Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)
The application of metabolomics technology to epidemiological studies is emerging as a new approach to elucidate disease etiology and for biomarker discovery. However, analysis of metabolomics data is complex and there is an urgent need for the standardization of analysis workflow and reporting of s...
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Format: | Article |
Language: | English |
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MDPI AG
2019-07-01
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Series: | Metabolites |
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Online Access: | https://www.mdpi.com/2218-1989/9/7/145 |
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doaj-960f957816d54d2aaead7f0ce8c260d0 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mary C. Playdon Amit D. Joshi Fred K. Tabung Susan Cheng Mir Henglin Andy Kim Tengda Lin Eline H. van Roekel Jiaqi Huang Jan Krumsiek Ying Wang Ewy Mathé Marinella Temprosa Steven Moore Bo Chawes A. Heather Eliassen Andrea Gsur Marc J. Gunter Sei Harada Claudia Langenberg Matej Oresic Wei Perng Wei Jie Seow Oana A. Zeleznik |
spellingShingle |
Mary C. Playdon Amit D. Joshi Fred K. Tabung Susan Cheng Mir Henglin Andy Kim Tengda Lin Eline H. van Roekel Jiaqi Huang Jan Krumsiek Ying Wang Ewy Mathé Marinella Temprosa Steven Moore Bo Chawes A. Heather Eliassen Andrea Gsur Marc J. Gunter Sei Harada Claudia Langenberg Matej Oresic Wei Perng Wei Jie Seow Oana A. Zeleznik Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) Metabolites metabolomics epidemiology statistical analysis reporting analytical methods data analysis pre-processing |
author_facet |
Mary C. Playdon Amit D. Joshi Fred K. Tabung Susan Cheng Mir Henglin Andy Kim Tengda Lin Eline H. van Roekel Jiaqi Huang Jan Krumsiek Ying Wang Ewy Mathé Marinella Temprosa Steven Moore Bo Chawes A. Heather Eliassen Andrea Gsur Marc J. Gunter Sei Harada Claudia Langenberg Matej Oresic Wei Perng Wei Jie Seow Oana A. Zeleznik |
author_sort |
Mary C. Playdon |
title |
Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) |
title_short |
Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) |
title_full |
Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) |
title_fullStr |
Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) |
title_full_unstemmed |
Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS) |
title_sort |
metabolomics analytics workflow for epidemiological research: perspectives from the consortium of metabolomics studies (comets) |
publisher |
MDPI AG |
series |
Metabolites |
issn |
2218-1989 |
publishDate |
2019-07-01 |
description |
The application of metabolomics technology to epidemiological studies is emerging as a new approach to elucidate disease etiology and for biomarker discovery. However, analysis of metabolomics data is complex and there is an urgent need for the standardization of analysis workflow and reporting of study findings. To inform the development of such guidelines, we conducted a survey of 47 cohort representatives from the Consortium of Metabolomics Studies (COMETS) to gain insights into the current strategies and procedures used for analyzing metabolomics data in epidemiological studies worldwide. The results indicated a variety of applied analytical strategies, from biospecimen and data pre-processing and quality control to statistical analysis and reporting of study findings. These strategies included methods commonly used within the metabolomics community and applied in epidemiological research, as well as novel approaches to pre-processing pipelines and data analysis. To help with these discrepancies, we propose use of open-source initiatives such as the online web-based tool COMETS Analytics, which includes helpful tools to guide analytical workflow and the standardized reporting of findings from metabolomics analyses within epidemiological studies. Ultimately, this will improve the quality of statistical analyses, research findings, and study reproducibility. |
topic |
metabolomics epidemiology statistical analysis reporting analytical methods data analysis pre-processing |
url |
https://www.mdpi.com/2218-1989/9/7/145 |
work_keys_str_mv |
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doaj-960f957816d54d2aaead7f0ce8c260d02020-11-25T01:17:03ZengMDPI AGMetabolites2218-19892019-07-019714510.3390/metabo9070145metabo9070145Metabolomics Analytics Workflow for Epidemiological Research: Perspectives from the Consortium of Metabolomics Studies (COMETS)Mary C. Playdon0Amit D. Joshi1Fred K. Tabung2Susan Cheng3Mir Henglin4Andy Kim5Tengda Lin6Eline H. van Roekel7Jiaqi Huang8Jan Krumsiek9Ying Wang10Ewy Mathé11Marinella Temprosa12Steven Moore13Bo Chawes14A. Heather Eliassen15Andrea Gsur16Marc J. Gunter17Sei Harada18Claudia Langenberg19Matej Oresic20Wei Perng21Wei Jie Seow22Oana A. Zeleznik23Department of Nutrition and Integrative Physiology, College of Health, University of Utah, Salt Lake City, UT 84112, USAClinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA 02114, USADivision of Medical Oncology, Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH 43210, USASmidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USACardiovascular Division, Brigham and Women’s Hospital, Boston, MA 02115, USACardiovascular Division, Brigham and Women’s Hospital, Boston, MA 02115, USADivision of Cancer Population Sciences, Huntsman Cancer Institute, Salt Lake City, UT 84112, USADepartment of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, The NetherlandsDivision of Cancer Epidemiology and Genetics, Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD 20850, USAInstitute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10021, USABehavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA 30303, USACollege of Medicine, Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USADepartment of Epidemiology and Biostatistics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052, USADivision of Cancer Epidemiology and Genetics, Metabolic Epidemiology Branch, National Cancer Institute, Rockville, MD 20850, USACOPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 1165 Copenhagen, DenmarkChanning Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USAInstitute of Cancer Research, Department of Medicine, Medical University of Vienna, 1090 Vienna, AustriaSection of Nutrition and Metabolism, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, FranceDepartment of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo 160-8582, JapanMRC Epidemiology Unit, Public Health, University of Cambridge, Cambridge CB2 1 TN, UKTurku Centre for Biotechnology, University of Turku, 20500 Turku, FinlandDepartment of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USASaw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, SingaporeChanning Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USAThe application of metabolomics technology to epidemiological studies is emerging as a new approach to elucidate disease etiology and for biomarker discovery. However, analysis of metabolomics data is complex and there is an urgent need for the standardization of analysis workflow and reporting of study findings. To inform the development of such guidelines, we conducted a survey of 47 cohort representatives from the Consortium of Metabolomics Studies (COMETS) to gain insights into the current strategies and procedures used for analyzing metabolomics data in epidemiological studies worldwide. The results indicated a variety of applied analytical strategies, from biospecimen and data pre-processing and quality control to statistical analysis and reporting of study findings. These strategies included methods commonly used within the metabolomics community and applied in epidemiological research, as well as novel approaches to pre-processing pipelines and data analysis. To help with these discrepancies, we propose use of open-source initiatives such as the online web-based tool COMETS Analytics, which includes helpful tools to guide analytical workflow and the standardized reporting of findings from metabolomics analyses within epidemiological studies. Ultimately, this will improve the quality of statistical analyses, research findings, and study reproducibility.https://www.mdpi.com/2218-1989/9/7/145metabolomicsepidemiologystatistical analysisreportinganalytical methodsdata analysispre-processing |