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Review
. 2010 Apr;21(2):136-40.
doi: 10.1097/MOL.0b013e3283377395.

PhenX: a toolkit for interdisciplinary genetics research

Patrick J Stover  1 , William R Harlan, Jane A Hammond, Tabitha Hendershot, Carol M Hamilton
Affiliations
Review

PhenX: a toolkit for interdisciplinary genetics research

Patrick J Stover et al. Curr Opin Lipidol. 2010 Apr.

Abstract

Purpose of review: To highlight standard PhenX (consensus measures for Phenotypes and eXposures) measures for nutrition, dietary supplements, and cardiovascular disease research and to demonstrate how these and other PhenX measures can be used to further interdisciplinary genetics research.

Recent findings: PhenX addresses the need for standard measures in large-scale genomic research studies by providing investigators with high-priority, well established, low-burden measurement protocols in a web-based toolkit (https://www.phenxtoolkit.org). Cardiovascular and Nutrition and Dietary Supplements are just 2 of 21 research domains and accompanying measures included in the PhenX Toolkit.

Summary: Genome-wide association studies (GWAS) provide promise for the identification of genomic markers associated with different disease phenotypes, but require replication to validate results. Cross-study comparisons typically increase statistical power and are required to understand the roles of comorbid conditions and environmental factors in the progression of disease. However, the lack of comparable phenotypic, environmental, and risk factor data forces investigators to infer and to compare metadata rather than directly combining data from different studies. PhenX measures provide a common currency for collecting data, thereby greatly facilitating cross-study analysis and increasing statistical power for identification of associations between genotypes, phenotypes, and exposures.

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Figures

Figure 1
Figure 1. Gene–environment interactions in the ontogeny of disease
The diagram illustrates how an individual’s genome and environment interact and contribute to risk phenotypes which are associated with the development of disease.
See this image and copyright information in PMC

References

    1. Pennisi E. Breakthrough of the year: human genetic variation. Science 2007; 318:1842–1843. - PubMed
    1. Pearson TA, Manolio TA. How to interpret a genome-wide association study. J Am Med Assoc 2008; 299:1335–1344. - PubMed

    1. Hamilton CM, Strader LC, Pratt JG, et al. The PhenX Toolkit: get the most from your measures. Paper presented at the American Society of Human Genetics (ASHG) Annual Meeting, October 20–24, 2009; Honolulu, HI.

      • This presentation highlighted the PhenX project. The goal of the project is to facilitate cross-study comparisons by providing standard measures of phenotype and environmental exposures for use in genome-wide association studies (GWAS) and other large-scale genomic studies.

    1. Smith CE, Ordovás JM. Fatty acid interactions with genetic polymorphisms for cardiovascular disease. Curr Opin Clin Nutr Metab Care 2009. [Epub ahead of print].

      •• This excellent review considers the limitations and challenges in investigating gene–diet associations.

    1. Stover PJ, Caudill M. Genetic and epigenetic contributions to human nutrition and health: managing genome-diet interactions. J Am Diet Assoc 2008; 108:1480–1487. - PMC - PubMed

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