{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["David Hervas"],"study_type":["methylation profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15459"],"description":["There is a growing recognition of the importance of conducting epigenome-wide analysis directly in cfDNA to identify specific, blood-measurable DNA methylation biomarkers. In this study, we ought to identify novel epigenetic biomarkers for lung cancer (LC) detection from blood-derived cfDNA. Using the Infinium MethylationEPIC BeadChip technology, which profiles over 850,000 CpG sites genome-wide, we analyzed cfDNA methylation profiles from patients with LC (stages  I-IV) and patients with non-neoplastic respiratory diseases (non-neoplastic)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Participants were recruited from the University Hospital La Fe (Valencia, Spain) and included 25 patients diagnosed with lung cancer (stages I–IV) and 8 non-cancer individuals. Peripheral blood samples were collected in PAXgene® Blood ccfDNA Tubes (Qiagen). A total of 30 mL of blood was obtained from each participant. Blood plasma was isolated within 1 to 24 hours of collection using double centrifugation at 4 °C (1,900 x g for 15 minutes; 1.900g for 10 minutes) and stored at −80 °C until further processing.","Labeling - Quantification of cfDNA was performed using the Qubit 1× dsDNA High-Sensitivity Assay Kit and a Qubit 4.0 Fluorometer (Thermo Fisher Scientific). Bisulfite-conversion of cfDNA was carried out using the the EZ DNA Methylation Lightning Kit (Zymo Research), following the manufacturer’s protocol.","Hybridization - Hybridization was performed following the manufacturer’s protocol with 10 µL of converted DNA.","Scaning - Arrays were scanned on the iScan SQ System (Illumina) and the raw data (IDAT files) were normalized using functional normalization as implemented in the R-package minfi (version 1.54.0). The methylation level of each cytosine was expressed as a beta value calculated as the fluorescence intensity ratio of the methylated to the unmethylated versions of the probes (according to a combination of the Cy3 and Cy5 fluorescence intensities).","Nucleic Acid Extraction - Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen) following the manufacturer’s instructions."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["David Hervas"],"additional_accession":[]},"is_claimable":false,"name":"Epigenome analysis of cfDNA samples from lung cancer patients and tumor free individuals with respiratory diseases","description":"There is a growing recognition of the importance of conducting epigenome-wide analysis directly in cfDNA to identify specific, blood-measurable DNA methylation biomarkers. In this study, we ought to identify novel epigenetic biomarkers for lung cancer (LC) detection from blood-derived cfDNA. Using the Infinium MethylationEPIC BeadChip technology, which profiles over 850,000 CpG sites genome-wide, we analyzed cfDNA methylation profiles from patients with LC (stages  I-IV) and patients with non-neoplastic respiratory diseases (non-neoplastic).","dates":{"release":"2026-09-01T00:00:00Z","modification":"2026-09-01T01:00:41.247Z","creation":"2025-08-06T14:20:35.613Z"},"accession":"E-MTAB-15459","cross_references":{"EFO":["EFO_0002944","EFO_0003814","EFO_0003813","EFO_0002759","EFO_0005518","EFO_0003815"]}}