Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review

Handle URI:
http://hdl.handle.net/10754/337011
Title:
Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review
Authors:
Emwas, Abdul-Hamid M.; Luchinat, Claudio; Turano, Paola; Tenori, Leonardo; Roy, Raja; Salek, Reza M.; Ryan, Danielle; Merzaban, Jasmeen S. ( 0000-0002-7276-2907 ) ; Kaddurah-Daouk, Rima; Zeri, Ana Carolina; Nagana Gowda, G. A.; Raftery, Daniel; Wang, Yulan; Brennan, Lorraine; Wishart, David S.
Abstract:
The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.
KAUST Department:
Advanced Nanofabrication, Imaging and Characterization Core Lab; Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review 2014 Metabolomics
Publisher:
Springer Science + Business Media
Journal:
Metabolomics
Issue Date:
21-Nov-2014
DOI:
10.1007/s11306-014-0746-7
PubMed ID:
26109927
PubMed Central ID:
PMC4475544
Type:
Article
ISSN:
1573-3882; 1573-3890
Additional Links:
http://link.springer.com/10.1007/s11306-014-0746-7
Appears in Collections:
Articles; Advanced Nanofabrication, Imaging and Characterization Core Lab; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorEmwas, Abdul-Hamid M.en
dc.contributor.authorLuchinat, Claudioen
dc.contributor.authorTurano, Paolaen
dc.contributor.authorTenori, Leonardoen
dc.contributor.authorRoy, Rajaen
dc.contributor.authorSalek, Reza M.en
dc.contributor.authorRyan, Danielleen
dc.contributor.authorMerzaban, Jasmeen S.en
dc.contributor.authorKaddurah-Daouk, Rimaen
dc.contributor.authorZeri, Ana Carolinaen
dc.contributor.authorNagana Gowda, G. A.en
dc.contributor.authorRaftery, Danielen
dc.contributor.authorWang, Yulanen
dc.contributor.authorBrennan, Lorraineen
dc.contributor.authorWishart, David S.en
dc.date.accessioned2014-12-10T06:57:22Zen
dc.date.available2014-12-10T06:57:22Zen
dc.date.issued2014-11-21en
dc.identifier.citationStandardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review 2014 Metabolomicsen
dc.identifier.issn1573-3882en
dc.identifier.issn1573-3890en
dc.identifier.pmid26109927en
dc.identifier.doi10.1007/s11306-014-0746-7en
dc.identifier.urihttp://hdl.handle.net/10754/337011en
dc.description.abstractThe metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.en
dc.language.isoenen
dc.publisherSpringer Science + Business Mediaen
dc.relation.urlhttp://link.springer.com/10.1007/s11306-014-0746-7en
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.en
dc.subjectNMRen
dc.subjectMetabolomicsen
dc.subjectMetabonomicsen
dc.subjectMetabolites profilingen
dc.subjectUrineen
dc.subjectBiomarkeren
dc.subjectHuman diseasesen
dc.subjectStandardizationen
dc.subjectDiagnosisen
dc.subjectRecommendationsen
dc.titleStandardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a reviewen
dc.typeArticleen
dc.contributor.departmentAdvanced Nanofabrication, Imaging and Characterization Core Laben
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalMetabolomicsen
dc.identifier.pmcidPMC4475544en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionCentro Risonanze Magnetiche – CERM, University of Florence, Florence, Italyen
dc.contributor.institutionFiorGen Foundation, 50019, Sesto Fiorentino, Florence, Italyen
dc.contributor.institutionCentre of Biomedical Research, Formerly known as Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, Indiaen
dc.contributor.institutionDepartment of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UKen
dc.contributor.institutionEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UKen
dc.contributor.institutionSchool of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, Australiaen
dc.contributor.institutionPharmacometabolomics Center, School of Medicine, Duke University, Durham, USAen
dc.contributor.institutionBrazilian Biosciences National Laboratory, LNBio, Campinas, SP, Brazilen
dc.contributor.institutionDepartment of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA, 98109, USAen
dc.contributor.institutionWuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Beijing, Chinaen
dc.contributor.institutionInstitute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Irelanden
dc.contributor.institutionDepartment of Computing Science, University of Alberta, Edmonton, Alberta, Canadaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorEmwas, Abdul-Hamid M.en
kaust.authorMerzaban, Jasmeen S.en

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