Wednesday, August 15, 2018

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 Cerebrovascular DiseaseType 2 Diabetes, or Cardiovascular Disease 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.

Wednesday, May 2, 2018

Join the Knowledge Portal Network team!

At the Knowledge Portal Network (currently consisting of the Type 2 Diabetes, Cerebrovascular Disease, and Cardiovascular Disease Knowledge Portals), we are looking for energetic, talented people to help us produce web portals that aggregate and serve genetic association results to the world in order to spark insights into complex diseases. There are positions open for a software engineer to help in developing and producing these web portals, and for a technical release manager to manage and coordinate tasks during production and maintenance of the portals.

The positions are located at the Broad Institute in Cambridge, MA, a dynamic and exciting work environment where cutting-edge science is applied to critical biomedical problems.

Find more details and apply for the software engineer or technical release manager positions at the Broad Careers site.

Monday, February 12, 2018

CDKP Publication

The Cerebrovascular Disease Knowledge Portal has an article describing its design and development available! This article has been published in Stroke’s February issue as a topical review. The article details the challenges and successes that the CDKP has faced during development and outlines plans for the future of the knowledge portal. The article is entitled “Cerebrovascular Disease Knowledge Portal: An Open-Access Data Resource to Accelerate Genomic Discoveries in Stroke” and is available through the journal website.



Tuesday, November 14, 2017

Announcing the Cardiovascular Disease Knowledge Portal

We are pleased to announce the launch of the Cardiovascular Disease Knowledge Portal (CVDKP). The Knowledge Portal team at the Broad Institute, in collaboration with Dr. Patrick Ellinor, Dr. Sek Kathiresan, and their colleagues in the Atrial Fibrillation, Global Lipids Genetics, Myocardial Infarction Genetics, and CARDIoGRAMPlusC4D consortia, has created a resource that offers world-wide open access to genetic and genomic information about atrial fibrillation, myocardial infarction, and related traits, with the goal of democratizing access to genomic data and accelerating cardiovascular genomics research.


CVDKP home page

The CVDKP is constructed on a software architecture originally developed for the Type 2 Diabetes Knowledge Portal (T2DKP), which is the central product of the Accelerating Medicines Partnership in Type 2 Diabetes (AMP T2D). AMP T2D is a public-private partnership between the National Institutes of Health, the U.S. Food and Drug Administration, biopharmaceutical companies, and non-profit organizations that is managed through the Foundation for the NIH. AMP seeks to harness collective capabilities, scale, and resources toward improving current efforts to develop new therapies for complex, heterogeneous diseases.

The ultimate goal of AMP T2D is to increase the number of new diagnostics and therapies for patients while reducing the time and cost of developing them, by jointly identifying and validating promising biological targets for type 2 diabetes. The T2DKP furthers that goal by aggregating, harmonizing, and displaying genetic association and epigenomic results along with user-friendly analysis tools, allowing research biologists who would not individually be able to amass and manipulate these large datasets to glean insights from the data.

Working towards these same goals for other complex diseases, the platform and analysis tools constructed for the T2DKP have been extended to other disease areas. The Cerebrovascular Disease Knowledge Portal, based on the same infrastructure, was recently created in partnership with the International Stroke Genetics Consortium. Now, with the advent of the Cardiovascular Disease Knowledge Portal, researchers may access a three-member Knowledge Portal Network for the genetics of cardiometabolic and cerebrovascular disease.

Data in the CVDKP directly relevant to heart disease include genetic associations with atrial fibrillation, electrocardiogram traits, plasma lipid levels, and myocardial infarction. Additional association datasets are available for type 2 diabetes and glycemic traits, anthropometric traits, measures of kidney function, and psychiatric traits. The complete list of datasets and their descriptions is available on the CVDKP Data page.

Like the Cerebrovascular Disease Knowledge Portal, the CVDKP is connected to the American Heart Association Precision Medicine Platform (PMP) to provide an additional avenue for accessing cardiovascular genetic data. Currently, summary statistics from the AFGen GWAS and AFGen exome chip analysis datasets are deposited in the PMP.

The CVDKP team welcomes all suggestions, comments, questions, and submission of relevant datasets. Please contact them at help@cvdgenetics.org!

