{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Anders Jacobsen Skanderup"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001001733"],"host":["EGA"],"description":["EGA DAC EGAC00001001733"],"repository":["EGA"],"email":["skanderupamj@gis.a-star.edu.sg"],"pubmed_abstract":["Profiling of circulating tumor DNA (ctDNA) may offer a non-invasive approach to monitor disease progression. Here, we develop a quantitative method, exploiting local tissue-specific cell-free DNA (cfDNA) degradation patterns, that accurately estimates ctDNA burden independent of genomic aberrations. Nucleosome-dependent cfDNA degradation at promoters and first exon-intron junctions is strongly associated with differential transcriptional activity in tumors and blood. A quantitative model, based on just 6 regulatory regions, could accurately predict ctDNA levels in colorectal cancer patients. Strikingly, a model restricted to blood-specific regulatory regions could predict ctDNA levels across both colorectal and breast cancer patients. Using compact targeted sequencing (<25 kb) of predictive regions, we demonstrate how the approach could enable quantitative low-cost tracking of ctDNA dynamics and disease progression."],"pubmed_title":["Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden."],"pubmed_authors":["Zhu Guanhua G, Guo Yu A YA, Ho Danliang D, Poon Polly P, Poh Zhong Wee ZW, Wong Pui Mun PM, Gan Anna A, Chang Mei Mei MM, Kleftogiannis Dimitrios D, Lau Yi Ting YT, Tay Brenda B, Lim Wan Jun WJ, Chua Clarinda C, Tan Tira J TJ, Koo Si-Lin SL, Chong Dawn Q DQ, Yap Yoon Sim YS, Tan Iain I, Ng Sarah S, Skanderup Anders J AJ"],"name_synonyms":["Plasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, thymus nucleic acid, Frozen Plasma, DNS, Fresh Frozen Plasma, (Deoxyribonucleotide)n, Deoxyribonucleic acids., Blood, DNAn+1, portion of plasma, Double Stranded, Deoxyribonucleic acid, Double-Stranded, Plasmas, (Deoxyribonucleotide)n+m, Frozen Plasmas, Deoxyribonucleic Acid, Blood Plasmas, ds DNA, Desoxyribonukleinsaeure, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, ds-DNA, desoxyribose nucleic acid, plasma"],"pubmed_title_synonyms":["Tumor DNA, dTAF[[II]]230, TAF[[II]]250, d230, TAF200, DNA catabolism, l(3)84Ab, dTAFII250, BG:DS00004.13, Circulating, Cell Free Tumor DNA, TAFII-250, TAF250/230, EfW1, Circulating Tumor, Cell, dTAF230, dmTAF[[II]]230, TAFII250, dmTAF1, Taf230, p230, DNA breakdown, Cell-Free, TAF[[II]]250/230, Cell-Free Tumor DNA, TFIID, simple tissue, DNA degradation, TAF250, Taf[[II]]250, Taf200, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, Tissue, Taf1p, TAF[II]250, Burden., CG17603, TAF[[II]], free, Specified, dTAF250, Cell-Free Tumor, DmelCG17603, Taf250, Specific, SR3-5, DNA, TAF, TAF230, TAF1"],"pubmed_abstract_synonyms":["Tumor DNA, Colorectal Neoplasm, Across, Invasive Lesion, Mini Exon, cfDNA, sci, Tumor, Circulating Tumor, invasive procedure, Cost-Minimization, dmTAF[[II]]230, Polynucleosome, Method, HOW, How, cancer of the breast, Analysis, Cost Comparison, Local-Regional, Progression, Colorectal Tumors, Transcriptional, BC, Project ENABLE, independent, thymus nucleic acid, TFIID TAF250, Analyses, cel, catabolism, Tissue, nuclear nucleosome, stru, Colorectal Carcinomas, Comparison, l(3)S053606, Colorectal Tumor, Based, D17Mit170, Cost Analysis, Independence, cancer of breast, Breast Malignant Neoplasms, colorectal (colon or rectal) cancer, Tumors, dTAF[[II]]230, Regional, Difference, TAF200, Procedure, Tl3, Tl2, Cell Free Ribonucleic Acid, Nucleosome, Cell-Free Tumor DNA, secretion, simple tissue, Circulating Nucleic Acids, Educate, Cell-Free Deoxyribonucleic Acid, Colorectal Cancers, desoxyribose nucleic acid, finances, Dinucleosome, Carcinomas, Acid, Moving from wheelchair to bed and return independent, Cell Free Nucleic Acids, Nucleic Acids, salaries, Methodological, \"mammary neoplasm\" RELATED [], cancer of large bowel, Genomic, Taf250, breast cancer, monitor, Breast Tumors, ds DNA, Breast Malignant Tumors, cancer of the large bowel, Acids, DNA, financial management, cancer, TAF230, Cost Analyses, transcription, Restricted, DNS, Colorectal Cancer, (Deoxyribonucleotide)n, Cell-Free Deoxyribonucleic, Conditional, Contingency, Different, Neoplasms, Traverse, number, Mammary Cancers, cellular catabolism, Human, Circulating Cell-Free Nucleic Acid, colorectal cancer, Breast Malignant Tumor, Deoxyribonucleic Acid, Dressing (includes tying shoes, Targeted Sequencing, Breast Tumor, Cell-Free RNA, Mini-Exon, breast tumor, Technique, Offered, Invasive Procedure, Tracking, Negation, Transcription, RNA Expression, dTAF[[II]]250, Clinical, Bathes with Help, cell, Mammary