{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Whole Genome Sequencing"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001007400"],"host":["EGA"],"description":["EGA study EGAS00001007400"],"dataset_title":["Xenograft cfDNA dataset"],"repository":["EGA"],"category":["restricted"],"description_synonyms":["IPP2A2, Feature, Measure, Tumor, Cost-Minimization, prevention, Mid(H15), 5730420M11Rik, dmTAF[[II]]230, Software Engineering, Relapses, Analysis, Transfer, Fs(3)Hor, Cost Comparison, prevention and control, Computer Program, SET, thymus nucleic acid, DmelCG2684, esophagus adenocarcinoma, TFIID TAF250, reference sample, Analyses, cel, TAF-I, Machine, Cost-Minimization Analyses, Open, Recurrences, Computer Programs and Programming, Comparison, NTef2, free, DmelCG4299, preventive measures, Cost Analysis, IGAAD, set, DmelCG10574, malignant neoplasm, Double-Stranded DNA, Malignancies, stage, deoxyribonucleic acids, Comparisons, DNAn, Affordabilities, adenocarcinoma of esophagus, Tumors, phapii, Relapse, dTAF[[II]]230, preventive therapy, Learning, TAF200, Genome Sequencing, StF-IT-1, Double-Stranded, TAFII-250, TAF250/230, Source Softwares, Software Tools, Fs(3)Sz11, Programs, (Deoxyribonucleotide)n+m, Program, Computer Applications, TAFII250, Benign, Complete Genome, Recrudescence, Computer Applications Software, Computer Applications Softwares, esophageal adenocarcinoma, Softwares, desoxyribose nucleic acid, END, finances, H15r/nmr2, Software Applications, HLA-DR-associated protein II, death rate, DI-2, Source Software, adenocarcinoma of oesophagus, I-2Dm, salaries, Benign Neoplasms, CG4299, adenocarcinoma of the esophagus, CG17603, Features, TAF[[II]], early, Malignant Neoplasms, I-2PP1, Applications, oesophageal adenocarcinoma, TAF-IBETA, Taf250, Patient, SR3-5, Horka, ds DNA, CG2684, Fs(3)Horka, adenocarcinoma of the oesophagus, TAF-Ibeta, DNA, financial management, other neoplasm, i2pp2a, TAF230, Cost Analyses, Computer Software Applications, d230, DNS, conformation, (Deoxyribonucleotide)n, Neoplasms, developmental stage, Benign Neoplasm, dTAFII250, Cost Comparisons, Computer, EfW1, Malignant, Deoxyribonucleic acids, PHAPII, adenocarcinoma - oesophagus, EAC, Deoxyribonucleic Acid, Cost Minimization Analysis, dmTAF1, Taf230, DmF2, Application, TAF250, lod, Open Source Softwares, Transfer Learning, Taf200, Complete, dTAF[[II]]250, Whole Genome, oesophagus adenocarcinoma, Malignancy, cell, Recrudescences, Cost Measures, Software Application, Affordability, ipp2a2, Complete Genome Sequencing, los, Open Source Software, Double Stranded, 2pp2a, Measures, Taf1p, Deoxyribonucleic acid, financing, Sequencing, CG10574, Computer Software Application, Neoplasias, dTAF250, funding, DmelCG6634, 2PP2A, Tools, taf-ibeta, time of survival, Clients, Whole, dSET, dSet, liquid, (Deoxyribonucleotide)m, Characteristics, TAF, HHT1, adenocarcinoma - esophagus, Controlled, Cancer, Applications Software, fees, Open Source, Controlling, TAF[[II]]250, Malignant Neoplasm, Computer Software, whole blood, Edg, DNAn+1, igaad, l(3)84Ab, BG:DS00004.13, Client, Cell, Tool, group, dTAF230, Software Tool, MT, survival, Characteristic, H15r, I-2PP2A, p230, Dm I-2, I2PP2A, Neoplasm, TAF[[II]]250/230, TFIID, ds-DNA, Software, Costs and Cost Analyses, Taf[[II]]250, Costs, primary cancer, TAF[[II]]230, ensemble, nmr2, prophylaxis, Cost, Engineering, CG6634, Cost-Minimization Analysis, TAF[II]250, Cancers, TBX20, extra, Pricing, Lds, Biopsies., malignant tumor, Computer Programs, dSET/TAF-Ibeta, cost, 2610030F17Rik, DmelCG17603, Applications Softwares, control, Desoxyribonukleinsaeure, ORW1, Cost Measure, AA407739, Neoplasia, TAF1"],"name_synonyms":["dTAF[[II]]230, TAF[[II]]250, d230, wide/broad, DNS, Malignant Neoplasm, (Deoxyribonucleotide)n, DNAn+1, Neoplasms, Benign Neoplasm, TAF200, l(3)84Ab, dTAFII250, BG:DS00004.13, broad, Double-Stranded, TAFII-250, Tumor, TAF250/230, EfW1, Malignant, Client, Cell, Deoxyribonucleic acids, dTAF230, (Deoxyribonucleotide)n+m, dmTAF[[II]]230, TAFII250, MT, Benign, Deoxyribonucleic Acid, dmTAF1, Taf230, p230, Neoplasm, TAF[[II]]250/230, TFIID, ds-DNA, desoxyribose nucleic acid, TAF250, Taf[[II]]250, Taf200, thymus nucleic acid, primary cancer, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, Genomes, Malignancy, cel, cell, Double Stranded, Benign Neoplasms, Taf1p, TAF[II]250, Deoxyribonucleic acid, whole genome, Cancers, CG17603, TAF[[II]], free, malignant tumor, Neoplasias, dTAF250, wide, DmelCG17603, Taf250, Patient, malignant neoplasm, SR3-5, Clients, ds DNA, Desoxyribonukleinsaeure, Double-Stranded DNA, Malignancies, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, TAF, Neoplasia, TAF230, TAF1, Cancer, Tumors, Malignant Neoplasms."],"additional_accession":[]},"is_claimable":false,"name":"Genome wide cell-free DNA biological patterns in patients with cancer","description":"The structure of cell-free DNA (cfDNA) is altered in the blood of cancer patients. From whole genome sequencing we retrieved the cfDNA fragment-end composition using a new software (FrEIA), as well as the cfDNA size and tumor fraction in three independent cohorts (n=925 cancer from >10 types and 321 control samples). At 95% specificity, we detect 72% of cancer samples using at least one cfDNA measure, including 64% of early-stage cancer (n=220). cfDNA detection correlates with a shorter overall (p=0.018) and recurrence-free (p=0.006) survival in patients with resectable esophageal adenocarcinoma. Integrating cfDNA measures with machine learning in an independent test set (n=396 cancer, 90 controls) achieve a detection accuracy of 82% and AUROC of 96%. In conclusion, harnessing the biological features of cfDNA can improve at no-extra cost the diagnostic performance of liquid biopsies.","dates":{"updated":"2023-07-13 09:23:22"},"accession":"EGAS00001007400","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001011128","EGAC00001003335"]}}