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!


Monday, October 15, 2018

Connect with the Knowledge Portal Network team at ASHG!

Next week, the human genetics research community will come together in San Diego for one of the most important conferences of the year: the annual American Society of Human Genetics meeting. The Knowledge Portal Network team will be there, and in addition to presenting all the new data and features in the Type 2 DiabetesCerebrovascular Disease, and Cardiovascular Disease Knowledge Portals (KPs), we'll be launching an entirely new Portal for the genetics of sleep disorders!

We'll also present an interactive workshop on Friday that will go over the basics of navigating the Knowledge Portal Network. Download the flyer here, and find more details below.

Here's the schedule of events for the week:

Tuesday, October 16
2:05-2:30 pm: Jason Flannick will present a talk, "Infrastructure for analyzing and disseminating large-scale genetic data for type 2 diabetes and other complex diseases," in the ASHG/IGES/ISCB Joint Symposium.
Room 6C - Upper Level/San Diego Convention Center

Wednesday, October 17
The Knowledge Portal team will be at our booth, #219, in the exhibit hall from 10am-4:30pm.
We'll also be at the Broad Institute Genomic Services booth, #1634, from 10:30-11:30am.

Thursday, October 18
The team will again be at our booth, #219, in the exhibit hall from 10am-4:30pm.

Friday, October 19
We'll again be at our booth, #219, in the exhibit hall from 10am- 4:30pm, but today the booth will be closed around lunchtime so that we can present a special tutorial session on the Knowledge Portals. See details and sign up below. After the session, we'll be back at our booth until 4:30pm and will also be at the Broad Institute Genomic Services booth, #1634, from 2:30 - 3:30pm.

At lunchtime on Friday, grab your laptop and come to a workshop on the Knowledge Portals:

Navigating complex disease genetics: using the Knowledge Portal Network to move from SNPs to functional insights
12:30-1:45pm
Room 28C, Upper Level, San Diego Convention Center

We'll go over some basics, illustrate workflows, and answer questions about how you can use KPs to investigate SNPs, genes, or regions of interest and turn genetic data into insights about complex diseases.

Please sign up so we can plan for refreshments. We'll send you a reminder a few days beforehand. We look forward to seeing you there! Please contact us with any questions or suggestions for topics you'd like to discuss.