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.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.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.doi http://dx.doi.org/10.1093/bib/bbac575
- dc.identifier.issn 1467-5463
- dc.identifier.uri http://hdl.handle.net/10230/56266
- dc.language.iso eng
- dc.publisher Oxford University Press
- dc.relation.ispartof Briefings in Bioinformatics. 2023 Jan;24(1):bbac575
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-119323RB-I00
- 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.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
- 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.title Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion