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A new pipeline for ...
A new pipeline for the normalization and pooling of metabolomics data
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- Viallon, Vivian (författare)
- International Agency for Research on Cancer, World Health Organization
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- His, Mathilde (författare)
- International Agency for Research on Cancer, World Health Organization
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- Rinaldi, Sabina (författare)
- International Agency for Research on Cancer, World Health Organization
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- Breeur, Marie (författare)
- International Agency for Research on Cancer, World Health Organization
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- Gicquiau, Audrey (författare)
- International Agency for Research on Cancer, World Health Organization
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- Hemon, Bertrand (författare)
- International Agency for Research on Cancer, World Health Organization
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- Overvad, Kim (författare)
- Aarhus University
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- Tjønneland, Anne (författare)
- Danish Cancer Society
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- Rostgaard-Hansen, Agnetha Linn (författare)
- Danish Cancer Society
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- Rothwell, Joseph A. (författare)
- Versailles Saint-Quentin-en-Yvelines University
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- Lecuyer, Lucie (författare)
- Versailles Saint-Quentin-en-Yvelines University
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- Severi, Gianluca (författare)
- University of Florence,Versailles Saint-Quentin-en-Yvelines University
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- Kaaks, Rudolf (författare)
- German Cancer Research Centre
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- Johnson, Theron (författare)
- German Cancer Research Centre
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- Schulze, Matthias B. (författare)
- German Institute of Human Nutrition,University of Potsdam
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- Palli, Domenico (författare)
- Institute for Cancer Research, Prevention and Clinical Network (ISPRO)
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- Agnoli, Claudia (författare)
- Istituto Nazionale dei Tumori
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- Panico, Salvatore (författare)
- University of Naples Federico II
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- Tumino, Rosario (författare)
- Provincial Health Authority (ASP) Ragusa
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- Ricceri, Fulvio (författare)
- University of Turin,Azienda Sanitaria Locale Torino 3
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- Monique Verschuren, W.M. (författare)
- National Institute for Public Health and the Environment (RIVM),University Medical Center Utrecht
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- Engelfriet, Peter (författare)
- National Institute for Public Health and the Environment (RIVM)
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- Onland-Moret, Charlotte (författare)
- University Medical Center Utrecht
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- Vermeulen, Roel (författare)
- University Medical Center Utrecht,Utrecht University
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- Nøst, Therese Haugdahl (författare)
- UiT The Arctic University of Norway, Tromsø
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- Urbarova, Ilona (författare)
- UiT The Arctic University of Norway, Tromsø
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- Zamora-Ros, Raul (författare)
- Bellvitge Biomedical Research Institute
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- Rodriguez-Barranco, Miguel (författare)
- Andalusian School Of Public Health (EASP)
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- Amiano, Pilar (författare)
- Biodonostia Health Research Institute
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- Huerta, José Maria (författare)
- Murcia Regional Health Council
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- Ardanaz, Eva (författare)
- Health Research Institute of Navarra (IDISNA)
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- Melander, Olle (författare)
- Lund University,Lunds universitet,Kardiovaskulär forskning - hypertoni,Forskargrupper vid Lunds universitet,Cardiovascular Research - Hypertension,Lund University Research Groups,Skåne University Hospital
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- Ottoson, Filip (författare)
- Lund University
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- Vidman, Linda (författare)
- Umeå University,Umeå universitet,Onkologi
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- Rentoft, Matilda (författare)
- Umeå University,Umeå universitet,Onkologi
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- Schmidt, Julie A. (författare)
- University of Oxford
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- Travis, Ruth C. (författare)
- University of Oxford
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- Weiderpass, Elisabete (författare)
- International Agency for Research on Cancer, World Health Organization
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- Johansson, Mattias (författare)
- International Agency for Research on Cancer, World Health Organization
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- Dossus, Laure (författare)
- International Agency for Research on Cancer, World Health Organization
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- Jenab, Mazda (författare)
- International Agency for Research on Cancer, World Health Organization
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- Gunter, Marc J. (författare)
- International Agency for Research on Cancer, World Health Organization
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- Bermejo, Justo Lorenzo (författare)
- Heidelberg University
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- Scherer, Dominique (författare)
- Heidelberg University
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- Salek, Reza M. (författare)
- International Agency for Research on Cancer, World Health Organization
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- Keski-Rahkonen, Pekka (författare)
- International Agency for Research on Cancer, World Health Organization
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- Ferrari, Pietro (författare)
- International Agency for Research on Cancer, World Health Organization
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(creator_code:org_t)
- 2021-09-17
- 2021
- Engelska.
