Grant Details
Grant Number: |
1R21ES020811-01 Interpret this number |
Primary Investigator: |
Mukherjee, Bhramar |
Organization: |
University Of Michigan At Ann Arbor |
Project Title: |
Efficient Design and Analytic Strategies for Enhancing the Power of Detecting G X |
Fiscal Year: |
2012 |
Abstract
DESCRIPTION (provided by applicant): This proposal is in response to the Funding Opportunity Announcement PAR- 11-032 on Methods and Approaches for Detection of Gene- Environment Interactions in Human Disease (R21). The proposal will be led by multiple PIs, Dr. Bhramar Mukherjee at the Department of Biostatistics, University of Michigan and Dr. Jinbo Chen at the Department of Biostatistics and Epidemiology, University of Pennsylvania. Dr. Stephen B. Gruber, Dr. Sung Kyun Park and Dr. Naisyin Wang from the University of Michigan are key clinical and methodological consultants on the project. In this proposal, we will have two specific aims: (i) Evaluate efficient two-phase design and analysis choices in the post genomewide association studies (GWAS) era where additional genotyping or biomarker data is collected on a prioritized selection of a sub-sample of study subjects in an existing study base. This includes the possibility of using supplementary data on cases and controls with only genetic or environmental data. The methods are guided by modern retrospective likelihood framework. (ii) Develop methods for screening of interaction in cohort studies using a novel technique developed by the PIs called "Principal Interactions Analysis". This method is based on a parsimonious low rank representation of the interaction matrix after fitting additive main effects of gene and environment. The proposal plans to extend this method to longitudinal studies to capture time- varying effects of interaction. Visual diagnostics to identify time-windows of critical importance will be developed as a byproduct. The planned work in this important proposal will meaningfully contribute to the mission of this FOA, and advance study design and analytical techniques for studying G x E effects. The proposal will involve active collaboration between Dr. Chen and Dr. Mukherjee, their doctoral/post-doctoral trainees and foster collaboration between two peer institutions: University of Pennsylvania and University of Michigan. The proposal lies in the intersection of statistics, medicine, epidemiology and human genetics in terms of methodology development. The broader impact is better understanding of disease etiology and identify potentials for targeted intervention strategies.
PUBLIC HEALTH RELEVANCE: This proposal is submitted in response to the Funding Opportunity Announcement PAR- 11-032 on Methods and Approaches for Detection of Gene-Environment Interactions in Human Disease (R21). The proposal is lead by multiple PD/PI, Dr. Bhramar Mukherjee at the University of Michigan and Dr. Jinbo Chen at the University of Pennsylvania. Synergism of genes and environment plays an important role in the etiology of complex diseases. This proposal addresses important study design and analytical challenges for efficient detection of gene-environment interactions in epidemiological studies. In the first specific aim, we consider design and analytical methods associated with strategies for selection of cases/controls for additional genotyping or collection of biomarker data in existing study bases. In the second specific aim, we consider a highly novel strategy for exploring interactions in longitudinal studies, based on a singular value decomposition of the residual interaction contrast matrix after removing additive effects. We call this analysis Principal Interactions Analysis, due to its similarity with Principal Components Analysis. The proposal is expected to contribute significantly to the existing literature on G x E studies.
Publications
Efficient inference of parent-of-origin effect using case-control mother-child genotype data.
Authors: Tian Y.
, Zhang H.
, Bureau A.
, Hochner H.
, Chen J.
.
Source: Journal Of Statistical Planning And Inference, 2024 Dec; 233, .
EPub date: 2024-05-09 00:00:00.0.
PMID: 38818512
Related Citations
A hierarchical integrative group least absolute shrinkage and selection operator for analyzing environmental mixtures.
Authors: Boss J.
, Rix A.
, Chen Y.H.
, Narisetty N.N.
, Wu Z.
, Ferguson K.K.
, McElrath T.F.
, Meeker J.D.
, Mukherjee B.
.
Source: Environmetrics, 2021 Dec; 32(8), .
EPub date: 2021-07-30 00:00:00.0.
PMID: 34899005
Related Citations
Covariate adjusted inference of parent-of-origin effects using case-control mother-child paired multilocus genotype data.
Authors: Zhang K.
, Zhang H.
, Hochner H.
, Chen J.
.
Source: Genetic Epidemiology, 2021-08-23 00:00:00.0; , .
EPub date: 2021-08-23 00:00:00.0.
