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Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
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Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
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Journal Article
Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis
2012
Overview
Carl Anderson and colleagues report dense genotyping, using the Immunochip array, of 2,861 primary biliary cirrhosis (PBC) cases and 8,514 controls. They identify three loci newly associated with PBC, and their fine-mapping of previous susceptibility loci identifies five regions with multiple independent common, low-frequency and rare variant associations.
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;
r
2
> 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 (
r
2
> 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.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ Adaptor Proteins, Signal Transducing
/ Animal Genetics and Genomics
/ Arrays
/ Biological and medical sciences
/ Biomedical and Life Sciences
/ Classical genetics, quantitative genetics, hybrids
/ Diabetes
/ Disease
/ DNA
/ Fundamental and applied biological sciences. Psychology
/ Gastroenterology. Liver. Pancreas. Abdomen
/ Genetic Predisposition to Disease
/ Genetics of eukaryotes. Biological and molecular evolution
/ Genome-Wide Association Study
/ Genomes
/ Genomics
/ Genotype
/ Humans
/ Intracellular Signaling Peptides and Proteins
/ letter
/ Liver Cirrhosis, Biliary - genetics
/ Liver. Biliary tract. Portal circulation. Exocrine pancreas
/ Methods
/ Methods, theories and miscellaneous
