Exploring Impact of Rare Variation in Systemic Lupus Erythematosus by a Genome Wide Imputation Approach

Abstract

The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. Genome-wide association studies are therefore, underpowered to detect rare variation. We have used a combined approach of genome-wide-based imputation with a highly stringent sequence kernel association (SKAT) test and a case-control burden test. We identified 98 candidate genes containing rare variation that in aggregate show association with SLE many of which have recognized immunological function, but also function and expression related to relevant tissues such as the joints, skin, blood or central nervous system. In addition we also find that there is a significant enrichment of genes annotated for disease-causing mutations in the OMIM database, suggesting that in complex diseases such as SLE, such mutations may be involved in subtle or combined phenotypes or could accelerate specific organ abnormalities found in the disease. We here provide an important resource of candidate genes for SLE.

Keywords: GWAS—genome-wide association study; SLE; aggregated case-control enrichment; imputated rare variation; sequence kernel association test; systemic lupus erythematosus.

Figure 1

After QC filtering, imputation provided a set of 5,305,811 markers: 2,595,206 with MAF > 1% (48.93%) and 2,709,605 with MAF < 1% (51.07%). A set of 1,549,436 independent markers was obtained by applying a threshold of r² < 0.1. Rare variation was less affected by the linkage disequilibrium than common variation, which resulted in 87,853 variants with MAF > 1% (5.56%) and 1,491,583 variants with MAF < 1% (94.44%). This last set of 1,491,583 independent rare-variants constituted our working set.

Figure 2

Numbers of variants were represented by dark columns: in the set of 1,306,324 independent (r² < 0.1) polymorphic rare variants (MAF < 0.1), 189,893 (14.5%) were singletons (in the 8,277 individuals sample this means a MAF = 0.006%), 676,621 (51.8%) were classified as “very rare-variants” (0.006% < MAF < 0.1%), and 439,810 (33.7%) considered as a rare variation in a “strict sense” (0.1% < MAF ≤ 1%); these numbers of variants were represented by dark columns. Lighter columns represented the sums of alleles of minor frequency in each of the 3 categories of rare variation, these 3 categories sum up 29,128,106 minor alleles: the 189,893 singletons represented only 0.65% of minor alleles; the 676,621 the markers, which were very rare variation, add up to 4,671,537 minor frequency alleles, it was the 16.04%; while the remaining markers, sum up to 24,266,676 of minor frequency alleles representing the 83.33%.

Figure 3

Functional annotation of rare variation. Note that the percentages of the different functional categories in rare variation with and without r² filtering was similar, being the intronic the most abundant category, 85% of the total.

Figure 4

Functional annotation of exonic rare variation. The exonic rare variants represented only 2%, and more than 98% of these exonic mutations were synonymous.