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Dealing with the Genomics and Health Information Overload: Introducing the CDC Public Health Genomics Knowledge Base

Posted on by Muin J. Khoury and Wei Yu, Office of Public Health Genomics, Centers for Disease Control and Prevention

home page of the PHGkb database

Understanding genetic information is increasingly becoming important for health decision making for a variety of health conditions across the lifespan.

The amount of genome-related information is growing exponentially, but it is scattered all over the web, peer-reviewed literature, and public and private databases. The CDC Office of Public Health Genomics has launched the beta version of the Public Health Genomics Knowledge Base (PHGKB), in an effort to continue capturing evolving snapshots of the field while tracking the translational trajectory of scientific discoveries into population health impact.

Twenty five years after the launch of the Human Genome Project, advances in genomics and related fields are proceeding at an ever accelerating pace. Resulting information is beginning to affect all facets of the practice of medicine and public health.  From the diagnosis of rare genetic diseases to the prevention of common chronic diseases, we are witnessing the growth of an unprecedented amount of information that will be increasingly useful in preventing and treating human diseases. The plethora of genomic information on human pathogens is already deeply affecting the landscape of the medical and public health fight against infectious diseases. In addition, the public has an increasing thirst for genetic information about themselves and their health. As the recently launched precision medicine initiative and other efforts will lead to millions of people having their genomes sequenced in the next decade, there is a need for credible and scientifically based information on what genomic information means for health and how it can be used to reduce the burden of human diseases.

For more than a decade, the CDC Office of Public Health Genomics has attempted to capture an emerging snapshot of the field through our weekly horizon scanning of genomics publications and products from CDC and elsewhere. In 2008, we launched the online searchable database- the Human Genome Epidemiology Navigator  – to monitor progress on the rapidly evolving literature on human genes and diseases. This database recently celebrated the milestone of surpassing 100,000 online curated publications. More recently, we started tracking the exploding field of pathogen genomics through the weekly advanced molecular detection clips.

The newly launched PHGKB collects and presents the new developing hot topics on public health and genomics insights and discoveries in a timely fashion through constant horizon scanning and curation of a variety data sources from CDC products, genetic practice guidelines and evidence synthesis, human genome epidemiology, infectious disease advanced molecular detection searches and others. The PHGKB is composed of multiple databases that the users can search independently or as a group as well as customized links to relevant external resources of information. Users can use one or more search terms using “and” “or” combinations.  The results are arranged according to type of information (see box for search results on “breast cancer” conducted October November 2).

screenshot of the PHGkb search results for breast cancer

The PHGKB information is currently far from complete or comprehensive. Many items are manually curated and were started in 2015. Other components, like contents of the HuGE Navigator are now fully automated using machine learning algorithms. We hope that “smarter” ways of searching will be integrated over time.  We are currently actively seeking user input to enhance the functionality of the database as well as tips on credible sources of information PHGB can link to. This is very much a work in progress and we ask readers for patience and more importantly feedback on PHGKB.

Ultimately, we hope that PHGKB can be beneficial to researchers, policy makers, practitioners and the general public interested in understanding the complicated landscape on genomics and health. We believe that genetically literate public and health practitioners are key to the responsible and effective translation of genomic sciences to improve population health. Send your comments to genetics@cdc.gov or post a comment below.

Posted on by Muin J. Khoury and Wei Yu, Office of Public Health Genomics, Centers for Disease Control and PreventionTags , , , ,

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