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

Autor: Trinidad EM; Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain., Vidal E; Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain., Coronado E; Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain., Esteve-Codina A; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), , Barcelona , Spain., Castel V; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain.; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain., Cañete A; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain.; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.; Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain., Gut M; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), , Barcelona , Spain., Heath S; CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), , Barcelona , Spain., Font de Mora J; Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.; Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain.
Jazyk: angličtina
Zdroj: Briefings in bioinformatics [Brief Bioinform] 2023 Jan 19; Vol. 24 (1).
DOI: 10.1093/bib/bbac575
Abstrakt: 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.
(© The Author(s) 2023. Published by Oxford University Press.)
Databáze: MEDLINE
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