Neoplasm, Cost Measures, Mammary Carcinoma, Double Stranded, Genetic Transcription, Deoxyribonucleic acid, Cell-Free Ribonucleic, Monitoring, cancer of the large intestine, Study, dTAF250, Clinical Course, LOCOREGIONAL, Malignant Tumor of Breast, genome, Intron, (Deoxyribonucleotide)m, Independent for Wheelchair Transfer, Cancer, cellular breakdown, fees, Breast Carcinoma, Human Mammary Neoplasm, ctdDNA, RNA, Breast Carcinomas, cou, whole blood, degradation, DNAn+1, colorectal, BG:DS00004.13, qkr, \"breast tumor\" EXACT [NCI2004_11_17:C2910], l(3)S090417, Cell, Conditionality, dTAF230, Circulating RNA, Sequences, Lr, KH93F, Bathing self with help, Neoplasm, TAF[[II]]250/230, Human Mammary Carcinoma, CRC, Approach, Trial Monitor, Cell-Free DNA, Costs and Cost Analyses, Taf[[II]]250, Costs, Regulator, Colorectal Carcinoma, Monitor, Exon, Cost-Minimization Analysis, Ribonucleic Acid, Cancers, Negated, Independent for Transfer Between Wheelchair and Bed, Dinucleosomes, plan specification, No, Differential, colon cancer, Specific, Dependent Bathing, Desoxyribonukleinsaeure, Bra, Restriction, Independent, Localized Disease, Cancer of Breast, Cost Measure, General activity, breast, biochemical pathways, Next Generation Targeted Sequencing, malignant tumor of the breast, NEXT GENERATION TARGETED SEQUENCING, Activity, Burden, mammary neoplasm, Human Mammary Neoplasms, Nurture, Circulating, Measure, Circulating DNA, Techniques, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], monitoring, Offering, Cell-Free Circulating Tumor DNA, Cell-Free, cellular degradation, Cell-Free Nucleic Acid, Cell Free Nucleic Acid, l(3)j5D5, 24B, Mammary Neoplasms, malignant neoplasm of breast, medical monitoring, me75, cirDNA, Cost-Minimization Analyses, Human Mammary Carcinomas, Study Monitor, CG10293, free, T1, large intestine cancer, Gene Transcription, l(3)j5B5, Monitor Device, Colon or Rectum, Methodological Studies, Disease., Exacerbation, biotransformation, Double-Stranded DNA, deoxyribonucleic acids, Comparisons, DNAn, mammary cancer, Affordabilities, somatic mutation, Dependent Dressing, Carcinoma, 0904/17, Constraint, \"breast neoplasm\" EXACT [MTH:120], Intervening Sequences, Disease Exacerbation, Limitation, Cell Free Tumor DNA, Double-Stranded, TAFII-250, TAF250/230, (Deoxyribonucleotide)n+m, TAFII250, Patient Monitoring, INSDC_feature:intron, SZ1, Circulating Tumor DNA, Non, Not, NOS, Offer, Conflict, Malignant Neoplasm of Breast, Circulating Cell Free Nucleic Acids, susceptibility to, CG17603, Methodological Study, TAF[[II]], Intervening, Dependent for Toilet Use, Patient, SR3-5, Base, anon-EST:Liang-2.39, cancer of large intestine, Contingent, primary breast cancer, Non-, d230, Procedures, Independent for Transfer, P62, Circulating Cell Free Nucleic Acid, dTAFII250, Cost Comparisons, fastening fasteners) with help, LOCAL, EfW1, presence, autosomal dominant, dependent, Deoxyribonucleic acids, Colorectal, method, Local, Cost Minimization Analysis, dmTAF1, Taf230, method used in an experiment, Clinical Progression, Studies, \"mammary tumor\" EXACT [CSP2005:2016-0671], Low, Cell Free DNA, Invasive, TAF250, Taf200, Cell Free Deoxyribonucleic Acid, Human Mammary, l(3)s2612, breakdown of chemical, Targeted NGS (sequencing of selected regions of the genome either via targeted capture or amplification), ctDNA, Affordability, Device Monitor, Measures, Taf1p, Circulating Tumor-Derived DNA, financing, Circulating Cell-Free Nucleic Acids, Cancer of the Breast, funding, Cell-Free Tumor, PATIENT MONITORING, Clients, Mammary, Mammary Cancer, DmelCG10293, TAF, Breast, mammary tumor, Disease, TAF[[II]]250, Regulatory, Dependent, clone 2.39, l(3)84Ab, Client, Breast Malignant Neoplasm, count in organism, Monitoring Device, Intervening Sequence, Mammary Carcinomas, Circulating Nucleic Acid, Sequence, ENABLE, p230, Nucleic Acid, TFIID, Polynucleosomes, ds-DNA, Cell Free RNA, breakdown of molecule, who, Basic, large bowel cancer, Protocol Monitor, Cross, Breast Neoplasm, TAF[[II]]230, biodegradation, exonic region, Mini-Exons, Cost, cytoplasmic nucleosome, Basis, cirRNA, TAF[II]250, Who/How, Pricing, Dresses with Help, Specified, cfRNA, cost, Circulating Nucleic, breakdown of substance, DmelCG17603, Cell-Free Ribonucleic Acid, Breast Cancer, qkr[93F], Genome, Advise Before Life Ends, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"Plasma DNA - GIS","description":"Data Access Committee EGAC00001001733","dates":{"output":"2025-1-9"},"accession":"EGAC00001001733","cross_references":{"TAXONOMY":["9606"],"pubmed":["33850132"],"EGA":["EGAS00001004657","EGAD00001006420","EGAD00001008352","EGAD00001006419","EGAD00001006421"]}}