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• W2783210076 abstract "HomeStrokeVol. 49, No. 2Cerebrovascular Disease Knowledge Portal Free AccessReview ArticlePDF/EPUBAboutView PDFView EPUBSections ToolsAdd to favoritesDownload citationsTrack citationsPermissions ShareShare onFacebookTwitterLinked InMendeleyReddit Jump toFree AccessReview ArticlePDF/EPUBCerebrovascular Disease Knowledge PortalAn Open-Access Data Resource to Accelerate Genomic Discoveries in Stroke Katherine M. Crawford, BS, Cristina Gallego-Fabrega, PhD, Christina Kourkoulis, BS, Laura Miyares, BS, Sandro Marini, MD, Jason Flannick, PhD, Noel P. Burtt, BS, Marcin von Grotthuss, PhD, Benjamin Alexander, BS, Maria C. Costanzo, PhD, Neil H. Vaishnav, JD, Rainer Malik, PhD, Jennifer L. Hall, PhD, Michael Chong, MSc, Jonathan Rosand, MD, MSc and Guido J. Falcone, MD, ScD, MPHon behalf of the International Stroke Genetics Consortium Katherine M. CrawfordKatherine M. Crawford From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Cristina Gallego-FabregaCristina Gallego-Fabrega From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Christina KourkoulisChristina Kourkoulis From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Laura MiyaresLaura Miyares From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Sandro MariniSandro Marini From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Jason FlannickJason Flannick From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Noel P. BurttNoel P. Burtt From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Marcin von GrotthussMarcin von Grotthuss From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Benjamin AlexanderBenjamin Alexander From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Maria C. CostanzoMaria C. Costanzo From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Neil H. VaishnavNeil H. Vaishnav From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Rainer MalikRainer Malik From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Jennifer L. HallJennifer L. Hall From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Michael ChongMichael Chong From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author , Jonathan RosandJonathan Rosand From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author and Guido J. FalconeGuido J. Falcone From the Center for Genomic Medicine (K.C., C.G.-F., C.K., S.M., N.V., J.R.), Division of Neurocritical Care and Emergency Neurology, Department of Neurology (J.R.), and J. Philip Kistler Stroke Research Center (J.R.), Massachusetts General Hospital, Boston; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (K.C., C.G.-F., C.K., S.M., J.F., N.B., M.v.G., B.A., M.C., N.V., J.R., G.J.F.); Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale University School of Medicine, New Haven, CT (L.M., G.J.F.); Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilian University, Munich, Germany (R.M.); Institute for Precision Cardiovascular Medicine, American Heart Association National Center, Dallas, TX (J.L.H.); Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis (J.L.H.); and McMaster University, Hamilton, Ontario, Canada (M.C.). Search for more papers by this author and on behalf of the International Stroke Genetics Consortium Originally published15 Jan 2018https://doi.org/10.1161/STROKEAHA.117.018922Stroke. 2018;49:470–475Other version(s) of this articleYou are viewing the most recent version of this article. Previous versions: January 1, 2018: Previous Version 1 Stroke is a leading cause of death and disability across the globe, affecting 15 million people each year.1 Stroke represents an archetypical common complex disease with both genetic and environmental determinants2,3 playing a role in its occurrence. The proportion of stroke risk that can be attributed to genetic variation has been estimated to be 30%.4–6 Although this estimate provides an indication of the overall importance of genetic variation in stroke, the key to developing new treatment strategies is to identify the specific genetic variants (mutations) that modify an individual’s risk of stroke. Genetic association studies (GWAS) seek to identify these variants and link them to specific genes, which, in turn, point to specific cellular processes to become therapeutic targets for drug development. In addition, newly discovered genetic risk loci can be used to improve existing phenotyping systems, enhance prediction tools aimed to identify high-risk patients, and aid in establishing causality for associations involving nongenetic exposures.Successfully identifying the range of genetic variants that cause stroke and leveraging these discoveries to reduce the suffering caused by this condition requires overcoming several key challenges. First, stroke is the final result of multiple different pathological processes and must, therefore, be accurately subtyped to identify underlying biology. Second, because large number of cases and controls are required to identify the culprit genetic variants, tens (even hundreds) of thousands of cases must be studied, requiring the collaboration of multiple centers, many of which use different ascertainment methods and criteria. Third, because genetic variation differs