{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:03Z","timestamp":1753875783520,"version":"3.41.2"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,6]],"date-time":"2023-01-06T00:00:00Z","timestamp":1672963200000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002704","name":"Fundaci\u00f3n Cient\u00edfica de la Asociaci\u00f3n Espa\u00f1ola Contra el C\u00e1ncer","doi-asserted-by":"publisher","award":["PRDVA19004CORO"],"award-info":[{"award-number":["PRDVA19004CORO"]}],"id":[{"id":"10.13039\/501100002704","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Instituto de Salud Carlos III (ISCIII), Spain and \u2018European Social Fund Plus (ESF+)\u2019 of the European Union","award":["CP20\/00179, ISCIII-MICINN"],"award-info":[{"award-number":["CP20\/00179, ISCIII-MICINN"]}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["PID2020-119323RB-I00"],"award-info":[{"award-number":["PID2020-119323RB-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002704","name":"Fundaci\u00f3n Cient\u00edfica de la Asociaci\u00f3n Espa\u00f1ola Contra el C\u00e1ncer","doi-asserted-by":"publisher","award":["TRNSC18001FON"],"award-info":[{"award-number":["TRNSC18001FON"]}],"id":[{"id":"10.13039\/501100002704","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>","DOI":"10.1093\/bib\/bbac575","type":"journal-article","created":{"date-parts":[[2023,1,8]],"date-time":"2023-01-08T04:42:38Z","timestamp":1673152958000},"source":"Crossref","is-referenced-by-count":3,"title":["Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6090-5205","authenticated-orcid":false,"given":"Eva Mar\u00eda","family":"Trinidad","sequence":"first","affiliation":[{"name":"Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4217-1807","authenticated-orcid":false,"given":"Enrique","family":"Vidal","sequence":"additional","affiliation":[{"name":"Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7487-6836","authenticated-orcid":false,"given":"Esther","family":"Coronado","sequence":"additional","affiliation":[{"name":"Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0361-2873","authenticated-orcid":false,"given":"Anna","family":"Esteve-Codina","sequence":"additional","affiliation":[{"name":"CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , , Barcelona , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3792-0615","authenticated-orcid":false,"given":"Victoria","family":"Castel","sequence":"additional","affiliation":[{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5669-5097","authenticated-orcid":false,"given":"Adela","family":"Ca\u00f1ete","sequence":"additional","affiliation":[{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Universitat Pompeu Fabra (UPF) , Barcelona 08002 , Spain"},{"name":"Pediatric Oncology Unit, La Fe University Hospital , Valencia , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4063-7159","authenticated-orcid":false,"given":"Marta","family":"Gut","sequence":"additional","affiliation":[{"name":"CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , , Barcelona , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9550-0897","authenticated-orcid":false,"given":"Simon","family":"Heath","sequence":"additional","affiliation":[{"name":"CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , , Barcelona , Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6816-2095","authenticated-orcid":false,"given":"Jaime","family":"Font de Mora","sequence":"additional","affiliation":[{"name":"Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe , Valencia , Spain"},{"name":"Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe , Valencia , Spain"}]}],"member":"286","published-online":{"date-parts":[[2023,1,5]]},"reference":[{"key":"2023011917120234500_ref1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-018-0071-5","article-title":"Current and future perspectives of liquid biopsies in genomics-driven oncology","volume":"20","author":"Heitzer","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2023011917120234500_ref2","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1038\/nprot.2010.190","article-title":"Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling","volume":"6","author":"Gu","year":"2011","journal-title":"Nat Protoc"},{"key":"2023011917120234500_ref3","doi-asserted-by":"crossref","DOI":"10.3390\/cancers12020309","article-title":"Investigation of the role of dinutuximab beta-based immunotherapy in the SIOPEN high-risk neuroblastoma 1 trial (HR-NBL1)","volume":"12","author":"Ladenstein","year":"2020","journal-title":"Cancers (Basel)"},{"key":"2023011917120234500_ref4","doi-asserted-by":"crossref","first-page":"2202","DOI":"10.1056\/NEJMra0804577","article-title":"Recent advances in neuroblastoma","volume":"362","author":"Maris","year":"2010","journal-title":"N Engl J Med"},{"key":"2023011917120234500_ref5","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1126\/science.aat6768","article-title":"A mechanistic classification of clinical phenotypes in neuroblastoma","volume":"362","author":"Ackermann","year":"2018","journal-title":"Science"},{"key":"2023011917120234500_ref6","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1126\/science.6719137","article-title":"Amplification of N-myc in untreated human neuroblastomas correlates with advanced disease stage","volume":"224","author":"Brodeur","year":"1984","journal-title":"Science"},{"key":"2023011917120234500_ref7","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1038\/nature14980","article-title":"Telomerase activation by genomic rearrangements