Informatics Research Seminar: The PhenX Toolkit: Get the Most from Your Measures

September 26 @ 4:00 – 5:00 pm

 

Speaker: Carol Hamilton, MD
Presented from Duke University

Broadcast Link: Seminar

 

 

Abstract:

The PhenX (consensus measures for Phenotypes and eXposures) Toolkit (https://www.phenxtoolkit.org/) is an online resource that catalogs broadly validated and well-established measures of phenotypes and exposures for use in genomic and other types of
studies involving human subjects.  The PhenX Toolkit currently includes 295 measures that provide assessments of phenotypes and exposures for 21 research domains and 44 measures selected to support Substance Abuse and Addiction (SAA) research.  Released in 2009, the Toolkit has logged 320,000 visits, and currently has almost 900 Registered Users.    Investigators can find measures of interest by browsing domains, collections or measures, or by searching using the Smart Query Tool.  For each measure, the Toolkit provides a description of the measure, the rationale for its inclusion, detailed protocol(s) for collecting the data, and supporting
documentation.  Another project, PhenX RISING (Real world, Implementation, SharING), brings together seven investigators awarded funds to incorporate PhenX measures into existing, population-based genomic studies.    The Toolkit provides tools to help investigators integrate PhenX measures into their study design, providing custom data collection worksheets to support data collection and custom data dictionaries to facilitate data submission to the database of Genotypes and Phenotypes (dbGaP).  In an
effort to link PhenX measures with data that is already in dbGaP, PhenX measures were mapped to 16 dbGaP studies in a pilot study.  The advanced search in dbGaP now includes PhenX as an option.  This approach will help investigators identify studies in dbGaP that may be well-suited for various cross-study analyses.

BioSketch:

Dr. Hamilton earned a BS in Botany at the University of CA, Davis, and a PhD in Genetics from the University of Georgia.  She has experience in biochemistry, molecular biology, technology development, data management, and analysis of genomic and clinical data.  She has been involved in the development of bioinformatics and analytic systems for a variety of technologies, including DNA sequencing, RNA expression profiling, metabolic profiling, and phenotype profiling. Research areas have included biomarker discovery for monitoring drug safety, efficacy, and target identification. Key areas of interest are the visualization and analysis of complex data sets that include genotype, phenotype (including “-omics”) and environmental exposures data.  Dr. Hamilton is currently the principal investigator of PhenX (pronounced “phoenix”; consensus measures for Phenotypes and eXposures), a
cooperative agreement funded by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH).  Led by RTI, and driven by the scientific community, PhenX has established a toolkit of standard measures for use in genome-wide association studies (GWAS) and other studies involving human subjects.