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.