A two-stage genome-wide association study of sporadic amyotrophic lateral sclerosis

Abstract

The cause of sporadic amyotrophic lateral sclerosis (ALS) is largely unknown, but genetic factors are thought to play a significant role in determining susceptibility to motor neuron degeneration. To identify genetic variants altering risk of ALS, we undertook a two-stage genome-wide association study (GWAS): we followed our initial GWAS of 545 066 SNPs in 553 individuals with ALS and 2338 controls by testing the 7600 most associated SNPs from the first stage in three independent cohorts consisting of 2160 cases and 3008 controls. None of the SNPs selected for replication exceeded the Bonferroni threshold for significance. The two most significantly associated SNPs, rs2708909 and rs2708851 [odds ratio (OR) = 1.17 and 1.18, and P-values = 6.98 x 10(-7) and 1.16 x 10(-6)], were located on chromosome 7p13.3 within a 175 kb linkage disequilibrium block containing the SUNC1, HUS1 and C7orf57 genes. These associations did not achieve genome-wide significance in the original cohort and failed to replicate in an additional independent cohort of 989 US cases and 327 controls (OR = 1.18 and 1.19, P-values = 0.08 and 0.06, respectively). Thus, we chose to cautiously interpret our data as hypothesis-generating requiring additional confirmation, especially as all previously reported loci for ALS have failed to replicate successfully. Indeed, the three loci (FGGY, ITPR2 and DPP6) identified in previous GWAS of sporadic ALS were not significantly associated with disease in our study. Our findings suggest that ALS is more genetically and clinically heterogeneous than previously recognized. Genotype data from our study have been made available online to facilitate such future endeavors.

Figure 1.

Association analysis of combined joints analysis in two-stage GWAS of ALS (n = 2289 ALS cases and 4532 controls) based on the logistic regression model correcting for age, gender and population. SNPs listed in Table 1 are represented by red dots.

Figure 2.

Location of the association signal and pairwise linkage disequilibrium (LD) surrounding the most associated SNPs on chromosome 7p12.3. LD pattern is depicted using stage 1 US data. Association signals are shown for all SNPs genotyped in (A) stage 1 US samples (blue squares, n = 1065); (B) stage 1 Italian samples (green triangles, n = 1456); (C) stage 2 all populations (orange circles, n = 4300), and the combined dataset (red diamonds, n = 6821). The most associated SNPs, rs2708909 and rs2708851, lie in or near gene SUNC1, and are in almost complete LD (D′ = 0.981, r² = 0.959 based on stage 1 US data). Plots were produced using the snp.plotter package within R version 2.6.1.

Figure 3.

Q-Q plot based on (A) genomic-controlled Cochran-Armitage Trend test P-values for 474 554 SNPs analyzed in the stage 1 271 North American ALS cases and 794 North American controls (genomic inflation factor λ = 1.002); (B) genomic-controlled Cochran-Armitage Trend test P-values for 466 131 SNPs analyzed in the stage 1 266 Italian ALS cases and 1190 Italian controls (genomic inflation factor λ = 1.147) and (C) logistic regression P-values for 6758 SNPs analyzed in the stage 2 1752 ALS cases and 2548 controls.