Copy number segmentations in ulcerative colitis, Gut 2025
Description
RDS files contain genomic copy number segmentations ("segmented") and copy number alteration (CNA) calls ("calls") for Discovery and Validation cohort datasets derived from low-coverage whole genome sequencing of tissue samples. Chromosomal locations of 4,401 bins of size 500kbp can be found in the "bin_locations_4401.Rdata" Rdata file. Datasets are described in Al Bakir I, Curtius K, et al. (2025) "Low-coverage whole genome sequencing of low-grade dysplasia strongly predicts advanced neoplasia risk in ulcerative colitis" Gut. Sample IDs of 270 total samples used for final analyses are located in Discovery_samples_used.csv and Validation_samples_used.csv
Files
Steps to reproduce
Methods are available in the manuscript outlining the generation of the WGS data and the pre-processing pipelines to obtain segmentations and CNA calls.
Institutions
- University of California San Diego
- Institute of Cancer Research