Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

Jimmy Z Liu, Mohamed A Almarri, Daniel J Gaffney, George F Mells, Luke Jostins, Heather J Cordell, Samantha J Ducker, Darren B Day, Michael A Heneghan, James M Neuberger, Peter T Donaldson, Andrew J Bathgate, Andrew Burroughs, Mervyn H Davies, David E Jones, Graeme J Alexander, Jeffrey C Barrett, Richard N Sandford, Carl A Anderson, UK Primary Biliary Cirrhosis (PBC) Consortium

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175 Citations (Scopus)


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 P0.8) 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.
Original languageEnglish
Pages (from-to)1137-41
Number of pages5
JournalNature Genetics
Issue number10
Publication statusPublished - Oct 2012


  • Case-Control Studies
  • Chromosome Mapping
  • Chromosomes, Human, Pair 19
  • Gene Frequency
  • Genetic Loci
  • Genetic Predisposition to Disease
  • Genome-Wide Association Study
  • Genotype
  • HLA Antigens
  • Humans
  • Linkage Disequilibrium
  • Liver Cirrhosis, Biliary
  • Polymorphism, Single Nucleotide
  • Proteins
  • Regression Analysis
  • Sequence Analysis, DNA
  • TYK2 Kinase


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