PMID: 34424572
Related Citations
Joint testing of donor and recipient genetic matching scores and recipient genotype has robust power for finding genes associated with transplant outcomes.
Authors: Arthur V.L.
, Guan W.
, Loza B.L.
, Keating B.
, Chen J.
.
Source: Genetic Epidemiology, 2020-08-11 00:00:00.0; , .
EPub date: 2020-08-11 00:00:00.0.
PMID: 32783273
Related Citations
A comprehensive gene-environment interaction analysis in Ovarian Cancer using genome-wide significant common variants.
Authors: Kim S.
, Wang M.
, Tyrer J.P.
, Jensen A.
, Wiensch A.
, Liu G.
, Lee A.W.
, Ness R.B.
, Salvatore M.
, Tworoger S.S.
, et al.
.
Source: International Journal Of Cancer, 2019-05-01 00:00:00.0; 144(9), p. 2192-2205.
EPub date: 2019-01-20 00:00:00.0.
PMID: 30499236
Related Citations
Selection of nonlinear interactions by a forward stepwise algorithm: Application to identifying environmental chemical mixtures affecting health outcomes.
Authors: Narisetty N.N.
, Mukherjee B.
, Chen Y.H.
, Gonzalez R.
, Meeker J.D.
.
Source: Statistics In Medicine, 2019-04-30 00:00:00.0; 38(9), p. 1582-1600.
EPub date: 2018-12-26 00:00:00.0.
PMID: 30586682
Related Citations
Distributed Lag Interaction Models with Two Pollutants.
Authors: Chen Y.H.
, Mukherjee B.
, Berrocal V.J.
.
Source: Journal Of The Royal Statistical Society. Series C, Applied Statistics, 2019 Jan; 68(1), p. 79-97.
EPub date: 2018-07-08 00:00:00.0.
PMID: 30636815
Related Citations
Associations of cumulative exposure to heavy metal mixtures with obesity and its comorbidities among U.S. adults in NHANES 2003-2014.
Authors: Wang X.
, Mukherjee B.
, Park S.K.
.
Source: Environment International, 2018 Dec; 121(Pt 1), p. 683-694.
EPub date: 2018-10-11 00:00:00.0.
PMID: 30316184
Related Citations
Empirical Bayes Estimation and Prediction Using Summary-Level Information From External Big Data Sources Adjusting for Violations of Transportability.
Authors: Estes J.P.
, Mukherjee B.
, Taylor J.M.G.
.
Source: Statistics In Biosciences, 2018 Dec; 10(3), p. 568-586.
EPub date: 2018-05-14 00:00:00.0.
PMID: 31123532
Related Citations
Robust Tests for Additive Gene-Environment Interaction in Case-Control Studies Using Gene-Environment Independence.
Authors: Liu G.
, Mukherjee B.
, Lee S.
, Lee A.W.
, Wu A.H.
, Bandera E.V.
, Jensen A.
, Rossing M.A.
, Moysich K.B.
, Chang-Claude J.
, et al.
.
Source: American Journal Of Epidemiology, 2018-02-01 00:00:00.0; 187(2), p. 366-377.
PMID: 28633381
Related Citations
Improving estimation and prediction in linear regression incorporating external information from an established reduced model.
Authors: Cheng W.
, Taylor J.M.G.
, Vokonas P.S.
, Park S.K.
, Mukherjee B.
.
Source: Statistics In Medicine, 2018-01-24 00:00:00.0; , .
EPub date: 2018-01-24 00:00:00.0.
PMID: 29365342
Related Citations
Rare-variant association tests in longitudinal studies, with an application to the Multi-Ethnic Study of Atherosclerosis (MESA).
Authors: He Z.
, Lee S.
, Zhang M.
, Smith J.A.
, Guo X.
, Palmas W.
, Kardia S.L.R.
, Ionita-Laza I.
, Mukherjee B.
.
Source: Genetic Epidemiology, 2017-10-27 00:00:00.0; , .
EPub date: 2017-10-27 00:00:00.0.
PMID: 29076270
Related Citations
Robust distributed lag models using data adaptive shrinkage.
Authors: Chen Y.H.
, Mukherjee B.
, Adar S.D.
, Berrocal V.J.
, Coull B.A.
.
Source: Biostatistics (oxford, England), 2017-10-12 00:00:00.0; , .
EPub date: 2017-10-12 00:00:00.0.
PMID: 29040386
Related Citations
Update on the State of the Science for Analytical Methods for Gene-Environment Interactions.
