Skip to main content
Premium Trial:

Request an Annual Quote

RTI to Use $5.3M NHGRI Grant to Expand Web-based Resource of Phenotype and Exposure Measures

Premium

RTI International has been awarded a $5.3 million, four-year grant from the National Human Genome Research Institute to expand and update the PhenX Toolkit, a free web-based resource that provides standard measures related to complex diseases, phenotypic traits, and environmental exposures.

According to the grant abstract, over the next four years, RTI will "implement a rolling review and update of the 21 research domains" contained in the toolkit, integrate Chinese and Spanish translations of Toolkit protocols, and make PhenX measures visible in all completed studies deposited in the National Center for Biotechnology Information's Database of Genotypes and Phenotypes. The non-profit institute will also take steps to attract additional users to the toolkit and raise awareness of its value to the scientific community.

Joe Pratt, project manager for the PhenX toolkit and an associate director at RTI, told BioInform that four new domains will be added to the toolkit. "We have a steering committee that we are in the process of selecting for this new award and they are the expert group that helps determine …what those domains are," he said.

RTI is also partnering with the dbGAP's developers to connect the PhenX measures to corresponding study data in the repository. The toolkit provides "access to the measures that are used for collection themselves [but] it's not a collection of the data," Pratt explained. "So, when a collection of data does occur, [in] dbGAP … we make the tie to those data elements that were collected … that are related to [current] PhenX measures," he said.

RTI has led efforts to develop the resource since it was launched in 2007, with a $6.8 million NHGRI grant to provide measures for large-scale genome-wide association and epidemiological studies (BI 11/16/2007). The toolkit — which has over 1,100 registered users — currently contains 339 measures grouped under 21 domains including cancer, cardiovascular, diabetes, and infectious diseases and immunity. The list of measures covers things like family history, blood pressure levels, stress, biological assays, substance abuse, vaccine use, and more.

The measures were selected by several working groups from institutions such as Roswell Park Cancer Institute, University of California, San Francisco, Mayo Clinic, Harvard University, Northwestern University, Emory University, and more with input from the community at large.

According to Carol Hamilton, RTI's director of bioinformatics and PhenX principal investigator, it is "a great resource" for investigators looking to expand their study design. "Because common, complex diseases share many risk factors, identification of these factors increases with the use of common measures in research studies," she said in a statement.

Since its launch, measures from the PhenX toolkit have supported studies like this one from researchers in the University of Oklahoma Health Sciences Center, which examined vitamin D efficiency and cardio-metabolic risk in a Northern India population with a high prevalence of type 2 diabetes. It was also used in a Pennsylvania State University-led study that explored gene-gene and gene-environment interactions in cataract cases.

Filed under

The Scan

Push Toward Approval

The Wall Street Journal reports the US Food and Drug Administration is under pressure to grant full approval to SARS-CoV-2 vaccines.

Deer Exposure

About 40 percent of deer in a handful of US states carry antibodies to SARS-CoV-2, according to Nature News.

Millions But Not Enough

NPR reports the US is set to send 110 million SARS-CoV-2 vaccine doses abroad, but that billions are needed.

PNAS Papers on CRISPR-Edited Cancer Models, Multiple Sclerosis Neuroinflammation, Parasitic Wasps

In PNAS this week: gene-editing approach for developing cancer models, role of extracellular proteins in multiple sclerosis, and more.