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  • Viallon, VivianInternational Agency for Research on Cancer, World Health Organization (author)

A new pipeline for the normalization and pooling of metabolomics data

  • Article/chapterEnglish2021

Publisher, publication year, extent ...

  • 2021-09-17
  • MDPI,2021
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:umu-188135
  • https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-188135URI
  • https://doi.org/10.3390/metabo11090631DOI
  • https://lup.lub.lu.se/record/13d41a4f-7812-4615-8ca3-76bee31b3125URI

Supplementary language notes

  • Language:English
  • Summary in:English

Part of subdatabase

Classification

  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • (This article belongs to the Special Issue Metabolomics Meets Epidemiology).
  • 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • His, MathildeInternational Agency for Research on Cancer, World Health Organization (author)
  • Rinaldi, SabinaInternational Agency for Research on Cancer, World Health Organization (author)
  • Breeur, MarieInternational Agency for Research on Cancer, World Health Organization (author)
  • Gicquiau, AudreyInternational Agency for Research on Cancer, World Health Organization (author)
  • Hemon, BertrandInternational Agency for Research on Cancer, World Health Organization (author)
  • Overvad, KimAarhus University (author)
  • Tjønneland, AnneDanish Cancer Society (author)
  • Rostgaard-Hansen, Agnetha LinnDanish Cancer Society (author)
  • Rothwell, Joseph A.Versailles Saint-Quentin-en-Yvelines University (author)
  • Lecuyer, LucieVersailles Saint-Quentin-en-Yvelines University (author)
  • Severi, GianlucaUniversity of Florence,Versailles Saint-Quentin-en-Yvelines University (author)
  • Kaaks, RudolfGerman Cancer Research Centre (author)
  • Johnson, TheronGerman Cancer Research Centre (author)
  • Schulze, Matthias B.University of Potsdam,German Institute of Human Nutrition (author)
  • Palli, DomenicoInstitute for Cancer Research, Prevention and Clinical Network (ISPRO) (author)
  • Agnoli, ClaudiaIstituto Nazionale dei Tumori (author)
  • Panico, SalvatoreUniversity of Naples Federico II (author)
  • Tumino, RosarioProvincial Health Authority (ASP) Ragusa (author)
  • Ricceri, FulvioUniversity of Turin,Azienda Sanitaria Locale Torino 3 (author)
  • Monique Verschuren, W.M.University Medical Center Utrecht,National Institute for Public Health and the Environment (RIVM) (author)
  • Engelfriet, PeterNational Institute for Public Health and the Environment (RIVM) (author)
  • Onland-Moret, CharlotteUniversity Medical Center Utrecht (author)
  • Vermeulen, RoelUniversity Medical Center Utrecht,Utrecht University (author)
  • Nøst, Therese HaugdahlUiT The Arctic University of Norway, Tromsø (author)
  • Urbarova, IlonaUiT The Arctic University of Norway, Tromsø (author)
  • Zamora-Ros, RaulBellvitge Biomedical Research Institute (author)
  • Rodriguez-Barranco, MiguelAndalusian School Of Public Health (EASP) (author)
  • Amiano, PilarBiodonostia Health Research Institute (author)
  • Huerta, José MariaMurcia Regional Health Council (author)
  • Ardanaz, EvaHealth Research Institute of Navarra (IDISNA) (author)
  • Melander, OlleLund University,Lunds universitet,Kardiovaskulär forskning - hypertoni,Forskargrupper vid Lunds universitet,Cardiovascular Research - Hypertension,Lund University Research Groups,Skåne University Hospital(Swepub:lu)endo-ome (author)
  • Ottoson, FilipLund University (author)
  • Vidman, LindaUmeå University,Umeå universitet,Onkologi(Swepub:umu)livi0018 (author)
  • Rentoft, MatildaUmeå University,Umeå universitet,Onkologi(Swepub:umu)maaret01 (author)
  • Schmidt, Julie A.University of Oxford (author)
  • Travis, Ruth C.University of Oxford (author)
  • Weiderpass, ElisabeteInternational Agency for Research on Cancer, World Health Organization (author)
  • Johansson, MattiasInternational Agency for Research on Cancer, World Health Organization (author)
  • Dossus, LaureInternational Agency for Research on Cancer, World Health Organization (author)
  • Jenab, MazdaInternational Agency for Research on Cancer, World Health Organization (author)
  • Gunter, Marc J.International Agency for Research on Cancer, World Health Organization (author)
  • Bermejo, Justo LorenzoHeidelberg University (author)
  • Scherer, DominiqueHeidelberg University (author)
  • Salek, Reza M.International Agency for Research on Cancer, World Health Organization (author)
  • Keski-Rahkonen, PekkaInternational Agency for Research on Cancer, World Health Organization (author)
  • Ferrari, PietroInternational Agency for Research on Cancer, World Health Organization (author)
  • International Agency for Research on Cancer, World Health OrganizationAarhus University (creator_code:org_t)

Related titles

  • In:Metabolites: MDPI11:92218-19892218-1989

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