Literature DB >> 28068484

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.

Arjun K Manrai1, Yuxia Cui2, Pierre R Bushel2, Molly Hall3, Spyros Karakitsios4, Carolyn J Mattingly5, Marylyn Ritchie3,6, Charles Schmitt7, Denis A Sarigiannis4, Duncan C Thomas8, David Wishart9, David M Balshaw2, Chirag J Patel1,10.   

Abstract

The complexity of the human exposome-the totality of environmental exposures encountered from birth to death-motivates systematic, high-throughput approaches to discover new environmental determinants of disease. In this review, we describe the state of science in analyzing the human exposome and provide recommendations for the public health community to consider in dealing with analytic challenges of exposome-based biomedical research. We describe extant and novel analytic methods needed to associate the exposome with critical health outcomes and contextualize the data-centered challenges by drawing parallels to other research endeavors such as human genomics research. We discuss efforts for training scientists who can bridge public health, genomics, and biomedicine in informatics and statistics. If an exposome data ecosystem is brought to fruition, it will likely play a role as central as genomic science has had in molding the current and new generations of biomedical researchers, computational scientists, and public health research programs.

Entities:  

Keywords:  bioinformatics; data standards; environment-wide association studies; exposures; genomics

Mesh:

Year:  2016        PMID: 28068484      PMCID: PMC5774331          DOI: 10.1146/annurev-publhealth-082516-012737

Source DB:  PubMed          Journal:  Annu Rev Public Health        ISSN: 0163-7525            Impact factor:   21.981


  63 in total

1.  Principal components analysis corrects for stratification in genome-wide association studies.

Authors:  Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal:  Nat Genet       Date:  2006-07-23       Impact factor: 38.330

2.  Designing a public square for research computing.

Authors:  Daniel R Masys; Paul A Harris; Paul A Fearn; Isaac S Kohane
Journal:  Sci Transl Med       Date:  2012-08-29       Impact factor: 17.956

3.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

4.  A nutrient-wide association study on blood pressure.

Authors:  Ioanna Tzoulaki; Chirag J Patel; Tomonori Okamura; Queenie Chan; Ian J Brown; Katsuyuki Miura; Hirotsugu Ueshima; Liancheng Zhao; Linda Van Horn; Martha L Daviglus; Jeremiah Stamler; Atul J Butte; John P A Ioannidis; Paul Elliott
Journal:  Circulation       Date:  2012-10-23       Impact factor: 29.690

5.  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.

Authors:  Joshua C Denny; Marylyn D Ritchie; Melissa A Basford; Jill M Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Dan R Masys; Dan M Roden; Dana C Crawford
Journal:  Bioinformatics       Date:  2010-03-24       Impact factor: 6.937

6.  An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus.

Authors:  Chirag J Patel; Jayanta Bhattacharya; Atul J Butte
Journal:  PLoS One       Date:  2010-05-20       Impact factor: 3.240

7.  Exposure science and the exposome: an opportunity for coherence in the environmental health sciences.

Authors:  Paul J Lioy; Stephen M Rappaport
Journal:  Environ Health Perspect       Date:  2011-11       Impact factor: 9.031

8.  Providing the missing link: the exposure science ontology ExO.

Authors:  Carolyn J Mattingly; Thomas E McKone; Michael A Callahan; Judith A Blake; Elaine A Cohen Hubal
Journal:  Environ Sci Technol       Date:  2012-03-12       Impact factor: 9.028

9.  The Comparative Toxicogenomics Database's 10th year anniversary: update 2015.

Authors:  Allan Peter Davis; Cynthia J Grondin; Kelley Lennon-Hopkins; Cynthia Saraceni-Richards; Daniela Sciaky; Benjamin L King; Thomas C Wiegers; Carolyn J Mattingly
Journal:  Nucleic Acids Res       Date:  2014-10-17       Impact factor: 16.971

10.  Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study.