Authors: Gauderman W.J.
, Mukherjee B.
, Aschard H.
, Hsu L.
, Lewinger J.P.
, Patel C.J.
, Witte J.S.
, Amos C.
, Tai C.G.
, Conti D.
, et al.
.
Source: American Journal Of Epidemiology, 2017-10-01 00:00:00.0; 186(7), p. 762-770.
PMID: 28978192
Related Citations
Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases.
Authors: McAllister K.
, Mechanic L.E.
, Amos C.
, Aschard H.
, Blair I.A.
, Chatterjee N.
, Conti D.
, Gauderman W.J.
, Hsu L.
, Hutter C.M.
, et al.
.
Source: American Journal Of Epidemiology, 2017-10-01 00:00:00.0; 186(7), p. 753-761.
PMID: 28978193
Related Citations
Construction of environmental risk score beyond standard linear models using machine learning methods: application to metal mixtures, oxidative stress and cardiovascular disease in NHANES.
Authors: Park S.K.
, Zhao Z.
, Mukherjee B.
.
Source: Environmental Health : A Global Access Science Source, 2017-09-26 00:00:00.0; 16(1), p. 102.
EPub date: 2017-09-26 00:00:00.0.
PMID: 28950902
Related Citations
Exposure enriched outcome dependent designs for longitudinal studies of gene-environment interaction.
Authors: Sun Z.
, Mukherjee B.
, Estes J.P.
, Vokonas P.S.
, Park S.K.
.
Source: Statistics In Medicine, 2017-08-15 00:00:00.0; 36(18), p. 2947-2960.
EPub date: 2017-05-11 00:00:00.0.
PMID: 28497531
Related Citations
Meta-analysis of gene-environment interaction exploiting gene-environment independence across multiple case-control studies.
Authors: Estes J.P.
, Rice J.D.
, Li S.
, Stringham H.M.
, Boehnke M.
, Mukherjee B.
.
Source: Statistics In Medicine, 2017-07-25 00:00:00.0; , .
EPub date: 2017-07-25 00:00:00.0.
PMID: 28744888
Related Citations
A New Variance Component Score Test for Testing Distributed Lag Functions with Applications in Time Series Analysis.
Authors: Chen Y.H.
, Mukherjee B.
.
Source: Statistics & Probability Letters, 2017 Apr; 123, p. 122-127.
EPub date: 2016-12-16 00:00:00.0.
PMID: 29200542
Related Citations
Set-Based Tests for the Gene-Environment Interaction in Longitudinal Studies.
Authors: He Z.
, Zhang M.
, Lee S.
, Smith J.A.
, Kardia S.L.R.
, Diez Roux A.V.
, Mukherjee B.
.
Source: Journal Of The American Statistical Association, 2017; 112(519), p. 966-978.
EPub date: 2016-12-16 00:00:00.0.
PMID: 29780190
Related Citations
Classification and Clustering Methods for Multiple Environmental Factors in Gene-Environment Interaction: Application to the Multi-Ethnic Study of Atherosclerosis.
Authors: Ko Y.A.
, Mukherjee B.
, Smith J.A.
, Kardia S.L.
, Allison M.
, Diez Roux A.V.
.
Source: Epidemiology (cambridge, Mass.), 2016 Nov; 27(6), p. 870-8.
PMID: 27479650
Related Citations
Efficient unified rare variant association test by modeling the population genetic distribution in case-control studies.
Authors: Li H.
, Chen J.
.
Source: Genetic Epidemiology, 2016 11; 40(7), p. 579-590.
PMID: 27550412
Related Citations
Using family members to augment genetic case-control studies of a life-threatening disease.
Authors: Chen L.
, Weinberg C.R.
, Chen J.
.
Source: Statistics In Medicine, 2016-07-20 00:00:00.0; 35(16), p. 2815-30.
EPub date: 2016-07-20 00:00:00.0.
PMID: 26866629
Related Citations
Mediation Formula for a Binary Outcome and a Time-Varying Exposure and Mediator, Accounting for Possible Exposure-Mediator Interaction.
Authors: Chen Y.H.
, Mukherjee B.
, Ferguson K.K.
, Meeker J.D.
, VanderWeele T.J.
.
Source: American Journal Of Epidemiology, 2016-07-15 00:00:00.0; 184(2), p. 157-9.
EPub date: 2016-07-15 00:00:00.0.
