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Julie Schmidt

A New Pipeline for the Normalization and Pooling of Metabolomics Data

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

DOI

  • Vivian Viallon, Nutrition and Metabolism Branch, Frankrig
  • Mathilde His, Nutrition and Metabolism Branch, Frankrig
  • Sabina Rinaldi, Nutrition and Metabolism Branch, Frankrig
  • Marie Breeur, Nutrition and Metabolism Branch
    • ,
  • Audrey Gicquiau, Nutrition and Metabolism Branch, Frankrig
  • Bertrand Hemon, Nutrition and Metabolism Branch, Frankrig
  • Kim Overvad
  • Anne Tjønneland, Kræftens Bekæmpelse, Danmark
  • Agnetha Linn Rostgaard-Hansen, Kræftens Bekæmpelse, Danmark
  • Joseph A Rothwell, UVSQ, Inserm, CESP U1018, “Exposome and Heredity” Team, Université Paris-Saclay, Gustave Roussy, 94800 Villejuif, Frankrig
  • Lucie Lecuyer, UVSQ, Inserm, CESP U1018, “Exposome and Heredity” Team, Université Paris-Saclay, Gustave Roussy, 94800 Villejuif, Frankrig
  • Gianluca Severi, UVSQ, Inserm, CESP U1018, “Exposome and Heredity” Team, Université Paris-Saclay, Gustave Roussy, 94800 Villejuif, University of Florence, Frankrig
  • Rudolf Kaaks, German Cancer Research Center, Tyskland
  • Theron Johnson, German Cancer Research Center, Tyskland
  • Matthias B Schulze, German Institute of Human Nutrition Potsdam-Rehbruecke, University of Potsdam, Tyskland
  • Domenico Palli, Institute for the Study and Prevention of Cancer (ISPRO), Italien
  • Claudia Agnoli, Epidemiology and Prevention Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy., Italien
  • Salvatore Panico, University of Naples Federico II, Italien
  • Rosario Tumino, Cancer Registry and Histopathology Department, 'Civic - M.P.Arezzo' Hospital, Italy., Italien
  • Fulvio Ricceri, University of Turin, Unit of Epidemiology, Regional Health Service ASL TO3, 10095 Grugliasco (Turin), Italy., Italien
  • W M Monique Verschuren, National Institute for Public Health and the Environment (RIVM), University Medical Centre Utrecht, Holland
  • Peter Engelfriet, National Institute for Public Health and the Environment (RIVM), Holland
  • Charlotte Onland-Moret, University Medical Centre Utrecht, Holland
  • Roel Vermeulen, University Medical Centre Utrecht, Utrecht University, Holland
  • Therese Haugdahl Nøst, UiT The Arctic University of Norway, Norge
  • Ilona Urbarova, UiT The Arctic University of Norway, Norge
  • Raul Zamora-Ros, Bellvitge Biomedical Research Institute - IDIBELL, Spanien
  • Miguel Rodriguez-Barranco, Escuela Andaluza de Salud Publica, University of Granada, CIBER - Center for Biomedical Research Network, Spanien
  • Pilar Amiano, CIBER - Center for Biomedical Research Network, Ministry of Health of the Basque Government, Instituto de Investigación Sanitaria Biodonostia, Spanien
  • José Maria Huerta, CIBER - Center for Biomedical Research Network, Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, 30007 Murcia, Spanien
  • Eva Ardanaz, CIBER - Center for Biomedical Research Network, Navarra Public Health Institute, IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spanien
  • Olle Melander, Lund University, Department of Emergency and Internal Medicine, Skåne University Hospital, SE-20 502 Malmö, Sverige
  • Filip Ottoson, Department of Immunotechnology, Lund University, SE-22 100 Lund, Sverige
  • Linda Vidman, Umeå University, Sverige
  • Matilda Rentoft, Umeå University, Sverige
  • Julie A Schmidt
  • Ruth C Travis, University of Oxford, Storbritannien
  • Elisabete Weiderpass, World Health Organization, Frankrig
  • Mattias Johansson, Genomic Epidemiology Branch, Frankrig
  • Laure Dossus, Nutrition and Metabolism Branch, Frankrig
  • Mazda Jenab, Nutrition and Metabolism Branch, Frankrig
  • Marc J Gunter, International Agency for Research on Cancer
    • ,
  • Justo Lorenzo Bermejo, Statistical Genetics Group, Institute of Medical Biometry, University of Heidelberg, Tyskland
  • Dominique Scherer, Statistical Genetics Group, Institute of Medical Biometry, University of Heidelberg, Tyskland
  • Reza M Salek, Nutrition and Metabolism Branch, Frankrig
  • Pekka Keski-Rahkonen, Nutrition and Metabolism Branch, Frankrig
  • Pietro Ferrari, Nutrition and Metabolism Branch, Frankrig

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.

OriginalsprogEngelsk
Artikelnummer631
TidsskriftMetabolites
Vol/bind11
Nummer9
Antal sider18
ISSN2218-1989
DOI
StatusUdgivet - sep. 2021

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