Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/46219
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dc.contributor.authorAnckaert, Jasper-
dc.contributor.authorCobos, Francisco Avila-
dc.contributor.authorDecock, Anneleen-
dc.contributor.authorDecruyenaere, Philippe-
dc.contributor.authorDeleu, Jill-
dc.contributor.authorDe Preter, Katleen-
dc.contributor.authorDe Wever, Olivier-
dc.contributor.authorDe Wilde , Jilke-
dc.contributor.authorDhondt, Bert-
dc.contributor.authorD'huyvetter, Thibaut-
dc.contributor.authorEveraert, Celine-
dc.contributor.authorFierro, Carolina-
dc.contributor.authorHelsmoortel, Hetty H.-
dc.contributor.authorHendrix, An-
dc.contributor.authorHulstaert, Eva-
dc.contributor.authorKuersten, Scott-
dc.contributor.authorKoster , Jan-
dc.contributor.authorMercer, Tim R.-
dc.contributor.authorMestdagh, Pieter-
dc.contributor.authorMorlion, Annelien-
dc.contributor.authorNuytens, Justine-
dc.contributor.authorPhilippron, Annouck-
dc.contributor.authorNijs , Nele-
dc.contributor.authorPiofczyk, Thomas-
dc.contributor.authorPoma-Soto, Franco-
dc.contributor.authorSchoofs, Kathleen-
dc.contributor.authorSchroth, Gary P.-
dc.contributor.authorTHAS, Olivier-
dc.contributor.authorVanden Eynde, Eveline-
dc.contributor.authorVandesompele, Jo-
dc.contributor.authorVan Maerken, Tom-
dc.contributor.authorVan Paemel, Ruben-
dc.contributor.authorVerniers, Kimberly-
dc.contributor.authorVerwilt, Jasper-
dc.contributor.authorYigit, Nurten-
dc.date.accessioned2025-06-18T08:54:51Z-
dc.date.available2025-06-18T08:54:51Z-
dc.date.issued2025-
dc.date.submitted2025-06-04T12:38:22Z-
dc.identifier.citationNature communications, 16 (1) (Art N° 4513)-
dc.identifier.urihttp://hdl.handle.net/1942/46219-
dc.description.abstractBlood-based extracellular RNA (cell-free RNA; exRNA) biomarkers require validated sample collection, processing, and quantification procedures. No study to date has systematically tested pre-analytical variables affecting transcriptome-wide exRNA analysis. By evaluating their impact on deep transcriptome profiling of microRNAs and mRNAs in blood plasma or serum, we compared ten blood collection tubes, three blood processing time intervals, and eight RNA purification methods. In addition, we assessed interactions among a selected pre-analytical variable set, resulting in 456 extracellular transcriptomes. Blood preservation tubes failed to stabilize exRNA and RNA purification methods differed significantly in performance, causing variations in concentration, detected gene numbers, replicability and observed transcriptome complexity. Critical interactions between tubes, purification methods and time intervals were identified. We provide 11 analytical performance metrics for exRNA quantification methods and put forward recommendations for both users and manufacturers of RNA purification methods and blood collection tubes, collectively, essential groundwork for exRNA-based precision medicine applications.-
dc.description.sponsorshipAcknowledgements This study was in part funded by Ghent University (BOF-GOA), Stand up to Cancer (Kom op tegen Kanker, the Flemish cancer society), the Foundation against Cancer, Research Foundation Flanders (FWO; G0B2820N), the Liquidhope Transcan-2 project, the International Waldenstroem Macroglobulinemia Foundation/Leukemia Lymphoma Society, and the European Union’s Horizon 2020 research and innovation program (grant agreement 826121). H.H.H., C.E., J.D.W., E.H., P.D., and R.V.P. were funded by a predoctoral fellowship grant from the FWO (12Q6217N, 1S07416N, 1S90621N, 1133120N,11H7523N, and 11B3718N). F.A.C was supported by a Special Research Fund postdoctoral scholarship from Ghent University (BOF21/PDO/007). A.M. was supported by a Special Research Fund scholarship from Ghent University (BOF19/ DOC/228), Stand up to Cancer and a predoctoral fellowship grant from the FWO (11C1621N). A.D. was supported by a postdoctoral fellowship grant from the Special Research Fund of Ghent University (BOF17/PDO/ 037) and the FWO (1224021N, 1266325N). K.S. was supported by a grant from Stand up to Cancer. J.D. was supported by the Special Research Fund of Ghent University (BOF22/CDV/077). We thank Illumina for sponsoring library preparation and sequencing reagents, and Qiagen, Promega and Roche for sponsoring blood collection tubes and/or RNA purification methods. The authors would like to thank Kathy Astrahantseff for the help in manuscript writing.-
dc.language.isoen-
dc.publisherNATURE PORTFOLIO-
dc.rightsThe Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creativecommons.org/licenses/by-nc-nd/4.0/.-
dc.subject.otherHumans-
dc.subject.otherTranscriptome-
dc.subject.otherRNA, Messenger-
dc.subject.otherMicroRNAs-
dc.subject.otherGene Expression Profiling-
dc.subject.otherBlood Specimen Collection-
dc.subject.otherCell-Free Nucleic Acids-
dc.titleBlood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling-
dc.typeJournal Contribution-
dc.identifier.issue1-
dc.identifier.volume16-
local.format.pages17-
local.bibliographicCitation.jcatA1-
dc.description.notesMestdagh, P; Vandesompele, J (corresponding author), Univ Ghent, OncoRNALab, Dept Biomol Med, Ghent, Belgium.; Mestdagh, P; Vandesompele, J (corresponding author), Canc Res Inst Ghent CRIG, Ghent, Belgium.; Mestdagh, P; Vandesompele, J (corresponding author), Biogazelle, Zwijnaarde, Belgium.-
dc.description.notespieter.mestdagh@ugent.be; jo.vandesompele@ugent.be-
local.publisher.placeHEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY-
local.type.refereedRefereed-
local.type.specifiedArticle-
local.bibliographicCitation.artnr4513-
local.type.programmeH2020-
local.relation.h2020826121-
dc.identifier.doi10.1038/s41467-025-58607-7-
dc.identifier.pmid40374609-
dc.identifier.isiWOS:001489557900012-
local.provider.typewosris-
local.description.affiliation[Anckaert, Jasper; Cobos, Francisco Avila; Decock, Anneleen; Decruyenaere, Philippe; Deleu, Jill; De Wilde, Jilke; D'huyvetter, Thibaut; Everaert, Celine; Helsmoortel, Hetty H.; Hulstaert, Eva; Mestdagh, Pieter; Morlion, Annelien; Nuytens, Justine; Poma-Soto, Franco; Schoofs, Kathleen; Vanden Eynde, Eveline; Vandesompele, Jo; Van Maerken, Tom; Van Paemel, Ruben; Verniers, Kimberly; Verwilt, Jasper; Yigit, Nurten] Univ Ghent, OncoRNALab, Dept Biomol Med, Ghent, Belgium.-
local.description.affiliation[Anckaert, Jasper; Cobos, Francisco Avila; Decock, Anneleen; Decruyenaere, Philippe; Deleu, Jill; De Preter, Katleen; De Wever, Olivier; De Wilde, Jilke; Dhondt, Bert; D'huyvetter, Thibaut; Everaert, Celine; Helsmoortel, Hetty H.; Hendrix, An; Hulstaert, Eva; Mestdagh, Pieter; Morlion, Annelien; Nuytens, Justine; Philippron, Annouck; Poma-Soto, Franco; Schoofs, Kathleen; Vanden Eynde, Eveline; Vandesompele, Jo; Van Maerken, Tom; Van Paemel, Ruben; Verniers, Kimberly; Verwilt, Jasper; Yigit, Nurten] Canc Res Inst Ghent CRIG, Ghent, Belgium.-
local.description.affiliation[Cobos, Francisco Avila; De Preter, Katleen; De Wilde, Jilke; Everaert, Celine; Schoofs, Kathleen; Van Paemel, Ruben] Univ Ghent, Ctr Med Genet, Dept Biomol Med, TOBI Lab, Ghent, BELARUS.-
local.description.affiliation[Decruyenaere, Philippe] Ghent Univ Hosp, Dept Hematol, Ghent, Belgium.-
local.description.affiliation[De Wever, Olivier; Dhondt, Bert; Hendrix, An] Univ Ghent, Lab Expt Canc Res, Ghent, Belgium.-
local.description.affiliation[Dhondt, Bert] Ghent Univ Hosp, Dept Urol, Ghent, Belgium.-
