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Open Access Research article

Validation of PhenX measures in the personalized medicine research project for use in gene/environment studies

Catherine A McCarty1*, Richard Berg2, Carla M Rottscheit2, Carol J Waudby2, Terrie Kitchner2, Murray Brilliant2 and Marylyn D Ritchie3

Author Affiliations

1 Division of Research, Essentia Institute of Rural Health, 502 East Second Street, Duluth, MN 55805, USA

2 Marshfield Clinic Research Foundation, Marshfield, USA

3 Pennsylvania State University, University Park, USA

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BMC Medical Genomics 2014, 7:3  doi:10.1186/1755-8794-7-3

Published: 14 January 2014

Abstract

Background

The purpose of this paper is to describe the data collection efforts and validation of PhenX measures in the Personalized Medicine Research Project (PMRP) cohort.

Methods

Thirty-six measures were chosen from the PhenX Toolkit within the following domains: demographics; anthropometrics; alcohol, tobacco and other substances; cardiovascular; environmental exposures; cancer; psychiatric; neurology; and physical activity and physical fitness. Eligibility criteria for the current study included: living PMRP subjects with known addresses who consented to future contact and were not currently living in a nursing home, available GWAS data from eMERGE I for subjects where age-related cataract, HDL, dementia and resistant hypertension were the primary phenotypes, thus biasing the sample to the older PMRP participants. The questionnaires were mailed twice. Data from the PhenX measures were compared with information from PMRP questionnaires and data from Marshfield Clinic electronic medical records.

Results

Completed PhenX questionnaires were returned by 2271 subjects for a final response rate of 70%. The mean age reported on the PhenX questionnaire (73.1 years) was greater than the PMRP questionnaire (64.8 years) because the data were collected at different time points. The mean self-reported weight, and subsequently calculated BMI, were less on the PhenX survey than the measured values at the time of enrollment into PMRP (PhenX means 173.5 pounds and BMI 28.2 kg/m2 versus PMRP 182.9 pounds and BMI 29.6 kg/m2). There was 95.3% agreement between the two questionnaires about having ever smoked at least 100 cigarettes. 139 (6.2%) of subjects indicated on the PhenX questionnaire that they had been told they had a stroke. Of them, only 15 (10.8%) had no electronic indication of a prior stroke or TIA. All of the age-and gender-specific 95% confidence limits around point estimates for major depressive episodes overlap and show that 31% of women aged 50–64 reported symptoms associated with a major depressive episode.

Conclusions

The approach employed resulted in a high response rate and valuable data for future gene/environment analyses. These results and high response rate highlight the utility of the PhenX Toolkit to collect valid phenotypic data that can be shared across groups to facilitate gene/environment studies.