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Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (∼26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ∼2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5×10(-8)) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT-assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.

Original publication

DOI

10.1371/journal.pgen.1001324

Type

Journal article

Journal

Plos genetics

Publication Date

10/03/2011

Volume

7

Addresses

Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, United States of America. espeliot@med.umich.edu

Keywords

NASH CRN, GIANT Consortium, MAGIC Investigators, GOLD Consortium, Humans, Fatty Liver, Insulin, Lipase, Blood Glucose, Adaptor Proteins, Signal Transducing, Lectins, C-Type, Membrane Proteins, Nerve Tissue Proteins, Tomography, X-Ray Computed, Case-Control Studies, Cohort Studies, Mutation, Missense, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Adult, Aged, Aged, 80 and over, Middle Aged, Male, Genome-Wide Association Study, Chondroitin Sulfate Proteoglycans, Non-alcoholic Fatty Liver Disease