Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
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We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P<5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2>0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.
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The presence of genetic susceptibility is supported by the increased concordance rate in monozygotic twins and confirmed by the identification of significant numbers of associated genetic loci in GWAS and other large-scale genetic approaches.
“The presence of genetic susceptibility is supported by the increased concordance rate in monozygotic twins44 and confirmed by the identification of significant numbers of associated genetic loci in Genome Wide Association Studies (GWAS) and other large-scale, high-quality genetic approaches.45–54”
From The British Society of Gastroenterology/UK-PBC primary biliary cholangitis treatment and management guidelines (2018) · cites this paper as [49]
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Self-citation
- Authors
- The UK Primary Biliary Cirrhosis (PBC) Consortium, Liu, J. Z., The Wellcome Trust Case Control Consortium 3, Almarri, M. A., Gaffney, D. J., Mells, G. F., Jostins, L., Cordell, H. J., Ducker, S. J., Day, D. B., Heneghan, M. A., Neuberger, J. M., Donaldson, P. T., Bathgate, A. J., Burroughs, A., Davies, M. H., Jones, D. E., Alexander, G. J., Barrett, J. C., Sandford, R. N., & Anderson, C. A.
- Affiliations
- Wellcome Sanger Institute (GB)
- National Health Service (GB)
- Newcastle University (GB)
- University of Cambridge (GB)
- King's College Hospital NHS Foundation Trust (GB)
- Queen Elizabeth Hospital Birmingham (GB)
- Edinburgh Royal Infirmary (GB)
- The Royal Free Hospital (GB)
- St James's University Hospital (GB)
- Corresponding author
- Anderson, Carl A
- ORCID
- Venue
- Nature Genetics
- Published
- 2012-09-09
- Volume
- 44
- Issue
- 10
- Pages
- 1137-1141
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3459817
- OpenAlex
- W1966382491
- Cited by
- 274
- References
- 42
- Citations by year
- 2026: 9 · 2025: 10 · 2024: 18 · 2023: 12 · 2022: 11 · 2021: 16 · 2020: 19 · 2019: 18 · 2018: 32 · 2017: 20 · 2016: 15 · 2015: 41 · 2014: 29 · 2013: 24
- FWCI
- 18.84
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- University of Birmingham Research Portal (University of Birmingham) (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- BOA (University of Milano-Bicocca) (submittedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Research Portal (Queen's University Belfast) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- Wellcome Trust (068545/Z/02), WT090355/B/09/Z, WT090355/A/09/Z, 061858, 085925/Z/08/Z, 090532, 098051, 076113/C/04/Z)
- National Institute for Health and Care Research (IS-BRC-0211-10046)
- National Institutes of Health
- NIHR Newcastle Biomedical Research Centre (BH121729)
- National Institute of Diabetes and Digestive and Kidney Diseases (U01DK062418)
- Topics
- Health Sciences › Medicine › Hepatology › Liver Diseases and Immunity
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Inflammatory Bowel Disease
- Keywords
- primary biliary cirrhosis, genetic susceptibility loci, fine mapping, TYK2, JAK/STAT signaling, cytokine signaling, non-synonymous mutations, rare variants, linkage disequilibrium, autoimmune disease genetics
- MeSH terms
- Chromosome Mapping, Chromosomes, Human, Pair 19, Gene Frequency, Genotype, HLA Antigens, Humans, Liver Cirrhosis, Biliary, Proteins, Regression Analysis, Linkage Disequilibrium, Case-Control Studies, Sequence Analysis, DNA, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Intracellular Signaling Peptides and Proteins, Adaptor Proteins, Signal Transducing, TYK2 Kinase, Genome-Wide Association Study, Genetic Loci
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