A large-scale international meta-analysis of paraoxonase gene polymorphisms in sporadic ALS

Abstract

Background: Six candidate gene studies report a genetic association of DNA variants within the paraoxonase locus with sporadic amyotrophic lateral sclerosis (ALS). However, several other large studies, including five genome-wide association studies, have not duplicated this finding.

Methods: We conducted a meta-analysis of 10 published studies and one unpublished study of the paraoxonase locus, encompassing 4,037 ALS cases and 4,609 controls, including genome-wide association data from 2,018 ALS cases and 2,425 controls.

Results: The combined fixed effects odds ratio (OR) for rs662 (PON1 Q192R) was 1.09 (95% confidence interval [CI], 1.02-1.16, p = 0.01); the genotypic OR for RR homozygotes at Q192R was 1.25 (95% CI, 1.07-1.45, p = 0.0004); the combined OR for rs854560 (PON1 L55M) was 0.97 (95% CI, 0.86-1.10, p = 0.62); the OR for rs10487132 (PON2) was 1.08 (95% CI, 0.92-1.27, p = 0.35). Although the rs662 polymorphism reached a nominal level of significance, no polymorphism was significant after multiple testing correction. In the subanalysis of samples with genome-wide data from which population outliers were removed, rs662 had an OR of 1.06 (95% CI, 0.97-1.16, p = 0.22).

Conclusions: In contrast to previous positive smaller studies, our genetic meta-analysis showed no significant association of amyotrophic lateral sclerosis (ALS) with the PON locus. This is the largest meta-analysis of a candidate gene in ALS to date and the first ALS meta-analysis to include data from whole genome association studies. The findings reinforce the need for much larger and more collaborative investigations of the genetic determinants of ALS.

Figure 1 Forest plots of nine studies of PON1 rs662 and six studies of rs854560 Study numbers refer to reference numbers. Published numbers include some duplicate samples, not included in the combined raw genotyping analysis. Areas of squares are proportional to the effective sample size, horizontal lines indicate confidence intervals (CI), and shaded diamonds denote grand totals. The horizontal axis is plotted on a log₁₀ scale. (A) Forest plot of paraoxonase PON1 Q192R/rs662 polymorphism in amyotrophic lateral sclerosis. The left side of the figure shows a forest plot based on the odds ratios (ORs) for the arginine allele in each study. The right side of the graph shows a forest plot based on the frequency of RR homozygotes from the same studies. The overall ORs for both were calculated using a fixed effects model due to low heterogeneity. Cochran's Q statistic (a test of heterogeneity which follows a χ² distribution) for the allelic analysis was not significant (12.12 with 8 degrees of freedom, p = 0.15) and the I² statistic equaled 35% (less than 50%). For the analysis of RR homozygotes, Cochran's Q statistic equaled 5.71 with 8 degrees of freedom (p = 0.68) and the I² statistic equaled 0%. (B) Funnel plot of the nine studies included in the rs662 analysis. The vertical axis shows the standard error of the log OR for each study, while the horizontal axis, the OR, is again plotted in a log scale. (C) Forest plot of the PON1 L55M/rs854560 polymorphism in amyotrophic lateral sclerosis. The overall OR was calculated using a random effects model due to significant heterogeneity (Cochran's Q statistic = 12.26 with 5 degrees of freedom, p = 0.03, and I² = 59.2%).

Figure 2 Association testing of seven single nucleotide polymorphisms within the PON cluster in 4,035 cases of sporadic amyotrophic lateral sclerosis and 4,603 controls (A) Negative log₁₀ of the unadjusted p value for each test in table 2 shown on y axis. (B) Exon mapping of the three paraoxonase genes, including the chromosomal location. (C) Pairwise linkage disequilibrium (D') and log of the odds ratio (lod) values were calculated using Haploview 4.0 for the seven tested single nucleotide polymorphisms. The color code on the Haploview plot follows the standard color scheme for Haploview: white (D' <1, lod <2); shades of pink/red (D' <1, lod >2); blue (D' = 1, lod <2).