Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL

Abstract

Resequencing genes provides the opportunity to assess the full spectrum of variants that influence complex traits. Here we report the first application of resequencing to a large population (n = 3,551) to examine the role of the adipokine ANGPTL4 in lipid metabolism. Nonsynonymous variants in ANGPTL4 were more prevalent in individuals with triglyceride levels in the lowest quartile than in individuals with levels in the highest quartile (P = 0.016). One variant (E40K), present in approximately 3% of European Americans, was associated with significantly lower plasma levels of triglyceride and higher levels of high-density lipoprotein cholesterol in European Americans from the Atherosclerosis Risk in Communities Study and in Danes from the Copenhagen City Heart Study. The ratio of nonsynonymous to synonymous variants was higher in European Americans than in African Americans (4:1 versus 1.3:1), suggesting population-specific relaxation of purifying selection. Thus, resequencing of ANGPTL4 in a multiethnic population allowed analysis of the phenotypic effects of both rare and common variants while taking advantage of genetic variation arising from ethnic differences in population history.

Figure 1

Schematic of the ANGPTL4 gene with location of nonsynonymous sequence variations identified in the upper and lower quartiles of Dallas Heart Study. The 406-residue protein comprises a signal sequence (SP), a coiled-coil domain (CC) and a fibrinogen-like domain. Sequence variants found among individuals in the low-triglyceride group (plasma triglyceride levels less than or equal to the 25th percentile) but not in individuals in the high-triglyceride group (plasma triglyceride levels greater than or equal to the 75th percentile) are shown below the protein. Sequence variants found in the high-triglyceride group but not in the low-triglyceride group are shown above the protein. Sequence variants found in African Americans are indicated by boxes. All variants were found in separate individuals in each group, except for R336C, which was found in three individuals in the low group (asterisk indicates n = 3). Thus, the number of individuals with nonsynonymous sequence variants in the bottom quartile (n = 13) was significantly greater than the number in the highest quartile (n = 2; P = 0.016). fs, frameshift.

Figure 2

Proportion of nonsynonymous and synonymous sequence variants in European Americans, African Americans and Hispanics in the Dallas Heart Study. (a) Number of nonsynonymous and synonymous variants expressed as a percentage of the total number of variants identified in the three ethnic groups in the DHS. (b) Number of nonsynonymous and synonymous variants identified per 596 individuals in each population. To adjust for the different numbers of individuals in each group, five subsamples of 596 individuals (corresponding to the total number of Hispanics from whom sequence data were obtained) were drawn at random from the 1,045 European Americans and from the 1,830 African Americans in the sample. The number of nonsynonymous and synonymous variants was determined in each subsample, and the average number across the five subsamples was calculated. This random selection process was repeated once, with essentially identical results.

Figure 3

Prevalence of the ANGPTL4[E40K] allele among individuals with low and high plasma triglyceride levels in the Dallas Heart Study and ARIC study. European American participants in the DHS were stratified by plasma triglyceride level (which was significantly associated with the E40K variant in all three populations) and by BMI (which was not associated with the variant in any of the three populations). The number of ANGPTL4[E40K] carriers in the upper and lower quartiles for each trait was determined. A corresponding analysis was performed in the ARIC study using the upper and lower 5% of the population distribution for the two traits. *P = 0.008; **P = 1.1 × 10 ⁻⁹.