Faster access to tools from the CVDKP home page

We've rearranged some of the links on the Cardiovascular Disease Knowledge Portal home page, as a first step towards offering a central location for analysis tools. The previous link to the Variant Finder tool has been replaced by a link to the new Analysis modules page:

The new page, shown below, offers access to two analysis tools.

The Interactive Manhattan plot allows you to choose a phenotype and view variant associations across the genome for that phenotype.  We've added phenotype selection options to both the Analysis modules page and the Manhattan plot page, making it easier to switch your view between phenotypes.  The default view on the Manhattan plot page shows the largest dataset for a phenotype, but when multiple datasets exist, you can select any one to display. For many datasets, LD clumping is available at several r2 thresholds. Clumping reduces redundancy due to association signals from linked variants, pinpointing the most strongly associated variant in a group…

Atrial fibrillation associations from whole-genome sequence data now available in the CVDKP

We are pleased to present in the Cardiovascular Disease Knowledge Portal the results of a new study, published today in the Journal of the American Medical Association, that used deep-coverage whole-genome sequencing to uncover genetic variants contributing to early-onset atrial fibrillation. As part of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium and the DiscovEHR study, first author Seung Hoan Choi and colleagues analyzed genetic associations with early-onset atrial fibrillation (AF) in 2,781 cases and 4,959 controls.

The study found multiple associations of common variants with AF, many of which supported previous reports. One particularly interesting association was found for a variant in an intron of the NAV2 gene. Since NAV2 is involved in nervous system development, this association may suggest a link between AF and development of the autonomic nervous system.

The researchers also took advantage of the whole-genome sequence data to assess the contribution of…

Heart failure and albuminuria associations across nearly 400,000 UK Biobank subjects now available in the CVDKP

Two new datasets now bring associations for heart failure and albuminuria from large UK Biobank subject pools to the Cardiovascular Disease Knowledge Portal (CVDKP). Both studies revealed important insights about the etiology of different aspects of cardiovascular disease. And the results of both studies are available now in the CVDKP--both integrated into the Portal, and as files of summary statistics for download.

The study of heart failure associations (Aragam et al. (2018), Circulation) looked at associations both with heart failure from any cause and with a more refined phenotype, nonischemic cardiomyopathy (NICM), defined as left ventricular dysfunction without coronary artery disease. The loci significantly associated with all-cause heart failure were predominantly those already known to be associated with heart failure risk factors, such as coronary artery disease and atrial fibrillation. However, refining the phenotype to NICM revealed a different spectrum of associations, ov…

See you at AHA!

This weekend, cardiovascular researchers from around the globe will be meeting in Chicago for the 2018 Scientific Sessions of the American Heart Association. For the Cardiovascular Disease Knowledge Portal team, this is an opportunity to meet and talk with the geneticists and biologists who use the site and get your input on how we can improve it.

Please come visit us at booth #2249 in the Exhibit Hall! We'll be there on Saturday, Nov. 10 from 11am-5pm; on Sunday, Nov. 11 from 10am-4:30pm; and on Monday, Nov. 12 from 10am-3pm.

Summary stat downloads and new features available in the CVDKP

We're pleased to announce the availability of summary statistic download files for several important association studies via the Cardiovascular Disease Knowledge Portal, as well as some new features in the Portal that help bring meaning to genetic association results.

Download files available

Full summary results from five studies may now be downloaded via the CVDKP Data page. Association results for atrial fibrillation, albuminuria, and several ECG traits are available, from these publications:

Haas et al. 2018, Genetic Association of Albuminuria with Cardiometabolic Disease and Blood Pressure.Prins et al. 2018, Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6.Lin et al. 2018, Common and Rare Coding Genetic Variation Underlying the Electrocardiographic PR Interval.Christophersen et al. 2017, Fifteen Genetic Loci Associated With the Electrocardiographic P Wave.Christophersen et al. 2017, Large-scale analyses of common and rare vari…

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 …

Sign up for a hands-on tutorial session on the Knowledge Portals

Are you attending the American Society of Human Genetics meeting in October? If so, save your Friday lunch break for a tutorial session on the Knowledge Portals!

Navigating complex disease genetics: using the Knowledge Portal Network to move from SNPs to functional insights
12:30pm - 1:45pm
Friday, October 19
San Diego Convention Center
Room 28C, Upper Level

Bring your laptop and your questions about the Cardiovascular DiseaseCerebrovascular Disease, or Type 2 Diabetes Knowledge Portals (KPs). 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.