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Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA

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dc.contributor.author Trinidad, Eva María
dc.contributor.author Vidal, Enrique
dc.contributor.author Coronado, Esther
dc.contributor.author Esteve-Codina, Anna
dc.contributor.author Castel, Victoria
dc.contributor.author Cañete, Adela
dc.contributor.author Gut, Marta
dc.contributor.author Heath, Simon
dc.contributor.author Font de Mora, Jaime
dc.date.accessioned 2023-03-20T07:19:18Z
dc.date.available 2023-03-20T07:19:18Z
dc.date.issued 2023
dc.identifier.citation Trinidad EM, Vidal E, Coronado E, Esteve-Codina A, Castel V, Cañete A, et al. Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA. Briefings in Bioinformatics. 2023 Jan;24(1):bbac575. DOI: 10.1093/bib/bbac575
dc.identifier.issn 1467-5463
dc.identifier.uri http://hdl.handle.net/10230/56266
dc.description.abstract Analysis of the methylome of tumor cell-free deoxyribonucleic acid (DNA; cfDNA) has emerged as a powerful non-invasive technique for cancer subtyping and prognosis. However, its application is frequently hampered by the quality and total cfDNA yield. Here, we demonstrate the feasibility of very low-input cfDNA for whole-methylome and copy-number profiling studies using enzymatic conversion of unmethylated cysteines [enzymatic methyl-seq (EM-seq)] to better preserve DNA integrity. We created a model for predicting genomic subtyping and prognosis with high accuracy. We validated our tool by comparing whole-genome CpG sequencing with in situ cohorts generated with bisulfite conversion and array hybridization, demonstrating that, despite the different techniques and sample origins, information on cfDNA methylation is comparable with in situ cohorts. Our findings support use of liquid biopsy followed by EM-seq to assess methylome of cancer patients, enabling validation in external cohorts. This advance is particularly relevant for rare cancers like neuroblastomas where liquid-biopsy volume is restricted by ethical regulations in pediatric patients.
dc.description.sponsorship TRANSCAN-2 consortium LIQUIDHOPE by Fundación Científica de la Asociación Española Contra el Cáncer (TRNSC18001FON); Spanish Ministry of Science and Innovation (MICINN, PID2020-119323RB-I00 grant); ‘Sumemos muchas manos por los niños enfermos’ non-profit organization; Instituto de Salud Carlos III (ISCIII), Spain and ‘European Social Fund Plus (ESF+)’ of the European Union (Miguel Servet Program, CP20/00179, ISCIII-MICINN to E.V.); Fundación Científica de la Asociación Española Contra el Cáncer (PRDVA19004CORO to E.C.).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Briefings in Bioinformatics. 2023 Jan;24(1):bbac575
dc.rights © The Author(s) 2023. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.title Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/bib/bbac575
dc.subject.keyword Neuroblastoma
dc.subject.keyword Liquid biopsy
dc.subject.keyword High-risk
dc.subject.keyword MYCN
dc.subject.keyword 11q
dc.subject.keyword DNA methylation
dc.subject.keyword Combined haploinsufficiency
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-119323RB-I00
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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