Authors:  Molly A Hall; Anurag Verma; Kristin D Brown-Gentry; Robert Goodloe; Jonathan Boston; Sarah Wilson; Bob McClellan; Cara Sutcliffe; Holly H Dilks; Nila B Gillani; Hailing Jin; Ping Mayo; Melissa Allen; Nathalie Schnetz-Boutaud; Dana C Crawford; Marylyn D Ritchie; Sarah A Pendergrass
Journal:  PLoS Genet       Date:  2014-12-04       Impact factor: 5.917

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  24 in total

Review 1.  Opportunities and Challenges for Environmental Exposure Assessment in Population-Based Studies.

Authors:  Chirag J Patel; Jacqueline Kerr; Duncan C Thomas; Bhramar Mukherjee; Beate Ritz; Nilanjan Chatterjee; Marta Jankowska; Juliette Madan; Margaret R Karagas; Kimberly A McAllister; Leah E Mechanic; M Daniele Fallin; Christine Ladd-Acosta; Ian A Blair; Susan L Teitelbaum; Christopher I Amos
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2017-07-14       Impact factor: 4.254

Review 2.  The Exposome Research Paradigm: an Opportunity to Understand the Environmental Basis for Human Health and Disease.

Authors:  Germaine M Buck Louis; Melissa M Smarr; Chirag J Patel
Journal:  Curr Environ Health Rep       Date:  2017-03

3.  The emerging landscape of health research based on biobanks linked to electronic health records: Existing resources, statistical challenges, and potential opportunities.

Authors:  Lauren J Beesley; Maxwell Salvatore; Lars G Fritsche; Anita Pandit; Arvind Rao; Chad Brummett; Cristen J Willer; Lynda D Lisabeth; Bhramar Mukherjee
Journal:  Stat Med       Date:  2019-12-20       Impact factor: 2.373

4.  Data Science in Environmental Health Research.

Authors:  Christine Choirat; Danielle Braun; Marianthi-Anna Kioumourtzoglou
Journal:  Curr Epidemiol Rep       Date:  2019-07-15

Review 5.  Social epigenomics: are we at an impasse?

Authors:  Amy L Non
Journal:  Epigenomics       Date:  2021-03-22       Impact factor: 4.778

6.  Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery.

Authors:  Ming Kei Chung; Stephen M Rappaport; Craig E Wheelock; Vy Kim Nguyen; Thomas P van der Meer; Gary W Miller; Roel Vermeulen; Chirag J Patel
Journal:  Environ Health Perspect       Date:  2021-08-26       Impact factor: 9.031

Review 7.  The Exposome and Toxicology: A Win-Win Collaboration.

Authors:  Robert Barouki; Karine Audouze; Christel Becker; Ludek Blaha; Xavier Coumoul; Spyros Karakitsios; Jana Klanova; Gary W Miller; Elliott J Price; Denis Sarigiannis
Journal:  Toxicol Sci       Date:  2022-02-28       Impact factor: 4.109

8.  Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections.

Authors:  Caroline H Johnson; Toby J Athersuch; Gwen W Collman; Suraj Dhungana; David F Grant; Dean P Jones; Chirag J Patel; Vasilis Vasiliou
Journal:  Hum Genomics       Date:  2017-12-08       Impact factor: 4.639

9.  Promise and pitfalls in the application of big data to occupational and environmental health.

Authors:  David M Stieb; Cécile R Boot; Michelle C Turner
Journal:  BMC Public Health       Date:  2017-05-09       Impact factor: 3.295

10.  Using methylome data to inform exposome-health association studies: An application to the identification of environmental drivers of child body mass index.

Authors:  Solène Cadiou; Mariona Bustamante; Lydiane Agier; Sandra Andrusaityte; Xavier Basagaña; Angel Carracedo; Leda Chatzi; Regina Grazuleviciene; Juan R Gonzalez; Kristine B Gutzkow; Léa Maitre; Dan Mason; Frédéric Millot; Mark Nieuwenhuijsen; Eleni Papadopoulou; Gillian Santorelli; Pierre-Jean Saulnier; Marta Vives; John Wright; Martine Vrijheid; Rémy Slama
Journal:  Environ Int       Date:  2020-03-14       Impact factor: 9.621

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