Friday, October 26, 2018

New features in the CDKP

Today the Cerebrovascular Disease Knowledge Portal has several new features that help bring meaning to genetic association results.

Calculated credible sets

Credible sets are useful because they assign to individual variants in a locus a probability of being causal for a phenotype. On Gene Pages, when viewing the type 2 diabetes (T2D) phenotype, the Credible sets tab displays credible sets generated by the MAGIC consortium. However, credible sets have not been generated by researchers for phenotypes in the CDKP other than T2D.

Now, the CDKP provides calculated credible sets for all phenotypes. When viewing a phenotype other than T2D on the Gene page, the Credible sets tab is replaced by a Calculated credible set tab. This LocusZoom module, developed by researchers at the University of Michigan, automatically calculates posterior probabilities from p-values. Calculated credible sets include up to 10 variants; the credible interval covered by the set may vary, depending on the strength of associations across the region.

UK Biobank PheWAS

The PheWAS display in the "Associations at a glance" section of Variant pages (see an example) is another LocusZoom module for displaying phenome-wide associations. The default PheWAS plot on the Variant page shows associations for a variant across all of the phenotypes included in the CDKP.

Now, by checking the "Use UKBB data" box, you can view associations for a variant across about 1,400 UK Biobank phenotypes from an analysis performed at the University of Michigan.

New LocusZoom visualization shows variant associations across UK Biobank phenotypes

Forest plot visualization of variant associations

We provide yet another LocusZoom visualization on a separate tab of the "Associations at a glance" section of the Variant page. The Forest plot is an alternative way to visualize phenotypic associations for a variant. In addition to displaying the significance of variant associations, the Forest plot also shows their direction of effect and confidence interval.

Forest plot on the Variant page

Check out a new portal!

We've just launched a new member of the Knowledge Portal Network: the Sleep Disorder Knowledge Portal for the genetics of sleep and circadian traits. Find a link to it on the CDKP home page:

We hope you enjoy the new data and features in the CDKP. Please contact us any time with suggestions or questions!