Abstract and Introduction
Abstract
Background Single nucleotide polymorphisms (SNPs) rs429358 (ε4) and rs7412 (ε2), both invoking changes in the amino-acid sequence of the apolipoprotein E (APOE) gene, have previously been tested for association with multiple sclerosis (MS) risk. However, none of these studies was sufficiently powered to detect modest effect sizes at acceptable type-I error rates. As both SNPs are only imperfectly captured on commonly used microarray genotyping platforms, their evaluation in the context of genome-wide association studies has been hindered until recently.
Methods We genotyped 12 740 subjects hitherto not studied for their APOE status, imputed raw genotype data from 8739 subjects from five independent genome-wide association studies datasets using the most recent high-resolution reference panels, and extracted genotype data for 8265 subjects from previous candidate gene assessments.
Results Despite sufficient power to detect associations at genome-wide significance thresholds across a range of ORs, our analyses did not support a role of rs429358 or rs7412 on MS susceptibility. This included meta-analyses of the combined data across 13 913 MS cases and 15 831 controls (OR=0.95, p=0.259, and OR 1.07, p=0.0569, for rs429358 and rs7412, respectively).
Conclusion Given the large sample size of our analyses, it is unlikely that the two APOE missense SNPs studied here exert any relevant effects on MS susceptibility.
Introduction
Multiple sclerosis (MS), the most common chronic inflammatory disease of the central nervous system, is likely caused by interplay of environmental and genetic factors. Recent genome-wide association studies (GWAS) have identified almost 60 putative risk loci apart from a well-established association with the human leukocyte antigen region on chromosome 6p21 (eg, refs.). Despite this recent progress, it has been estimated that approximately 80% or more of the genetic variance remains unexplained by the currently known loci. The failure to decipher the full genetic spectrum of MS susceptibility may in part be due to incomplete coverage of the genome by the available GWAS arrays. Along these lines, two single nucleotide polymorphisms (SNPs) frequently tested for association with MS risk in the pre-GWAS era, that is, rs429358 (a.k.a. 'ε4') and rs7412 ('ε2') in encoding apolipoprotein E (APOE), are absent from most GWAS genotyping platforms. Thus, these two APOE SNPs could not be directly assessed in previous MS GWAS and GWAS meta-analyses. The most recent release of whole-genome sequence data from the 1000 Genomes Project now makes it possible to impute genotypes at both sites for data from most GWAS genotyping platforms.
The investigation of APOE, the single most important risk locus for Alzheimer's disease, in MS has been motivated by reports of genetic linkage to the APOE-containing region on chromosome 19q13 (eg, ref.) as well as by its functional role in lipid transport, immunoregulation, neuroplasticity and repair mechanisms. However, APOE association studies in MS have yielded mostly negative results to date with some studies reporting significant effects while most others were unable to confirm these associations. These inconsistencies can at least in part be attributed to small sample sizes of the individual datasets. As a matter of fact, none of the previously performed APOE association studies in MS included more than 450 cases (see supplementary table S1 for an overview of study-specific sample sizes). Even two previous meta-analyses combining published data were limited in power to detect modest effects (ie, ORs at or below 1.2) at acceptable type-1 error rates, eg, at a genome-wide significance threshold (typically defined as α=5×10).
To provide a more conclusive assessment of the potential association between the two most commonly studied APOE SNPs and MS susceptibility in populations of European descent, we performed a large-scale association study of rs429358 and rs7412 using MS risk as outcome. To this end, we collected and genotyped 12 740 subjects hitherto not studied for their APOE status, imputed raw genotype data from 8739 subjects from five independent GWAS datasets using the most recent high-resolution reference panels, and extracted genotype data for 8265 subjects from previous candidate gene assessments to arrive at an overall samples size of up to 13 913 MS cases and 15 831 controls.