PMID: 27325886
Related Citations
Tests for Gene-Environment Interactions and Joint Effects With Exposure Misclassification.
Authors: Boonstra P.S.
, Mukherjee B.
, Gruber S.B.
, Ahn J.
, Schmit S.L.
, Chatterjee N.
.
Source: American Journal Of Epidemiology, 2016-02-01 00:00:00.0; 183(3), p. 237-47.
EPub date: 2016-02-01 00:00:00.0.
PMID: 26755675
Related Citations
Retrospective likelihood-based methods for analyzing case-cohort genetic association studies.
Authors: Shen Y.
, Cai T.
, Chen Y.
, Yang Y.
, Chen J.
.
Source: Biometrics, 2015 Dec; 71(4), p. 960-8.
PMID: 26177343
Related Citations
Set-based tests for genetic association in longitudinal studies.
Authors: He Z.
, Zhang M.
, Lee S.
, Smith J.A.
, Guo X.
, Palmas W.
, Kardia S.L.
, Diez Roux A.V.
, Mukherjee B.
.
Source: Biometrics, 2015 Sep; 71(3), p. 606-15.
PMID: 25854837
Related Citations
The impact of exposure-biased sampling designs on detection of gene-environment interactions in case-control studies with potential exposure misclassification.
Authors: Stenzel S.L.
, Ahn J.
, Boonstra P.S.
, Gruber S.B.
, Mukherjee B.
.
Source: European Journal Of Epidemiology, 2015 May; 30(5), p. 413-23.
PMID: 24894824
Related Citations
Latent variable models for gene-environment interactions in longitudinal studies with multiple correlated exposures.
Authors: Tao Y.
, Sánchez B.N.
, Mukherjee B.
.
Source: Statistics In Medicine, 2015-03-30 00:00:00.0; 34(7), p. 1227-41.
EPub date: 2015-03-30 00:00:00.0.
PMID: 25545894
Related Citations
Statistical methods for modeling repeated measures of maternal environmental exposure biomarkers during pregnancy in association with preterm birth.
Authors: Chen Y.H.
, Ferguson K.K.
, Meeker J.D.
, McElrath T.F.
, Mukherjee B.
.
Source: Environmental Health : A Global Access Science Source, 2015-01-26 00:00:00.0; 14, p. 9.
EPub date: 2015-01-26 00:00:00.0.
PMID: 25619201
Related Citations
Association between Stress Response Genes and Features of Diurnal Cortisol Curves in the Multi-Ethnic Study of Atherosclerosis: A New Multi-Phenotype Approach for Gene-Based Association Tests.
Authors: He Z.
, Payne E.K.
, Mukherjee B.
, Lee S.
, Smith J.A.
, Ware E.B.
, Sánchez B.N.
, Seeman T.E.
, Kardia S.L.
, Diez Roux A.V.
.
Source: Plos One, 2015; 10(5), p. e0126637.
PMID: 25993632
Related Citations
Testing departure from additivity in Tukey's model using shrinkage: application to a longitudinal setting.
Authors: Ko Y.A.
, Mukherjee B.
, Smith J.A.
, Park S.K.
, Kardia S.L.
, Allison M.A.
, Vokonas P.S.
, Chen J.
, Diez-Roux A.V.
.
Source: Statistics In Medicine, 2014-12-20 00:00:00.0; 33(29), p. 5177-91.
EPub date: 2014-12-20 00:00:00.0.
PMID: 25112650
Related Citations
Longitudinal profiling of inflammatory cytokines and C-reactive protein during uncomplicated and preterm pregnancy.
Authors: Ferguson K.K.
, McElrath T.F.
, Chen Y.H.
, Mukherjee B.
, Meeker J.D.
.
Source: American Journal Of Reproductive Immunology (new York, N.y. : 1989), 2014 Sep; 72(3), p. 326-36.
PMID: 24807462
Related Citations
Variability in urinary phthalate metabolite levels across pregnancy and sensitive windows of exposure for the risk of preterm birth.
Authors: Ferguson K.K.
, McElrath T.F.
, Ko Y.A.
, Mukherjee B.
, Meeker J.D.
.
Source: Environment International, 2014 Sep; 70, p. 118-24.
PMID: 24934852
Related Citations
The role of environmental heterogeneity in meta-analysis of gene-environment interactions with quantitative traits.
Authors: Li S.
, Mukherjee B.
, Taylor J.M.
, Rice K.M.
, Wen X.
, Rice J.D.
