Exome specificity with varying exome site density.

<p>We see an increase in specificity of exome generated IBD segments in detecting data verified by GWAS IBD as we increase the threshold of site density.</p

Exome sensitivity with varying segment length.

<p>Exome sequencing IBD data is shown to have low sensitivity with GWAS IBD data. The sensitivity decreases as the threshold increases for allowed segment length.</p

Exome sensitivity with varying exome site density.

<p>We see a decrease in sensitivity of exome generated IBD segments in their ability to cover the segments discovered from GWAS IBD as we increase the threshold of site density.</p

Exome specificity with varying sites and segment length.

<p>Exome specificity as a function of both with varying site frequency and segment length. Using specificity data generated for the 50 bit size data seen, we examine here the relationship between the specificity and the site density. Areas of high specificity (color coded green) are concentrated in the portion of the graph where segments demonstrate site density, with high site frequency and low length. Based on the figure, a qualitative observation can be made about how increased site density correlates with increased specificity.</p

Concordance between GWAS IBD and whole-exome sequencing data.

a<p>Minimum genotype quality threshold for variant call.</p>b<p>Sites not present in dbSNP 130.</p>c<p>Sites present in dbSNP 130.</p>d<p>Expected concordance measured across all loci.</p>e<p>800000 genotype sites, 155327 exome sites, and 28145 filtered exome sites are compared.</p

Exome specificity with varying segment length.

<p>Exome sequencing IBD data is shown to have low specificity with GWAS IBD data. Even at lengths of 30 cM and with stringent IBD segment generation parameters, the specificity remains low at under 3%.</p

Newly discovered protein-QTLs (10% FDR): protein probe and lead significant SNP.

<p>Newly discovered protein-QTLs (10% FDR): protein probe and lead significant SNP.</p

Locuszoom plot of MST1, CD and UC association pvalues around the MST1 gene.

<p>It is worth noting that our proteomics platform has 4 probes in this chromosomal region, targeting 4 different proteins: IMPDH2 (probe SL010928), MST1 (probe SL005202), MST1R (probe SL004637) and MAPKAPK3 (probe SL004765). Of these, MST1 is most significantly associated with the IBD GWAS SNP in this locus (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006565#pgen.1006565.s003" target="_blank">S3 Fig</a>), and the association pattern was highly consistent with the CD and UC GWAS peaks (Fig 5).</p

Overlaps between blood serum protein-QTLs and previously published eQTLs from several tissues (10% FDR).

<p>Overlaps between blood serum protein-QTLs and previously published eQTLs from several tissues (10% FDR).</p

Increase of Albumin levels with aging in CD and UC.

<p>Scatterplot of the Albumin protein level vs patients age, separately for UC patients (left panel) and CD patients (baseline data only is displayed, right panel). Age in years on the horizontal axis; mean-centered and adjusted log2-protein expression on the vertical axis (adjusted for sex and plateID).</p