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. 2012 May;33(5):849-57.
doi: 10.1002/humu.22074. Epub 2012 Apr 3.

Using PhenX measures to identify opportunities for cross-study analysis

Huaqin Pan  1 , Kimberly A Tryka, Daniel J Vreeman, Wayne Huggins, Michael J Phillips, Jayashri P Mehta, Jacqueline H Phillips, Clement J McDonald, Heather A Junkins, Erin M Ramos, Carol M Hamilton
Affiliations

Using PhenX measures to identify opportunities for cross-study analysis

Huaqin Pan et al. Hum Mutat. 2012 May.

Abstract

The PhenX Toolkit provides researchers with recommended, well-established, low-burden measures suitable for human subject research. The database of Genotypes and Phenotypes (dbGaP) is the data repository for a variety of studies funded by the National Institutes of Health, including genome-wide association studies. The dbGaP requires that investigators provide a data dictionary of study variables as part of the data submission process. Thus, dbGaP is a unique resource that can help investigators identify studies that share the same or similar variables. As a proof of concept, variables from 16 studies deposited in dbGaP were mapped to PhenX measures. Soon, investigators will be able to search dbGaP using PhenX variable identifiers and find comparable and related variables in these 16 studies. To enhance effective data exchange, PhenX measures, protocols, and variables were modeled in Logical Observation Identifiers Names and Codes (LOINC® ). PhenX domains and measures are also represented in the Cancer Data Standards Registry and Repository (caDSR). Associating PhenX measures with existing standards (LOINC® and caDSR) and mapping to dbGaP study variables extends the utility of these measures by revealing new opportunities for cross-study analysis.

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Conflict of interest statement

Conflicts of interest - none.

Figures

Figure 1
Figure 1
Screen shot of the report page for dbGaP variable phv00111936. In the column “Mapping,” a green circle indicates that the mapping result is “comparable”; a half-filled yellow circle indicates that the mapping result is “related.” The links below “PhenX Variable” take the user to a complete list of dbGaP variables with mapping to the PhenX variable. The “Measure” links take the user to the PhenX website Measures page.
Figure 2
Figure 2
A plot that shows the number of dbGaP mappings to PhenX as a function of the PhenX measure.
Figure 3
Figure 3
An example of accessory (image) content for a PhenX variable as represented in (Logical Observation Identifiers Names and Codes) LOINC.
Figure 4
Figure 4
Common Data Elements (CDEs) for PhenX domains listed in CDE Browser.
See this image and copyright information in PMC

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