Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy
Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiotherapy And Oncology 2024, 197: 110364. PMID: 38834154, DOI: 10.1016/j.radonc.2024.110364.Peer-Reviewed Original ResearchCopy number alterationsCell-free DNACancer patientsTumor fractionHead and neck cancer patientsPlasma cell-free DNAAssociated with tumor aggressivenessSCCHN patient samplesSystemic tumor spreadTumor-agnostic approachHigh-dose radiotherapyPlasma cfDNA samplesWhole-genome sequencingHead and neckCell-free DNA sequencing dataDetect viral DNAViral DNAOligometastatic patientsSCCHN patientsRadiotherapy guidelinesTumor spreadTumor aggressivenessImaging findingsCfDNA samplesTreatment strategiesFragmentstein—facilitating data reuse for cell-free DNA fragment analysis
Balázs Z, Gitchev T, Ivanković I, Krauthammer M. Fragmentstein—facilitating data reuse for cell-free DNA fragment analysis. Bioinformatics 2024, 40: btae017. PMID: 38224549, PMCID: PMC10805340, DOI: 10.1093/bioinformatics/btae017.Peer-Reviewed Original ResearchConceptsCopy number variantsNucleotide-level informationCell-free DNA sequencing dataDNA fragmentation analysisCell-free DNASensitive genomic dataFragment length analysisNucleosome occupancyBAM filesCommand-line toolSequence dataGenomic dataAnalysis of cell-free DNASequence informationGNU GPLv3Bioinformatics softwareFragment analysisFunctional analysisAlignment mapData sharingLength analysisFragmentsSimplified formatLimited data sharingGenome