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Published March 21, 2022 | Version v1
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Comprehensive epigenomic profiling reveals disease-specific chromatin states and enhances therapeutic target discovery in ankylosing spondylitis

Authors/Creators

  • 1. Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
  • 2. Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK
  • 3. Université Paris-Saclay, UVSQ, INSERM UMR1173, Infection et inflammation, Laboratory of Excellence INFLAMEX, France
  • 4. Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
  • 5. Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
  • 6. Computational Sciences, Population analytics team. Janssen R&D, Spring House PA, USA
  • 7. Computational Sciences, J&J Innovation Centre, London, W1G 0BG, UK

Description

We performed comprehensive epigenetic profiling in immune cell samples from patients with ankylosing spondylitis and healthy controls. 

We used ChromHMM to integrate epigenomic data. ChromHMM filenames are in the format ChromHMM_sampleID_celltype_n.bed.gz where n is the number of states in the ChromHMM emission model.

We performed Capture-C to detect chromosome looping interactions between gene promoters and SNPs associated with ankylosing spondylitis. 

Capture-C count data are shown in the format: CaptureC_celltype_gene_Pro/SNP_normalised.unionbdg

We used PeakY to calculate a score for each interaction. PeakY scores are given in the following format: PeakY_AS/HV_celltype_tier_chrloc_gene_Pro/SNP.txt

gene_Pro and gene_SNP relate to the baitsets given in Table S8.

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Additional details

Funding

Wellcome Trust
Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics. 090532
Wellcome Trust
A systematic approach to understanding the biology underpinning GWAS hits. 106130
Wellcome Trust
Characterising extreme innate immune response phenotypes informative for disease using a functional genomics approach 204969