in high-risk neuroblastoma","volume":"526","author":"Peifer","year":"2015","journal-title":"Nature"},{"key":"2023011917120234500_ref8","doi-asserted-by":"crossref","first-page":"6875","DOI":"10.1158\/1078-0432.CCR-17-0593","article-title":"Deletion of 11q in neuroblastomas drives sensitivity to PARP inhibition","volume":"23","author":"Sanmartin","year":"2017","journal-title":"Clin Cancer Res"},{"key":"2023011917120234500_ref9","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1002\/1878-0261.12868","article-title":"Intratumoral immunosuppression profiles in 11q-deleted neuroblastomas provide new potential therapeutic targets","volume":"15","author":"Coronado","year":"2021","journal-title":"Mol Oncol"},{"key":"2023011917120234500_ref10","doi-asserted-by":"crossref","first-page":"3229","DOI":"10.1200\/JCO.21.00278","article-title":"Revised neuroblastoma risk classification system: a report from the Children's Oncology Group","volume":"39","author":"Irwin","year":"2021","journal-title":"J Clin Oncol"},{"key":"2023011917120234500_ref11","doi-asserted-by":"crossref","first-page":"3122","DOI":"10.1200\/JCO.2009.26.7955","article-title":"Accumulation of segmental alterations determines progression in neuroblastoma","volume":"28","author":"Schleiermacher","year":"2010","journal-title":"J Clin Oncol"},{"key":"2023011917120234500_ref12","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1158\/1078-0432.CCR-15-1449","article-title":"Targeting MYCN-driven transcription by BET-bromodomain inhibition","volume":"22","author":"Henssen","year":"2016","journal-title":"Clin Cancer Res"},{"key":"2023011917120234500_ref13","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.ccell.2018.11.005","article-title":"Resistance to epigenetic-targeted therapy engenders tumor cell vulnerabilities associated with enhancer remodeling","volume":"34","author":"Iniguez","year":"2018","journal-title":"Cancer Cell"},{"key":"2023011917120234500_ref14","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1158\/2159-8290.CD-12-0418","article-title":"Targeting MYCN in neuroblastoma by BET bromodomain inhibition","volume":"3","author":"Puissant","year":"2013","journal-title":"Cancer Discov"},{"key":"2023011917120234500_ref15","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1093\/jnci\/djh224","article-title":"Clustering of gene hypermethylation associated with clinical risk groups in neuroblastoma","volume":"96","author":"Alaminos","year":"2004","journal-title":"J Natl Cancer Inst"},{"key":"2023011917120234500_ref16","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/75007","article-title":"Caspase 8 is deleted or silenced preferentially in childhood neuroblastomas with amplification of MYCN","volume":"6","author":"Teitz","year":"2000","journal-title":"Nat Med"},{"key":"2023011917120234500_ref17","first-page":"2157","article-title":"Tumor-specific down-regulation of the tumor necrosis factor-related apoptosis-inducing ligand decoy receptors DcR1 and DcR2 is associated with dense promoter hypermethylation","volume":"62","author":"Noesel","year":"2002","journal-title":"Cancer Res"},{"key":"2023011917120234500_ref18","doi-asserted-by":"crossref","first-page":"8493","DOI":"10.1158\/1078-0432.CCR-04-1331","article-title":"Association of epigenetic inactivation of RASSF1A with poor outcome in human neuroblastoma","volume":"10","author":"Yang","year":"2004","journal-title":"Clin Cancer Res"},{"key":"2023011917120234500_ref19","doi-asserted-by":"crossref","first-page":"1738","DOI":"10.1200\/PO.21.00130","article-title":"Novel circulating hypermethylated RASSF1A ddPCR for liquid biopsies in patients with pediatric solid tumors","volume":"5","author":"Zogchel","year":"2021","journal-title":"JCO Precis Oncol"},{"key":"2023011917120234500_ref20","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1186\/1471-2407-11-66","article-title":"Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma","volume":"11","author":"Caren","year":"2011","journal-title":"BMC Cancer"},{"key":"2023011917120234500_ref21","doi-asserted-by":"crossref","first-page":"1960","DOI":"10.18632\/oncotarget.6477","article-title":"Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma","volume":"7","author":"Decock","year":"2016","journal-title":"Oncotarget"},{"key":"2023011917120234500_ref22","doi-asserted-by":"crossref","first-page":"R95","DOI":"10.1186\/gb-2012-13-10-r95","article-title":"Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers","volume":"13","author":"Decock","year":"2012","journal-title":"Genome Biol"},{"key":"2023011917120234500_ref23","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1093\/bioinformatics\/bty690","article-title":"gemBS: high throughput processing for DNA methylation data from bisulfite sequencing","volume":"35","author":"Merkel","year":"2019","journal-title":"Bioinformatics"},{"key":"2023011917120234500_ref24","doi-asserted-by":"crossref","first-page":"E1317","DOI":"10.1073\/pnas.1500076112","article-title":"Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients","volume":"112","author":"Jiang","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023011917120234500_ref25","doi-asserted-by":"crossref","first-page":"e1004868","DOI":"10.1371\/journal.pgen.1004868","article-title":"Genome-wide analysis of DNA methylation dynamics during early human development","volume":"10","author":"Okae","year":"2014","journal-title":"PLoS Genet"},{"key":"2023011917120234500_ref26","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.2217\/epi.15.49","article-title":"DNA methylation fingerprint of neuroblastoma reveals new biological and clinical insights","volume":"7","author":"Gomez","year":"2015","journal-title":"Epigenomics"},{"key":"2023011917120234500_ref27","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1016\/j.celrep.2016.10.054","article-title":"Distinct trends of DNA methylation patterning in the innate and adaptive immune systems","volume":"17","author":"Schuyler","year":"2016","journal-title":"Cell Rep"},{"key":"2023011917120234500_ref28","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1007\/s12038-017-9714-5","article-title":"Induction of morphological and functional differentiation of human neuroblastoma cells by miR-124","volume":"42","author":"Sharif","year":"2017","journal-title":"J Biosci"},{"key":"2023011917120234500_ref29","doi-asserted-by":"crossref","DOI":"10.3390\/cancers14092080","article-title":"Circulating cell-free DNA assessment in biofluids from children with neuroblastoma demonstrates feasibility and potential for minimally invasive molecular diagnostics","volume":"14","author":"Lodrini","year":"2022","journal-title":"Cancers (Basel)"},{"key":"2023011917120234500_ref30","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.ejca.2021.09.022","article-title":"The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples","volume":"160","author":"Van Paemel","year":"2022","journal-title":"Eur J Cancer"},{"key":"2023011917120234500_ref31","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1080\/15592294.2016.1138195","article-title":"Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors","volume":"11","author":"Olsson","year":"2016","journal-title":"Epigenetics"},{"key":"2023011917120234500_ref32","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/cercor\/bhz137","article-title":"Nyap1 regulates multipolar-bipolar transition and morphology of migrating neurons by Fyn phosphorylation during corticogenesis","volume":"30","author":"Wang","year":"2020","journal-title":"Cereb Cortex"},{"key":"2023011917120234500_ref33","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1111\/j.1471-4159.2012.07779.x","article-title":"Lmx1a regulates dopamine transporter gene expression during ES cell differentiation and mouse embryonic development","volume":"122","author":"Chung","year":"2012","journal-title":"J Neurochem"},{"key":"2023011917120234500_ref34","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1111\/j.1349-7006.2010.01804.x","article-title":"Hypermethylation-mediated reduction of LMX1A expression in gastric cancer","volume":"102","author":"Dong","year":"2011","journal-title":"Cancer Sci"},{"key":"2023011917120234500_ref35","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1002\/ijc.23519","article-title":"Identification of novel DNA methylation markers in cervical cancer","volume":"123","author":"Lai","year":"2008","journal-title":"Int J Cancer"},{"key":"2023011917120234500_ref36","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1002\/ijc.23957","article-title":"An epigenetic marker panel for screening and prognostic prediction of ovarian cancer","volume":"124","author":"Su","year":"2009","journal-title":"Int J Cancer"},{"key":"2023011917120234500_ref37","doi-asserted-by":"crossref","first-page":"e35175","DOI":"10.1371\/journal.pone.0035175","article-title":"Methylcap-seq reveals novel DNA methylation markers for the diagnosis and recurrence prediction of bladder cancer in a Chinese population","volume":"7","author":"Zhao","year":"2012","journal-title":"PLoS One"},{"key":"2023011917120234500_ref38","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1593\/neo.06670","article-title":"Tissue microenvironment modulates CXCR4 expression and tumor metastasis in neuroblastoma","volume":"9","author":"Zhang","year":"2007","journal-title":"Neoplasia"},{"key":"2023011917120234500_ref39","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1002\/ijc.31532","article-title":"Colony stimulating factor 1 receptor blockade improves the efficacy of chemotherapy against human neuroblastoma in the absence of T lymphocytes","volume":"143","author":"Webb","year":"2018","journal-title":"Int J Cancer"},{"key":"2023011917120234500_ref40","doi-asserted-by":"crossref","first-page":"95135","DOI":"10.18632\/oncotarget.19619","article-title":"Inhibition of chemerin\/CMKLR1 axis in neuroblastoma cells reduces clonogenicity and cell viability in vitro and impairs tumor growth in vivo","volume":"8","author":"Tummler","year":"2017","journal-title":"Oncotarget"},{"key":"2023011917120234500_ref41","doi-asserted-by":"crossref","first-page":"2721","DOI":"10.1038\/onc.2014.226","article-title":"Autocrine CSF1R signaling mediates switching between invasion and proliferation downstream of TGFbeta in claudin-low breast tumor cells","volume":"34","author":"Patsialou","year":"2015","journal-title":"Oncogene"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac575\/48782689\/bbac575.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/24\/1\/bbac575\/48782689\/bbac575.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,19]],"date-time":"2023-01-19T17:37:03Z","timestamp":1674149823000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac575\/6972296"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1]]},"references-count":41,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,19]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac575","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2023,1]]},"published":{"date-parts":[[2023,1]]},"article-number":"bbac575"}}