The CDC Public Health Genomics and Precision Health Knowledge Base (PHGKB) is an online, continuously updated, searchable database of published scientific literature, CDC resources, and other materials that address the translation of genomics and precision health discoveries into improved health care and disease prevention. The Knowledge Base is curated by CDC staff and is regularly updated to reflect ongoing developments in the field. This compendium of databases can be searched for genomics and precision health related information on any specific topic. We will continue to add additional features to the knowledge base and are interested in your feedback via email.
Database Content (Last Updated: Oct 25, 2020)
COVID-19 GPH is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other materials that captures emerging discoveries and applications of genomics, molecular and other precision medicine and precision public health tools in the investigation and control of COVID-19. Contents include PubMed records via an automated pubmed search algorithm, the relevant information picked by experts, and linkages to contents from our curated PHGKB databases.
This database includes general CDC and NIH public health information on specific diseases and health related topics. When available, the database displays genomic information from various CDC and NIH web pages. Users are also encouraged to conduct searches of CDC and NIH websites for additional information.
This database contains CDC-authored scientific publications on genomics and precision health-related topics, and includes articles on infectious diseases, reproductive health, newborn screening, birth defects, developmental disabilities, genetic testing, chronic diseases such as cancer and diabetes, environmental and occupational health, laboratory methods, bioinformatics, and statistical methods.
This database includes published scientific literature on evidence-based translation of genomic and precision health discoveries into improved health care and population health. The database features information on topics that include reproductive health, birth defects, newborn screening, chronic diseases such as cancer and diabetes, pharmacogenomics, and family health history, guidelines and recommendations.
This database contains guidelines from the Genomics and Precision Health Database, sorted according to the highest evidence tier level that could be assigned to recommendations from each guideline. The sorting process is based on our previous method for classifying genomic applications (described in Clinical Pharmacology and Therapeutics, 2014), except that guideline documents rather than clinical scenarios are sorted according to evidence level'
The State Public Health Genomics Programs database has information about state public health programs and activities relevant to genomics. States have implemented genomics applications for Hereditary Breast and Ovarian Cancer syndrome, Lynch Syndrome, Familial Hypercholesterolemia, newborn screening, and more. Find relevant information from your own state or learn about what's been accomplished in other states. You can filter results by condition and resource type (data, programs, education, policy, tools, and general information. You can also view the content of the database using State Public Health Genomics Programs Map
This database includes published scientific literature, popular press articles, tools, and databases on the emerging role of pathogen genomics and host-pathogen interactions in infectious disease control and prevention. It includes information on methods, evolution and pathogenicity, detection and diagnosis, outbreaks, epidemiology and transmission, antimicrobials, and vaccines and host-pathogen interactions. The database contains items from all previous weekly editions of Advanced Molecular Detection Clips, as well as from the current edition. Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media.
HuGE Literature Finder is a search engine for finding published literature on genetic associations and other human genome epidemiology. The search query can include disease/outcome, environmental factors, genes,author's name, affiliation, etc. The results can be further refined by the filtering feature.The list of selected articles can be redirected to the PubMed website to take advantage of the functionalityit provides, such as uploading to reference software.
Variant Variant Name Mapper maps common gene variant names to their corresponding rs numbers using information compiled from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, OMIM, HuGE Navigator, LSDBs.
Genomics & Health Impact Weekly Scan This weekly update features emerging roles of human genomics, testing and interventions in a wide variety of noncommunicable diseases across the life span, including, birth defects, newborn screening, reproductive health, childhood diseases, cancer, chronic diseases, pharmacogenomics, family health history, guidelines and recommendations. The weekly sweep also includes news, reviews, commentaries, tools and databases.
Advanced Molecular Detection Clips Advanced Molecular Detection(AMD) Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in public health surveillance, investigation, and development of new diagnostics and interventions. The collection is not comprehensive but aims to capture highlights, while surveying a wide range of topics. CDC-authored articles are flagged.
Non-Genomics Precision Health Update The latest information and publications on the impact of big data science, machine learning and predictive analytics on public health.
CDC-authored Publications Update The latest CDC publications in genomics and precision health.
COVID-19 Genomics and Precision Public Health Weekly UpdateThis weekly update contains the latest information and publications on the impact of genomics and precision health technologies on the investigation and control of COVID-19. Items that are selected by staff from the CDC Office of Genomics and Precision Public Health daily from the COVID-19 GPH
Specialized PHGKBs are the subset databases of the overall PHGKB for specific domains. Currently four specialized PHGKBs are available. We will make more specialized PHGKBs in the future.
- Cancer PHGKB
- Diabetes PHGKB
HLBS-PopOmics is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other materials that address the translation of genomic discoveries into improved health care and prevention related to Heart and Vascular Diseases(H), Lung Diseases(L), Blood Diseases(B), and Sleep Disorders(S). HLBS-PopOmics is a specialized database of the overall PHGKB.
