• Jonnie Albertsen posted an update 1 year, 8 months ago

    Standard quality control procedures were applied to each dataset prior to combining summary statistics for meta-analysis. In brief, samples were excluded if they had call rates less than 95%, phenotype-genotype gender discordance, demonstrated cryptic relatedness (defined as pi_hat greater than 12.5%, effectively removing all first or second degree relatives), or outliers from the populations with European ancestry (defined as > 3 standard deviations away from the combined European Caucasians [HapMap 3 release 3, 2010 (International HapMap 3 Consortium, 2010)] population mean in components vectors 1 and 2, using PLINK Multidimensional scaling plot). SNPs were excluded if they had a minor allele frequency (MAF) < 0.01, Hardy-Weinberg equilibrium p-value < 10−6 in controls, missing by haplotype p value < 10−4, or evidence of nonrandom missingness in cases versus controls (p SNS-032 clinical trial value < 10−4). Meta-analyses were performed with METAL ( Willer et al., 2010) for fixed-effect and PLINK ( Purcell et al., 2007) for random-effects model. Haplotype analysis was performed using Haploview 4.2 to evaluate the possibility of population-based differences ( Barrett et al., 2005). Additional statistical analyses were performed using R (version 2.11.1, R Development Core Team, 2010). Subsequently, we tested families where phased genotype data generated on various SNP chips was available to establish the relationship between the 9p21 susceptibility region and the Mendelian linkage regions. We performed a meta-analysis of 5 ALS genome-wide association studies involving a total of 2017 cases and 3639 controls drawn from the 5 datasets. As expected, meta-analysis confirmed the presence of previously identified locus on chromosome 9p21 (most significantly with imputed SNP = rs2477521, p value = 4.51 × 10−11 based on fixed-effect model with heterogeneity p value of 1.5 × 10−4, and an overall p value = 0.00876 based on more conservative random-effects model). Heterogeneity estimates suggested significant variation in the effect size from different populations, with the Italian population being a frequent outlier. Secondary analysis without the Italian cohort yielded a markedly more robust p value for the same SNP (p value for rs2477521 under the fixed effect model = 1.24 × 10−13; rs10967973 with p value under the random effects model = 1.55 × 10−10). This suggests that the effect at this SNP differs markedly when comparing between populations of Northern and Southern European ancestry. The original risk haplotype identified within the Finnish ALS population consisted of 42 SNPs stretching over a 232 kb region of chromosome 9p21 (Laaksovirta et al., 2010). This block of linkage disequilibrium was shorter in the European Caucasians HapMap data (24 SNPs over a 140 kb region), as would be expected in an outbred European population compared with the genetically homogeneous Finnish population (Shifman and Darvasi, 2001).