Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.

ABSTRACT: Multiplexed DNA FISH (also known as FISH Omics) is a powerful imaging technology to map three-dimensional (3D) genome organization in thousands of single cells at kilobase resolution. However, existing computational approaches to identify 3D genome features, such as A/B compartments, topologically associating domains (TADs) and chromatin loops, have been mainly adapted from Hi-C and do not account for the distinct measurement errors across the three XYZ physical axes. Here we present ArcFISH (accurate and robust chromatin analysis from FISH data), which explicitly models axis-specific measurement errors in a unified statistical framework to detect multi-level 3D genome features. Comprehensive evaluations using multiple simulated as well as experimental datasets show th

SUBMITTER: Yu H 

PROVIDER: S-EPMC12697545 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature