Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank

Molly Hall, Scott M. Dudek, Robert Goodloe, Dana C. Crawford, Sarah A. Pendergrass, Peggy Peissig, Murray Brilliant, Catherine A. McCarty, Marylyn Deriggi Ritchie

Research output: Contribution to journalConference article

22 Citations (Scopus)

Abstract

Environment-wide association studies (EWAS) provide a way to uncover the environmental mechanisms involved in complex traits in a high-throughput manner. Genome-wide association studies have led to the discovery of genetic variants associated with many common diseases but do not take into account the environmental component of complex phenotypes. This EWAS assesses the comprehensive association between environmental variables and the outcome of type 2 diabetes (T2D) in the Marshfield Personalized Medicine Research Project Biobank (Marshfield PMRP). We sought replication in two National Health and Nutrition Examination Surveys (NHANES). The Marshfield PMRP currently uses four tools for measuring environmental exposures and outcome traits: 1) the PhenX Toolkit includes standardized exposure and phenotypic measures across several domains, 2) the Diet History Questionnaire (DHQ) is a food frequency questionnaire, 3) the Measurement of a Person's Habitual Physical Activity scores the level of an individual's physical activity, and 4) electronic health records (EHR) employs validated algorithms to establish T2D case-control status. Using PLATO software, 314 environmental variables were tested for association with T2D using logistic regression, adjusting for sex, age, and BMI in over 2,200 European Americans. When available, similar variables were tested with the same methods and adjustment in samples from NHANES III and NHANES 1999-2002. Twelve and 31 associations were identified in the Marshfield samples at p<0.01 and p<0.05, respectively. Seven and 13 measures replicated in at least one of the NHANES at p<0.01 and p<0.05, respectively, with the same direction of effect. The most significant environmental exposures associated with T2D status included decreased alcohol use as well as increased smoking exposure in childhood and adulthood. The results demonstrate the utility of the EWAS method and survey tools for identifying environmental components of complex diseases like type 2 diabetes. These high-throughput and comprehensive investigation methods can easily be applied to investigate the relation between environmental exposures and multiple phenotypes in future analyses.

Original languageEnglish (US)
Pages (from-to)200-211
Number of pages12
JournalPacific Symposium on Biocomputing
StatePublished - Jan 1 2014
Event19th Pacific Symposium on Biocomputing, PSB 2014 - Kohala Coast, United States
Duration: Jan 3 2014Jan 7 2014

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Precision Medicine
Nutrition
Medical problems
Type 2 Diabetes Mellitus
Nutrition Surveys
Medicine
Health
Environmental Exposure
Research
Throughput
Phenotype
Social Adjustment
Electronic Health Records
Genome-Wide Association Study
Logistics
Alcohols
Software
Genes
Logistic Models
Smoking

All Science Journal Classification (ASJC) codes

  • Medicine(all)

Cite this

Hall, M., Dudek, S. M., Goodloe, R., Crawford, D. C., Pendergrass, S. A., Peissig, P., ... Ritchie, M. D. (2014). Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank. Pacific Symposium on Biocomputing, 200-211.
Hall, Molly ; Dudek, Scott M. ; Goodloe, Robert ; Crawford, Dana C. ; Pendergrass, Sarah A. ; Peissig, Peggy ; Brilliant, Murray ; McCarty, Catherine A. ; Ritchie, Marylyn Deriggi. / Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank. In: Pacific Symposium on Biocomputing. 2014 ; pp. 200-211.
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abstract = "Environment-wide association studies (EWAS) provide a way to uncover the environmental mechanisms involved in complex traits in a high-throughput manner. Genome-wide association studies have led to the discovery of genetic variants associated with many common diseases but do not take into account the environmental component of complex phenotypes. This EWAS assesses the comprehensive association between environmental variables and the outcome of type 2 diabetes (T2D) in the Marshfield Personalized Medicine Research Project Biobank (Marshfield PMRP). We sought replication in two National Health and Nutrition Examination Surveys (NHANES). The Marshfield PMRP currently uses four tools for measuring environmental exposures and outcome traits: 1) the PhenX Toolkit includes standardized exposure and phenotypic measures across several domains, 2) the Diet History Questionnaire (DHQ) is a food frequency questionnaire, 3) the Measurement of a Person's Habitual Physical Activity scores the level of an individual's physical activity, and 4) electronic health records (EHR) employs validated algorithms to establish T2D case-control status. Using PLATO software, 314 environmental variables were tested for association with T2D using logistic regression, adjusting for sex, age, and BMI in over 2,200 European Americans. When available, similar variables were tested with the same methods and adjustment in samples from NHANES III and NHANES 1999-2002. Twelve and 31 associations were identified in the Marshfield samples at p<0.01 and p<0.05, respectively. Seven and 13 measures replicated in at least one of the NHANES at p<0.01 and p<0.05, respectively, with the same direction of effect. The most significant environmental exposures associated with T2D status included decreased alcohol use as well as increased smoking exposure in childhood and adulthood. The results demonstrate the utility of the EWAS method and survey tools for identifying environmental components of complex diseases like type 2 diabetes. These high-throughput and comprehensive investigation methods can easily be applied to investigate the relation between environmental exposures and multiple phenotypes in future analyses.",
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Hall, M, Dudek, SM, Goodloe, R, Crawford, DC, Pendergrass, SA, Peissig, P, Brilliant, M, McCarty, CA & Ritchie, MD 2014, 'Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank', Pacific Symposium on Biocomputing, pp. 200-211.

Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank. / Hall, Molly; Dudek, Scott M.; Goodloe, Robert; Crawford, Dana C.; Pendergrass, Sarah A.; Peissig, Peggy; Brilliant, Murray; McCarty, Catherine A.; Ritchie, Marylyn Deriggi.

In: Pacific Symposium on Biocomputing, 01.01.2014, p. 200-211.

Research output: Contribution to journalConference article

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T1 - Environment-wide association study (EWAS) for type 2 diabetes in the Marshfield Personalized Medicine Research Project Biobank

AU - Hall, Molly

AU - Dudek, Scott M.

AU - Goodloe, Robert

AU - Crawford, Dana C.

AU - Pendergrass, Sarah A.

AU - Peissig, Peggy

AU - Brilliant, Murray

AU - McCarty, Catherine A.

AU - Ritchie, Marylyn Deriggi

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N2 - Environment-wide association studies (EWAS) provide a way to uncover the environmental mechanisms involved in complex traits in a high-throughput manner. Genome-wide association studies have led to the discovery of genetic variants associated with many common diseases but do not take into account the environmental component of complex phenotypes. This EWAS assesses the comprehensive association between environmental variables and the outcome of type 2 diabetes (T2D) in the Marshfield Personalized Medicine Research Project Biobank (Marshfield PMRP). We sought replication in two National Health and Nutrition Examination Surveys (NHANES). The Marshfield PMRP currently uses four tools for measuring environmental exposures and outcome traits: 1) the PhenX Toolkit includes standardized exposure and phenotypic measures across several domains, 2) the Diet History Questionnaire (DHQ) is a food frequency questionnaire, 3) the Measurement of a Person's Habitual Physical Activity scores the level of an individual's physical activity, and 4) electronic health records (EHR) employs validated algorithms to establish T2D case-control status. Using PLATO software, 314 environmental variables were tested for association with T2D using logistic regression, adjusting for sex, age, and BMI in over 2,200 European Americans. When available, similar variables were tested with the same methods and adjustment in samples from NHANES III and NHANES 1999-2002. Twelve and 31 associations were identified in the Marshfield samples at p<0.01 and p<0.05, respectively. Seven and 13 measures replicated in at least one of the NHANES at p<0.01 and p<0.05, respectively, with the same direction of effect. The most significant environmental exposures associated with T2D status included decreased alcohol use as well as increased smoking exposure in childhood and adulthood. The results demonstrate the utility of the EWAS method and survey tools for identifying environmental components of complex diseases like type 2 diabetes. These high-throughput and comprehensive investigation methods can easily be applied to investigate the relation between environmental exposures and multiple phenotypes in future analyses.

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