Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers

Abstract

We report ∼17.6 million genetic variants from whole-genome sequencing of 2,120 Sardinians; 22% are absent from previous sequencing-based compilations and are enriched for predicted functional consequences. Furthermore, ∼76,000 variants common in our sample (frequency >5%) are rare elsewhere (<0.5% in the 1000 Genomes Project). We assessed the impact of these variants on circulating lipid levels and five inflammatory biomarkers. We observe 14 signals, including 2 major new loci, for lipid levels and 19 signals, including 2 new loci, for inflammatory markers. The new associations would have been missed in analyses based on 1000 Genomes Project data, underlining the advantages of large-scale sequencing in this founder population.

Figure 1. Geographical differentiation based on common and rare sites

The figure show allele sharing among the Sardinian and the 1000 Genomes European populations. In panel a) differentiation is represented for three different frequency intervals over the geographic map of Europe. The thickness and the color of the lines connecting the dots are proportional to the allele sharing statistic as indicated in the color map. In panel b) we instead represent the relationship between the frequency (X axis) and the sharing ratio (on the Y axis) for different 1000 Genomes Project populations (continuous lines). Results are plotted separately for the Lanusei valley sample (left panel) and the case control samples (right panel). The dotted line are used as comparison to show the sharing ratio between the TSI and other 1000 Genomes Project populations.

Figure 2. Length of shared haplotypes surrounding f₂ variants within Sardinians and populations in 1000 Genomes

Length of shared haplotypes surrounding f₂ variants shared between one of our sequenced individuals and one of 100 randomly selected individuals sampled from our study or from a particular 1000 Genomes Project population. Panel a) shows the length of these shared haplotypes, in kilobases, in comparisons between Sardinia and several 1000 Genomes Project populations. Panel b) shows the number of f₂ haplotypes in each comparison. Panel c) shows the number of f₂ haplotypes in comparisons within Sardinia (note the wider Y-axis range).

Figure 3. Regional association plots for novel lipids loci

Regional association plots at the HBB locus for LDL-c, and at APOA5 for triglycerides for imputation performed using the Sardinian (panels a and c) and 1000 Genomes (panels b and d) reference panels, respectively. At each locus, we plotted the association strength (Y axis shows the –log 10 pvalue) versus the genomic positions (on the hg19/GRCh37 genomic build) around the most significant SNP, which is indicated with a purple dot. Other SNPs in the region are color-coded to reflect their LD with the top SNP as in the inset (taken from pairwise r² values calculated on Sardinian and 1000 Genomes haplotypes for left and right panels, respectively). Symbols reflect genomic functional annotation, as indicated in the inner box of panel A. Genes and the position of exons, as well as the direction of transcription, are noted in lower boxes. This plot was drawn using the standalone version of the LocusZoom package ().

Figure 4. Regional association plot at chromosome 12 for hSCRP and ESR

Regional association plots at the chromosome 12 locus for hsCRP and for ESR, using the Sardinian (panels a and c) and 1000 Genomes (panels b and d) reference panels for imputation, respectively. For the plot style, see Figure 3 legend.