local.description.affiliation[Fierro, Carolina; Mestdagh, Pieter; Nijs, Nele; Piofczyk, Thomas; Vandesompele, Jo] Biogazelle, Zwijnaarde, Belgium.-
local.description.affiliation[Hulstaert, Eva] Ghent Univ Hosp, Dept Dermatol, Ghent, Belgium.-
local.description.affiliation[Koster, Jan] Univ Amsterdam, Amsterdam Univ Med Ctr, Ctr Expt & Mol Med CEMM, Amsterdam, Netherlands.-
local.description.affiliation[Kuersten, Scott; Schroth, Gary P.] Illumina, San Diego, CA USA.-
local.description.affiliation[Mercer, Tim R.] Univ Queensland, Australian Inst Bioengn & Nanotechnol, Brisbane, Qld, Australia.-
local.description.affiliation[Mercer, Tim R.] Garvan Inst Med Res, Kinghorn Ctr Clin Genom, Sydney, NSW, Australia.-
local.description.affiliation[Philippron, Annouck] Univ Ghent, Lab Expt Surg, Ghent, Belgium.-
local.description.affiliation[Philippron, Annouck] Ghent Univ Hosp, Dept Gastrointestinal Surg, Ghent, Belgium.-
local.description.affiliation[Thas, Olivier] Hasselt Univ, Data Sci Inst DSI, Interuniv Inst Biostat & Stat Bioinformat I BioSta, Hasselt, Belgium.-
local.description.affiliation[Thas, Olivier] Univ Ghent, Dept Appl Math Comp Sci & Stat, Ghent, Belgium.-
local.description.affiliation[Thas, Olivier] Univ Wollongong, Natl Inst Appl Stat Res Australia NIASRA, Wollongong, Australia.-
local.description.affiliation[Van Maerken, Tom] AZ Groeninge, Dept Lab Med, Kortrijk, Belgium.-
local.description.affiliation[Van Paemel, Ruben] Ghent Univ Hosp, Dept Pediat, Ghent, Belgium.-
local.uhasselt.internationalyes-
item.fullcitationAnckaert, Jasper; Cobos, Francisco Avila; Decock, Anneleen; Decruyenaere, Philippe; Deleu, Jill; De Preter, Katleen; De Wever, Olivier; De Wilde , Jilke; Dhondt, Bert; D'huyvetter, Thibaut; Everaert, Celine; Fierro, Carolina; Helsmoortel, Hetty H.; Hendrix, An; Hulstaert, Eva; Kuersten, Scott; Koster , Jan; Mercer, Tim R.; Mestdagh, Pieter; Morlion, Annelien; Nuytens, Justine; Philippron, Annouck; Nijs , Nele; Piofczyk, Thomas; Poma-Soto, Franco; Schoofs, Kathleen; Schroth, Gary P.; THAS, Olivier; Vanden Eynde, Eveline; Vandesompele, Jo; Van Maerken, Tom; Van Paemel, Ruben; Verniers, Kimberly; Verwilt, Jasper & Yigit, Nurten (2025) Blood collection tube and RNA purification method recommendations for extracellular RNA transcriptome profiling. In: Nature communications, 16 (1) (Art N° 4513).-
item.contributorAnckaert, Jasper-
item.contributorCobos, Francisco Avila-
item.contributorDecock, Anneleen-
item.contributorDecruyenaere, Philippe-
item.contributorDeleu, Jill-
item.contributorDe Preter, Katleen-
item.contributorDe Wever, Olivier-
item.contributorDe Wilde , Jilke-
item.contributorDhondt, Bert-
item.contributorD'huyvetter, Thibaut-
item.contributorEveraert, Celine-
item.contributorFierro, Carolina-
item.contributorHelsmoortel, Hetty H.-
item.contributorHendrix, An-
item.contributorHulstaert, Eva-
item.contributorKuersten, Scott-
item.contributorKoster , Jan-
item.contributorMercer, Tim R.-
item.contributorMestdagh, Pieter-
item.contributorMorlion, Annelien-
item.contributorNuytens, Justine-
item.contributorPhilippron, Annouck-
item.contributorNijs , Nele-
item.contributorPiofczyk, Thomas-
item.contributorPoma-Soto, Franco-
item.contributorSchoofs, Kathleen-
item.contributorSchroth, Gary P.-
item.contributorTHAS, Olivier-
item.contributorVanden Eynde, Eveline-
item.contributorVandesompele, Jo-
item.contributorVan Maerken, Tom-
item.contributorVan Paemel, Ruben-
item.contributorVerniers, Kimberly-
item.contributorVerwilt, Jasper-
item.contributorYigit, Nurten-
item.fulltextWith Fulltext-
item.accessRightsOpen Access-
crisitem.journal.eissn2041-1723-
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