across the globe, representative populations from all ethnicities must be studied. Finally, all these data must be shared rapidly and widely to ensure the most expedited progress in research and enable investigators with the brightest ideas to utilize these data provided by patients to facilitate stroke research. The Cerebrovascular Disease Knowledge Portal (CDKP) has been created by the International Stroke Genetics Consortium (ISGC) to overcome these challenges and enable data sharing as freely and rapidly as possible.Evolution of the Revolution: Open Access to Data From High Throughput TechnologiesIn the past decade, the introduction of high throughput genotyping technologies revolutionized the way we think about, and work with, genomic data. Genome-wide genotyping arrays, whole exome sequencing, and whole genome sequencing allow us collect massive amounts of common and rare genetic data from the entire genome and agnostically test these variants for association with human disease. These new technologies have been potentiated by the creation of large collaboration networks that allow the assembly of sample sizes unimaginable not long ago. Importantly, the experience accumulated with other complex diseases indicates that the field of stroke genomics is now approaching a breakthrough point. Concretely, because the overall sample size for stroke approximates the order of 100 000 cases, and sequencing technologies are applied to existing samples, it is expected that the discovery pace for new susceptibility loci will accelerate exponentially (Figure 1).7–11 This discovery power will be especially helpful in successfully identifying low frequency and rare mutations, as well as hard-to-detect risk alleles for specific stroke subtypes and ethnic groups.12 Formed in 2007, the ISGC was created to bring together clinicians, investigators, geneticists, and statisticians to assemble the sample sizes and expertise necessary to understand the genetic underpinnings of cerebrovascular disease and leverage these discoveries to help patients.13 Through its launch of collaborative studies, including METASTROKE, the NINDS-SiGN Consortium (National Institute of Neurological Disorders and Stroke–Stroke Genetics Network), and MEGASTROKE and its partnership with the CHARGE consortium (Cohorts for Heart and Aging Research in Genomic Epidemiology),14,15 the ISGC has been responsible for most of the confirmed stroke risk loci discovered in the era of GWAS.16Download figureDownload PowerPointFigure 1. Number of genome-wide significant loci for different complex traits.Open data access is an opportunity to accelerate scientific discoveries in stroke. The CDKP is a comprehensive web-based resource that enables access and exploration of genetic and phenotypic data related to cerebrovascular diseases (available at www.cerebrovascularportal.org). The mission of the CDKP is to potentiate stroke research by democratizing access to high-quality genetic, phenotypic, and imaging data on large number of stroke patients. To accomplish this mission, the CDKP collects, securely stores, harmonizes, displays, and shares stroke genomic data with investigators from around the world. The CDKP houses 2 substantially different types of data: summary-level data and individual-level data. Summary-level data (summary statistics) consist of full sets of association results by single-nucleotide polymorphisms that form the basis of published genetic association studies; they generally cannot be used to identify individual subjects. Individual-level data consist of complete datasets containing phenotypic and genotypic information by subject. Subjects must give broad consent to allow for the sharing of their individual-level data, in part, because of the risk of identifiability.These 2 types of data are accessed through different paths (Figure 2). Summary-level data are accessed through the CDKP web-based platform itself, whereas the CDKP will direct the user to the American Heart Association Precision Medicine Platform (PMP; www.precision.heart.org) to access individual-level data. Within the PMP, individual-level data are hosted in a secure environment that allows investigators to implement complex genetic analyses without downloading the data. These analyses are run in a cloud computing-based workspace powered by Amazon Web Services. This workspace is simple to use and was specifically designed to guide and teach first-time users on how to migrate to a cloud-based ecosystem. New data and tools are constantly being incorporated to both the CDKP and the PMP.Download figureDownload PowerPointFigure 2. Data access through the Cerebrovascular Disease Knowledge Portal (CDKP). Data flow describes the generalized path that all data take through the CDKP. The end-user experience details how a user interacts with the resources. Summary-level data can be accessed through the CDKP web-based graphical user interphase designed to run queries and allow for download of data, whereas individual-level data can be accessed through the PMP to run custom analysis.Here, we describe the design and available features of this new resource, emphasizing opportunities and challenges that may arise in the near future.Design and