- Rare Diseases PHGKB
Rare Disease PHGKB is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other information that address the public health impact and translation of genomic discoveries into improved health outcomes related to rare diseases. Rare Diseases PHGKB is a specialized database of the overall PHGKB and was developed with direct links to the NIH Genetics and Rare Disease Information Center. In the United States, a rare disease is defined as a condition that affects fewer than 200,000 people. There may be as many as 7,000 rare diseases. Only a few types of rare diseases are tracked when a person is diagnosed. These include certain infectious diseases, birth defects, and cancers. It also includes the diseases on state newborn screening tests. Browse the full list of A-Z list of rare diseases on the NIH website.
- Infectious Diseases PHGKB
Cancer PHGKB is an online, continuously updated, searchable database of published scientificliterature, CDC and NIH resources, and other materials thataddress the translation of genomic discoveries into improved health care and prevention related to cancer. Cancer PHGKB is a specialized database of the overall PHGKB.
Cancer PHGKB is an online, continuously updated, searchable database of published scientificliterature, CDC and NIH resources, and other materials thataddress the translation of genomic discoveries into improved health care and prevention related to diabetes. Cancer PHGKB is a specialized database of the overall PHGKB.
Infectious Diseases Cancer PHGKB is an online, continuously updated, searchable database of published scientific literature, CDC and NIH resources, and other materials that address the impact of genomics, advanced molecular detection, and precision health technologies on the control and prevention of infectious diseases. Infectious Diseases PHGKB is a specialized database of the overall PHGKB.
- Wei Yu, Marta Gwinn, Muin J. Khoury. A New Resource for Genomics and Precision Health Information and Publications on the Investigation and Control of COVID-19 and other Coronaviruses. BIORXIV, April 21, 2020.
- Mensah GA, Yu W, Barfield WL, Clyne M, Engelgau MM, Khoury MJ. HLBS-PopOmics: an online knowledge base to accelerate dissemination and implementation of research advances in population genomics to reduce the burden of heart, lung, blood, and sleep disorders. Genet Med. 2018 Sep 10. doi: 10.1038/s41436-018-0118-1
- Genomics and Health Impact Blog Posted on November 20, 2017 by Wei Yu and Muin J. Khoury Public health genomics information is now easily accessible online
- Yu W, Gwinn M, Dotson WD, Green RF, Clyne M, Wulf A, Bowen S, Kolor K, Khoury MJ. A knowledge base for tracking the impact of genomics on population health Genet Med.2016 Dec;18(12):1312-1314
- Genomics and Health Impact Blog Posted on November 4, 2015 by Muin J. Khoury and Wei Yu, Dealing with the Genomics and Health Information Overload: Introducing the CDC Public Health Genomics Knowledge Base
- Clyne M, Schully SD, Dotson WD, Douglas MP, Gwinn M, Kolor K, Wulf A, Bowen MS, Khoury MJ. Horizon scanning for translational genomic research beyond bench to bedside. Genet Med. 2014 Jan 9.
- Dotson WD, Douglas MP, Kolor K, Stewart AC, Bowen MS, Gwinn M, Wulf A, Anders HM, Chang CQ, Clyne M, Lam TK, Schully SD, Marrone M, Feero WG, Khoury MJ. Prioritizing genomic applications for action by level of evidence: a horizon-scanning method. Clin Pharmacol Ther. 2014 Apr;95(4):394-402.
- Yu W, Yesupriya A, Wulf A, Hindorff LA, Dowling N, Khoury MJ, Gwinn M. GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies. Eur J Hum Genet. 2011 Oct;19(10):1095-9.
- Yu W, Clyne M, Khoury MJ, Gwinn M. Phenopedia and Genopedia: Disease-centered and Gene-centered Views of the Evolving Knowledge of Human Genetic Associations. Bioinformatics. 2010 Jan 1;26(1):145-6. Epub 2009 Oct 27.
- Yu W, Ned R, Wulf A, Liu T, Khoury MJ, Gwinn M. The need for genetic variant naming standards in published abstracts of human genetic association studies. BMC Res Notes. 2009 Apr 14; 2:56.
- Yu W, Clyne M, Dolan SM, Yesupriya A, Wulf A, Liu T, Khoury MJ, Gwinn M. GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique. BMC Bioinformatics. 2008 Apr 22;9:205.
- Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ. A navigator for human genome epidemiology. Nat Genet. 2008 Feb;40(2):124-5.
- Yu W, Wulf A, Liu T, Khoury MJ, Gwinn M. Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases. BMC Bioinformatics. 2008 Dec 8; 9:528.
- Yu W, Yesupriya A, Wulf A, Qu J, Gwinn M, Khoury MJ. An automatic method to generate domain-specific investigator networks using PubMed abstracts. BMC Med Inform Decis Mak 2007 Jun 20;7(1):17.
- Yu W, Yesupriya A, Wulf A, Qu J, Khoury MJ, Gwinn M. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. BMC Bioinformatics. 2007 Nov 9;8:436.