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Ingår i: Metabolites. - : MDPI. - 2218-1989. ; 11:9
- Relaterad länk:
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https://doi.org/10.3...
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visa fler...
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https://umu.diva-por... (primary) (Raw object)
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https://www.mdpi.com...
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http://dx.doi.org/10... (free)
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https://urn.kb.se/re...
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https://doi.org/10.3...
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https://lup.lub.lu.s...
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Abstract
Ämnesord
Stäng
- Pooling metabolomics data across studies is often desirable to increase the statistical power of the analysis. However, this can raise methodological challenges as several preanalytical and analytical factors could introduce differences in measured concentrations and variability between datasets. Specifically, different studies may use variable sample types (e.g., serum versus plasma) collected, treated, and stored according to different protocols, and assayed in different laboratories using different instruments. To address these issues, a new pipeline was developed to normalize and pool metabolomics data through a set of sequential steps: (i) exclusions of the least informative observations and metabolites and removal of outliers; imputation of missing data; (ii) identification of the main sources of variability through principal component partial R-square (PC-PR2) analysis; (iii) application of linear mixed models to remove unwanted variability, including samples’ originating study and batch, and preserve biological variations while accounting for potential differences in the residual variances across studies. This pipeline was applied to targeted metabolomics data acquired using Biocrates AbsoluteIDQ kits in eight case-control studies nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Comprehensive examination of metabolomics measurements indicated that the pipeline improved the comparability of data across the studies. Our pipeline can be adapted to normalize other molecular data, including biomarkers as well as proteomics data, and could be used for pooling molecular datasets, for example in international consortia, to limit biases introduced by inter-study variability. This versatility of the pipeline makes our work of potential interest to molecular epidemiologists.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Cancer epidemiology
- Metabolites
- Metabolomics
- Normalization
- Pooling
- Technical variability
- onkologi
- Oncology
- Cancer epidemiology
- Metabolites
- Metabolomics
- Normalization
- Pooling
- Technical variability
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
Hitta via bibliotek
Till lärosätets databas
- Av författaren/redakt...
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Viallon, Vivian
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His, Mathilde
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Rinaldi, Sabina
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Breeur, Marie
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Gicquiau, Audrey
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Hemon, Bertrand
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visa fler...
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Overvad, Kim
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Tjønneland, Anne
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Rostgaard-Hansen ...
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Rothwell, Joseph ...
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Lecuyer, Lucie
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Severi, Gianluca
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Kaaks, Rudolf
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Johnson, Theron
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Schulze, Matthia ...
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Palli, Domenico
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Agnoli, Claudia
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Panico, Salvator ...
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Tumino, Rosario
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Ricceri, Fulvio
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Monique Verschur ...
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Engelfriet, Pete ...
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Onland-Moret, Ch ...
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Vermeulen, Roel
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Nøst, Therese Ha ...
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Urbarova, Ilona
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Zamora-Ros, Raul
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Rodriguez-Barran ...
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Amiano, Pilar
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Huerta, José Mar ...
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Ardanaz, Eva
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Melander, Olle
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Ottoson, Filip
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Vidman, Linda
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Rentoft, Matilda
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Schmidt, Julie A ...
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Travis, Ruth C.
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Weiderpass, Elis ...
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Johansson, Matti ...
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Dossus, Laure
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Jenab, Mazda
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Gunter, Marc J.
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Bermejo, Justo L ...
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Scherer, Dominiq ...
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Salek, Reza M.
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Keski-Rahkonen, ...
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Ferrari, Pietro
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- Om ämnet
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- MEDICIN OCH HÄLSOVETENSKAP
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MEDICIN OCH HÄLS ...
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och Klinisk medicin
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och Cancer och onkol ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Data och informa ...
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och Bioinformatik
- Artiklar i publikationen
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Metabolites
- Av lärosätet
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Umeå universitet
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Lunds universitet