Development of the CDKPThe creation of the CDKP, funded by the National Institute of Neurological Disorders and Stroke, has been a joint effort of the ISGC, the Broad Institute, and the American Heart Association Institute for Precision Cardiovascular Medicine. Given its extensive experience with similar projects, the Broad Institute hosts the data available through the platform and developed the informatic framework and analytic tools used by the CDKP. A dedicated steering committee, consisting of ISGC members who have contributed data to the portal, oversees the CDKP. An operations committee, consisting of ISGC members and Broad Institute staff, is responsible for the everyday operations of the CDKP. In addition, the ISGC has created a Data Access Committee that is responsible for ensuring access to all data. Any investigator wishing to contribute data to the CDKP can contact the Operations Committee at [email protected]. Several different types of data can be deposited in the CDKP, including summary statistics, raw individual-level genetic data, and postprocessing (eg, post-quality control and imputation) individual-level genetic data. Furthermore, as the CDKP evolves, there will be opportunities to deposit a broad range of phenotypic data, including imaging. Before transfer to the CDKP, proper institutional review board and legal approval for each data set is required, including assurance from the originating institution that all subjects are consented for this type of data sharing. Datasets transferred to the portal are harmonized following a standardized pipeline that evaluates the presence of important data points (such as a unique identifier for each subject) and identifies systematic errors. Phenotype–genotype harmonization takes place at the Broad Institute, which serves as the Data Coordinating Center. Individual-level data are subsequently transferred to the secure working space of the PMP.Specific Tools Available Through the CDKPWithin the CDKP and PMP, genomic data can be accessed through 3 main tools: (1) a graphical user interphase that allows quick and easy exploration of both individual- and summary-level data contained in the portal, (2) a repository of full sets of summary-level data produced by landmark-published studies in the field, and (3) a repository of individual-level data that investigators can analyze directly in a secure workspace (Figure 2).Web-Based Graphical User InterphaseThe graphical user interphase offers users a wide menu of integrated tools for data visualization and analysis, as well as the possibility to implement on-the-fly descriptive and association analyses focused on specific items of interest: base-pair positions, genomic regions, genes, or single-nucleotide polymorphisms, to name a few possibilities. Users can also explore descriptive and association results from GWAS of other related (hypercholesterolemia, hypertension, diabetes mellitus, and coronary artery disease) and unrelated traits (psychiatric conditions). Figures, tables, and results generated with this tool can be easily exported and downloaded. This functionality does not require a formal request, although users are required to register to use the portal.Summary-Level Data (Summary Statistics)The CDKP contains full sets of summary statistics from landmark-published studies. Because all association results are provided without filtering for specific P value thresholds, several million results are available for each specific study. These summary-level data can be accessed through a single mouse click, without submitting a formal application. The rationale for this strategy is to encourage and accelerate preliminary analyses to evaluate different working hypotheses. By providing summary-level results from published studies only, users can easily identify the methods and study populations that were used to generate the summary statistics. Although the majority of currently available stroke data comes from subjects of European descent, data from populations of African-American, African, and Asian descent are scheduled to be added in the coming year. Each set of summary statistics has an accompanying document that describes the rules and limitations of use, including (1) data are provided as-is, meaning each user is responsible for the design, implementation, and interpretation of any analyses based on this summary-level data; (2) commercial use of these data is prohibited (including deposition of these data into commercial databases); (3) cohorts of stroke cases and matched controls are usually used by >1 study; consequently, it is the user’s responsibility to check for possible overlaps when using summary statistics from different studies; and (4) scientific communications based on CDKP data must acknowledge the use of the portal. Currently, the CDKP contains full sets of results from 4 landmark papers (Table 1), and this list will rapidly grow in coming months.Table 1. Summary-Level Data (Summary Statistics) Contained in the International Stroke Genetics Consortium Cerebrovascular Disease Knowledge PortalReference NumberAuthorYearPhenotypeDiscovered LociTitlePMC3980413Woo et al201" @default.
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