A new pipeline for the normalization and pooling of metabolomics data

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A new pipeline for the normalization and pooling of metabolomics data

Viallon, Vivian (författare): International Agency for Research on Cancer, World Health Organization

His, Mathilde (författare): International Agency for Research on Cancer, World Health Organization

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

Gicquiau, Audrey (författare): International Agency for Research on Cancer, World Health Organization

Hemon, Bertrand (författare): International Agency for Research on Cancer, World Health Organization

Overvad, Kim (författare): Aarhus University

Tjønneland, Anne (författare): Danish Cancer Society

Rostgaard-Hansen, Agnetha Linn (författare): Danish Cancer Society

Rothwell, Joseph A. (författare): Versailles Saint-Quentin-en-Yvelines University

Lecuyer, Lucie (författare): Versailles Saint-Quentin-en-Yvelines University

Severi, Gianluca (författare): University of Florence,Versailles Saint-Quentin-en-Yvelines University

Kaaks, Rudolf (författare): German Cancer Research Centre

Johnson, Theron (författare): German Cancer Research Centre

Schulze, Matthias B. (författare): University of Potsdam,German Institute of Human Nutrition

Palli, Domenico (författare): Institute for Cancer Research, Prevention and Clinical Network (ISPRO)

Agnoli, Claudia (författare): Istituto Nazionale dei Tumori

Panico, Salvatore (författare): University of Naples Federico II

Tumino, Rosario (författare): Provincial Health Authority (ASP) Ragusa

Ricceri, Fulvio (författare): University of Turin,Azienda Sanitaria Locale Torino 3

Monique Verschuren, W.M. (författare): University Medical Center Utrecht,National Institute for Public Health and the Environment (RIVM)

Engelfriet, Peter (författare): National Institute for Public Health and the Environment (RIVM)

Onland-Moret, Charlotte (författare): University Medical Center Utrecht

Vermeulen, Roel (författare): University Medical Center Utrecht,Utrecht University

Nøst, Therese Haugdahl (författare): UiT The Arctic University of Norway, Tromsø

Urbarova, Ilona (författare): UiT The Arctic University of Norway, Tromsø

Zamora-Ros, Raul (författare): Bellvitge Biomedical Research Institute

Rodriguez-Barranco, Miguel (författare): Andalusian School Of Public Health (EASP)

Amiano, Pilar (författare): Biodonostia Health Research Institute

Huerta, José Maria (författare): Murcia Regional Health Council

Ardanaz, Eva (författare): Health Research Institute of Navarra (IDISNA)

Melander, Olle (författare): Lund University,Lunds universitet,Kardiovaskulär forskning - hypertoni,Forskargrupper vid Lunds universitet,Cardiovascular Research - Hypertension,Lund University Research Groups,Skåne University Hospital

Ottoson, Filip (författare): Lund University

Vidman, Linda (författare): Umeå University,Umeå universitet,Onkologi

Rentoft, Matilda (författare): Umeå University,Umeå universitet,Onkologi

Schmidt, Julie A. (författare): University of Oxford

Travis, Ruth C. (författare): University of Oxford

Weiderpass, Elisabete (författare): International Agency for Research on Cancer, World Health Organization

Johansson, Mattias (författare): International Agency for Research on Cancer, World Health Organization

Dossus, Laure (författare): International Agency for Research on Cancer, World Health Organization

Jenab, Mazda (författare): International Agency for Research on Cancer, World Health Organization

Gunter, Marc J. (författare): International Agency for Research on Cancer, World Health Organization

Bermejo, Justo Lorenzo (författare): Heidelberg University

Scherer, Dominique (författare): Heidelberg University

Salek, Reza M. (författare): International Agency for Research on Cancer, World Health Organization

Keski-Rahkonen, Pekka (författare): International Agency for Research on Cancer, World Health Organization

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.
Ingår i: Metabolites. - : MDPI. - 2218-1989 .- 2218-1989. ; 11:9

Relaterad länk:: https://doi.org/10.3...; visa fler...; https://umu.diva-por... (primary) (Raw object); https://www.mdpi.com...; http://dx.doi.org/10... (free); https://urn.kb.se/re...; https://doi.org/10.3...; https://lup.lub.lu.s...; visa färre...

Tidskriftsartikel (refereegranskat)

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
Oncology
onkologi
Cancer epidemiology
Metabolites
Metabolomics
Normalization
Pooling
Technical variability

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Av författaren/redakt...: Viallon, Vivian; His, Mathilde; Rinaldi, Sabina; Breeur, Marie; Gicquiau, Audrey; Hemon, Bertrand; visa fler...; Overvad, Kim; Tjønneland, Anne; Rostgaard-Hansen ...; Rothwell, Joseph ...; Lecuyer, Lucie; Severi, Gianluca; Kaaks, Rudolf; Johnson, Theron; Schulze, Matthia ...; Palli, Domenico; Agnoli, Claudia; Panico, Salvator ...; Tumino, Rosario; Ricceri, Fulvio; Monique Verschur ...; Engelfriet, Pete ...; Onland-Moret, Ch ...; Vermeulen, Roel; Nøst, Therese Ha ...; Urbarova, Ilona; Zamora-Ros, Raul; Rodriguez-Barran ...; Amiano, Pilar; Huerta, José Mar ...; Ardanaz, Eva; Melander, Olle; Ottoson, Filip; Vidman, Linda; Rentoft, Matilda; Schmidt, Julie A ...; Travis, Ruth C.; Weiderpass, Elis ...; Johansson, Matti ...; Dossus, Laure; Jenab, Mazda; Gunter, Marc J.; Bermejo, Justo L ...; Scherer, Dominiq ...; Salek, Reza M.; Keski-Rahkonen, ...; Ferrari, Pietro; visa färre...

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Klinisk medicin; och Cancer och onkol ...

NATURVETENSKAP: NATURVETENSKAP; och Data och informa ...; och Bioinformatik

Artiklar i publikationen: Metabolites

Av lärosätet: Umeå universitet; Lunds universitet

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