Friday, September 22, 2017

Data Sharing from Our Collaborators

Dr. Benjamin Neale of the Broad Institute’s Medical and Population program and the Population Genetics for the Stanley Center for Psychiatric Research has made the results of his lab’s UK Biobank GWAS available for download. Dr. Neale works alongside Drs. Daniel Macarthur and Mark Daly in the Analytic and Translational Genetics Unit (ATGU) at Massachusetts General Hospital. ATGU, along with the CDKP, is committed to advancing science through open data sharing and dissemination of scientific advances. We encourage our users to check out their data available for download here.

Thursday, August 10, 2017

Welcome to the Cerebrovascular Disease Knowledge Portal

We are pleased to announce the launch of the Cerebrovascular Disease Knowledge Portal (CDKP). This open-access resource brings stroke genomic information to the world.

About the Cerebrovascular Disease Knowledge Portal project

Funded by the National Institute of Neurological Disorders and Stroke, the Cerebrovascular Disease Knowledge Portal has been developed by a team of clinicians, scientists and software engineers from the Broad Institute of MIT and Harvard, Massachusetts General Hospital, Yale University, and many collaborators within the International Stroke Genetics consortium. The goal of the platform is to democratize access to genomic data and accelerate stroke genomics research by providing open access to genetic, phenotypic and imaging data on large numbers of patients with stroke from around the world.

History

In the past decade, the introduction of high throughput genotyping technologies revolutionized the way we think about, and work with, genomic data. These new technologies have been potentiated by the creation of large collaboration networks that allow the assembly of sample sizes unimaginable not long ago. Launched in 2007, the International Stroke Genetics Consortium (ISGC) brought together a global community of investigators. Working groups within the ISGC have been responsible for the discovery of dozens of genetic susceptibility loci for stroke and continue to pursue further discoveries. To capitalize fully on the unique opportunities available through the generation of genetic and phenotypic data on large numbers of individuals with cerebrovascular disease, the ISGC launched the CDKP (www.cerebrovascularportal.org), a comprehensive web-based resource that facilitates exploration of and access to the rich genetic and phenotypic data related to cerebrovascular disease that has been generated by the stroke research community.  It is built with the Knowledge Portal architecture developed at the Broad Institute and powered by the rich human genetics data of the stroke research community. The CDKP expands on this architecture with additional features and partnerships.

The Cerebrovascular Disease Knowledge Portal

The CDKP houses two substantially different types of data: summary level data and individual level data. Summary level data (summary statistics) consist of full sets of results described in published genetic association studies in stroke genomics. Individual level data consist of complete datasets containing phenotypic and genotypic information from cohorts of stroke patients and controls enrolled as part of one of the constituent studies within the ISGC.

The Knowledge Portal is designed to serve three key functions:
To be a central repository for large datasets of human genetic information linked to cerebrovascular disease and related traits.
To function as a scientific discovery engine that can be harnessed by the community at large, and ultimately assist in the selection of new targets for cerebrovascular drug design.
To facilitate the conduct of customized analyses by any interested user around the world, doing so in a secure manner that provides high quality results while protecting the integrity of the data.

The Knowledge Portal is intended to be secure, compliant with pertinent ethical regulations, accessible to a wide user base, inviting to researchers who may want to contribute data and participate in analyses, organic in the continuous incorporation of scientific advances, modular in its analytical capabilities and user interfaces, automated, rigorous in the quality of data aggregation and returned results, versatile, and sustainable.

The CDKP is constructed on a software architecture originally developed for the Type 2 Diabetes Knowledge Portal, built as the central product of the Accelerating Medicines Partnership in Type 2 Diabetes. It expands upon the Knowledge Portal (KP) framework by providing two additional avenues for accessing stroke genetic data, beyond the KP web interfaces and tools. The first avenue offers the public the ability to download published datasets of stroke GWAS summary statistics. The second avenue offers authorized researchers access to individual-level data in the Precision Medicine Platform of the American Heart Association (see below).

Partnership with the American Heart Association (AHA)

The developers of the CKDP have partnered with the AHA Institute for Precision Cardiovascular Medicine. The AHA Institute for Precision Cardiovascular Medicine is committed to advancing precision medicine through mechanisms such as the CKDP. Through this partnership a resource has been developed that allows scientists to query and analyze individual level data on a secure platform which prevents the download of data. This workspace will help to enable liberal but secure data sharing, to better enable scientists and doctors to find underlying mechanisms of stroke and cardiovascular disease.