freely available to the research community for advancing genomic studies.