The PhenX Toolkit for Biomedical Research

A catalog of consensus measures for phenotypes and exposures for use in biomedical research

National Human Genome Research Institute

Until recently, doctors have been unable to customize treatments based on individual variations in genes, environment, and lifestyle. Achieving this tailored approach, known as precision medicine, depends on gathering and analyzing large amounts of data on human genetics, health status, and lifestyle.

As genotyping technology advanced in the mid-2000s, the scientific community confronted a problem. Genome-wide association studies (GWAS) dramatically increased because investigators realized the technology’s potential to impact medicine. However, the numbers of study participants were often too low to get the statistical power needed to identify associations between genotypes, environmental exposures, disease susceptibility, and outcomes.

When investigators looked for collaborators with whom to combine and compare their results, they noticed they had almost no measures in common. For example, there are many ways to ask about income—personal, household, monthly, annual—but unless the question is asked the same way with the same answer choices, it is quite challenging to compare results across studies.

Recognizing this, the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) sought to fund a project to identify standard measures for GWAS. In 2007, RTI was engaged to lead a consensus-based process under a project now known as PhenX (consensus measures for Phenotypes and eXposures).

Bringing Together Experts to Create a Catalog of High-Priority, Low-Burden Measures

A community driven project, PhenX assembles working groups of domain experts who identify measures with the highest priority and lowest burden for investigators conducting GWAS and other biomedical studies. Input from the Steering Committee and the NIH Institutes and Centers helps guide the content and the process. This has resulted in the PhenX Toolkit, a web-based catalog of standard measures for use in biomedical research.

To date, the PhenX Toolkit includes nearly 500 measures across 23 research domains in the areas of medicine, public health, and social science.

These measures range from medical tests, such as Complete Blood Count, to questionnaires dealing with mental conditions, social circumstances, and environmental exposures. The PhenX Toolkit is publicly available at no cost to researchers. By using measures in the PhenX Toolkit, scientists in a variety of fields can collect data using the same methodology, thus facilitating cross-study analysis and increasing the overall impact of their study. 

Broad Adoption of PhenX Measures in Medical Research 

Since its release in 2009, the PhenX Toolkit has drawn more than 2,000 registered users from 155 nations. The site currently draws more than 300 visitors per day.

PhenX Toolkit measures are being broadly adopted in medical research, including

  • The GuLF study – An assessment of the human health effects of the BP/Deepwater Horizon oil spill by the National Institute of Environmental Health Sciences
  • The NEIGHBOR Consortium – A collaborative effort to identify genetic variants that contribute to glaucoma, funded by the National Eye Institute
  • Children’s Health After the Storm (CHATS) – An investigation by the Centers for Disease Control and Prevention of environmental exposures in children who lived in temporary housing provided by the Federal Emergency Management Agency (FEMA) during Hurricanes Katrina and Rita

The Toolkit includes a place for researchers to register studies to help build their networking capabilities. There is also an annotation tool to gather information from clinicians about how they are using PhenX measures to care for people with rare genetic conditions, sickle cell disease, and other conditions for which the measures might also be used. This type of information provides greater utility to the measures in the Toolkit.

The Future of PhenX

Under our leadership, PhenX continues to grow and evolve.  Interest from the National Institute on Drug Abuse and other NIH institutes has supported expansion of the toolkit into special collections of measures in such fields as substance abuse and addiction, sickle cell disease, tobacco regulatory research, and mental health research. We are adding Spanish and Chinese translations, and have made PhenX protocols available in a format compatible with REDCap (Research Electronic Data Capture), a secure Web application for building and managing online surveys and databases.

As we continue to expand the PhenX Toolkit, our aim is to increase its relevance and utility in support of genetic research and the future of precision medicine.