Characterization of European ancestry nonalcoholic fatty liver disease-associated variants in individuals of African and Hispanic descent

Abstract

Nonalcoholic fatty liver disease (NAFLD) is an obesity-related condition affecting over 50% of individuals in some populations and is expected to become the number one cause of liver disease worldwide by 2020. Common, robustly associated genetic variants in/near five genes were identified for hepatic steatosis, a quantifiable component of NAFLD, in European ancestry individuals. Here we tested whether these variants were associated with hepatic steatosis in African- and/or Hispanic-Americans and fine-mapped the observed association signals. We measured hepatic steatosis using computed tomography in five African American (n = 3,124) and one Hispanic American (n = 849) cohorts. All analyses controlled for variation in age, age(2) , gender, alcoholic drinks, and population substructure. Heritability of hepatic steatosis was estimated in three cohorts. Variants in/near PNPLA3, NCAN, LYPLAL1, GCKR, and PPP1R3B were tested for association with hepatic steatosis using a regression framework in each cohort and meta-analyzed. Fine-mapping across African American cohorts was conducted using meta-analysis. African- and Hispanic-American cohorts were 33.9/37.5% male, with average age of 58.6/42.6 years and body mass index of 31.8/28.9 kg/m(2) , respectively. Hepatic steatosis was 0.20-0.34 heritable in African- and Hispanic-American families (P < 0.02 in each cohort). Variants in or near PNPLA3, NCAN, GCKR, PPP1R3B in African Americans and PNPLA3 and PPP1R3B in Hispanic Americans were significantly associated with hepatic steatosis; however, allele frequency and effect size varied across ancestries. Fine-mapping in African Americans highlighted missense variants at PNPLA3 and GCKR and redefined the association region at LYPLAL1.

Conclusion: Multiple genetic variants are associated with hepatic steatosis across ancestries. This explains a substantial proportion of the genetic predisposition in African- and Hispanic-Americans. Missense variants in PNPLA3 and GCKR are likely functional across multiple ancestries.

Figure 1. Forest plot of the effect for hepatic steatosis index variants in European-Ancestry, African-American, and Hispanic-American populations

For each race and a pooled analysis, the effect allele (EA) and frequency (EAF) are listed with the corresponding p-value (p), beta value (beta) and 95% confidence interval (95% CI) for association with hepatic steatosis adjusting for age, age², gender, alcoholic drinks, and population substructure. Values greater than zero indicate an increase in the amount of hepatic steatosis. The solid vertical line represents no effect (beta=0).

Figure 2. Allele frequency distribution for hepatic steatosis index variants in European-Ancestry, African-American, and Hispanic-American populations

For each index variant, the effect allele is listed with a corresponding bar denoting the frequency observed in European-Ancestry (gray), African-American (white), and Hispanic-American (black) populations as well as in the pooled analysis (dark gray).

Figure 3. Weighted average of the variance explained by each SNP for European-Ancestry, African-American, and Hispanic-American populations

For each index variant, the corresponding bars represent the proportion of variance explained in European-Ancestry (gray), African-American (white), and Hispanic-American (black) populations as well as in the pooled analysis (dark gray).

Figure 4. Regional plots of loci robustly assoicated with NAFLD in European-ancestry population and fine-mapped in the African-American population

A) PNPLA3 in African Americans, B) PNPLA3 in European Americans, C) GCKR in African Americans, D) GCKR in European Americans, E) LYPLAL1 in African Americans, F) LYPLAL1 in European Americans. The variant most robustly associated is denoted in purple annotated by SNP ID with additional genotyped and imputed SNPs passing study-specific quality controls. SNPs are plotted with their meta-analysis p-values as a function of position (hg19). Shape of the data point is indicative of function, i.e. non-synonymous (▼) and no annotation (●), and color indicates LD (r²) with the previously identified variant taken from HapMap (red, r²=0.8–1.0; yellow, r²=0.6–0.8; green, r²=0.4–0.6; cyan, r²=0.2–0.4, and blue, r²<0.2). Estimated recombination rates (HapMap) reflect the local LD structure. Gene annotations were taken from the University of California Santa Cruz genome browser.