, Stringham H.M.
, Boehnke M.
.
Source: Genetic Epidemiology, 2014 Jul; 38(5), p. 416-29.
PMID: 24801060
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A space-time point process model for analyzing and predicting case patterns of diarrheal disease in northwestern Ecuador.
Authors: Ahn J.
, Johnson T.D.
, Bhavnani D.
, Eisenberg J.N.
, Mukherjee B.
.
Source: Spatial And Spatio-temporal Epidemiology, 2014 Jun; 9, p. 23-35.
PMID: 24889991
Related Citations
Personal black carbon exposure influences ambulatory blood pressure: air pollution and cardiometabolic disease (AIRCMD-China) study.
Authors: Zhao X.
, Sun Z.
, Ruan Y.
, Yan J.
, Mukherjee B.
, Yang F.
, Duan F.
, Sun L.
, Liang R.
, Lian H.
, et al.
.
Source: Hypertension, 2014 Apr; 63(4), p. 871-7.
PMID: 24420543
Related Citations
Propensity score-based diagnostics for categorical response regression models.
Authors: Boonstra P.S.
, Bondarenko I.
, Park S.K.
, Vokonas P.S.
, Mukherjee B.
.
Source: Statistics In Medicine, 2014-02-10 00:00:00.0; 33(3), p. 455-69.
EPub date: 2014-02-10 00:00:00.0.
PMID: 23934948
Related Citations
Environmental risk score as a new tool to examine multi-pollutants in epidemiologic research: an example from the NHANES study using serum lipid levels.
Authors: Park S.K.
, Tao Y.
, Meeker J.D.
, Harlow S.D.
, Mukherjee B.
.
Source: Plos One, 2014; 9(6), p. e98632.
PMID: 24901996
Related Citations
Bayesian analysis of time-series data under case-crossover designs: posterior equivalence and inference.
Authors: Li S.
, Mukherjee B.
, Batterman S.
, Ghosh M.
.
Source: Biometrics, 2013 Dec; 69(4), p. 925-36.
PMID: 24289144
Related Citations
BAYESIAN SHRINKAGE METHODS FOR PARTIALLY OBSERVED DATA WITH MANY PREDICTORS.
Authors: Boonstra P.S.
, Mukherjee B.
, Taylor J.M.
.
Source: The Annals Of Applied Statistics, 2013-12-01 00:00:00.0; 7(4), p. 2272-2292.
PMID: 24436727
Related Citations
Statistical strategies for constructing health risk models with multiple pollutants and their interactions: possible choices and comparisons.
Authors: Sun Z.
, Tao Y.
, Li S.
, Ferguson K.K.
, Meeker J.D.
, Park S.K.
, Batterman S.A.
, Mukherjee B.
.
Source: Environmental Health : A Global Access Science Source, 2013-10-04 00:00:00.0; 12(1), p. 85.
EPub date: 2013-10-04 00:00:00.0.
PMID: 24093917
Related Citations
Novel likelihood ratio tests for screening gene-gene and gene-environment interactions with unbalanced repeated-measures data.
Authors: Ko Y.A.
, Saha-Chaudhuri P.
, Park S.K.
, Vokonas P.S.
, Mukherjee B.
.
Source: Genetic Epidemiology, 2013 Sep; 37(6), p. 581-91.
PMID: 23798480
Related Citations
Incorporating auxiliary information for improved prediction in high-dimensional datasets: an ensemble of shrinkage approaches.
Authors: Boonstra P.S.
, Taylor J.M.
, Mukherjee B.
.
Source: Biostatistics (oxford, England), 2013 Apr; 14(2), p. 259-72.
PMID: 23087411
Related Citations
BAYESIAN SEMIPARAMETRIC ANALYSIS FOR TWO-PHASE STUDIES OF GENE-ENVIRONMENT INTERACTION.
Authors: Ahn J.
, Mukherjee B.
, Gruber S.B.
, Ghosh M.
.
Source: The Annals Of Applied Statistics, 2013 Mar; 7(1), p. 543-569.
PMID: 24587840
Related Citations
Principal Interactions Analysis For Repeated Measures Data: Application To Gene-gene And Gene-environment Interactions
Authors: Mukherjee B.
, Ko Y.A.
, Vanderweele T.
, Roy A.
, Park S.K.
, Chen J.
.
Source: Statistics In Medicine, 2012-09-28 00:00:00.0; 31(22), p. 2531-51.
PMID: 22415818
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