{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["NextSeq 550;, Illumina MiSeq;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001002215"],"sample_count":["108"],"description":["EGA dataset EGAD00001002215"],"repository":["EGA"],"title":["Low coverage WGS from plasma DNA"],"pubmed_abstract":["The analysis of cell-free DNA (cfDNA) in plasma represents a rapidly advancing field in medicine. cfDNA consists predominantly of nucleosome-protected DNA shed into the bloodstream by cells undergoing apoptosis. We performed whole-genome sequencing of plasma DNA and identified two discrete regions at transcription start sites (TSSs) where nucleosome occupancy results in different read depth coverage patterns for expressed and silent genes. By employing machine learning for gene classification, we found that the plasma DNA read depth patterns from healthy donors reflected the expression signature of hematopoietic cells. In patients with cancer having metastatic disease, we were able to classify expressed cancer driver genes in regions with somatic copy number gains with high accuracy. We were able to determine the expressed isoform of genes with several TSSs, as confirmed by RNA-seq analysis of the matching primary tumor. Our analyses provide functional information about cells releasing their DNA into the circulation."],"pubmed_title":["Inferring expressed genes by whole-genome sequencing of plasma DNA."],"pubmed_authors":["Ulz Peter P, Thallinger Gerhard G GG, Auer Martina M, Graf Ricarda R, Kashofer Karl K, Jahn Stephan W SW, Abete Luca L, Pristauz Gunda G, Petru Edgar E, Geigl Jochen B JB, Heitzer Ellen E, Speicher Michael R MR"],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MUG., uracil mismatch repair protein, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, GU mismatch-specific uracil-DNA glycosylase activity, ENA/VASP"],"description_synonyms":["Fresh, primary breast cancer, malignant tumor of the breast, DNS, Fresh Frozen Plasma, (Deoxyribonucleotide)n, determination, Blood, Neoplasms, Benign Neoplasm, mammary neoplasm, Mammary Cancers, Human Mammary Neoplasms, Tumor, Malignant, Deoxyribonucleic acids, Human, Breast Malignant Tumor, Deoxyribonucleic Acid, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], Breast Tumor, \"mammary tumor\" EXACT [CSP2005:2016-0671], breast tumor, cancer of the breast, Low, (2Z)-but-2-enedioate, male, BC, Mammary Neoplasms, malignant neoplasm of breast, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, me75, thymus nucleic acid, Human Mammary, Complete, Whole Genome, Malignancy, Mammary Neoplasm, Mammary Carcinoma, Complete Genome Sequencing, Tissue, Human Mammary Carcinomas, Double Stranded, Deoxyribonucleic acid, D17Mit170, T1, Sequencing, Cancer of the Breast, Transplant Donors, Neoplasias, malignant neoplasm, cancer of breast, Malignant Tumor of Breast, Clients, Mammary, Mammary Cancer, Whole, Blood Plasmas, Double-Stranded DNA, Malignancies, Tissue Donor, (Deoxyribonucleotide)m, deoxyribonucleic acids, Ovum Donor, DNAn, Breast, mammary cancer, mammary tumor, plasma, Cancer, Tumors, Organ, Breast Carcinoma, Human Mammary Neoplasm, Carcinoma, Frozen Plasma, Transplant Donor, Breast Carcinomas, cou, Malignant Neoplasm, \"breast neoplasm\" EXACT [MTH:120], female human body, Males, DNAn+1, Transplant, Genome Sequencing, Semen Donors, Double-Stranded, Tl3, \"breast tumor\" EXACT [NCI2004_11_17:C2910], Tl2, Plasmas, female, Client, (Deoxyribonucleotide)n+m, Breast Malignant Neoplasm, Frozen Plasmas, Lr, Complete Genome, MT, Benign, Mammary Carcinomas, chemical analysis, Neoplasm, Human Mammary Carcinoma, NOS, Donor, Donors, ds-DNA, desoxyribose nucleic acid, Malignant Neoplasm of Breast, Carcinomas, Plasma, primary cancer, Breast Neoplasm, Organ Donor, maleate, portion of plasma, Benign Neoplasms, Cancers, Breast Malignant Neoplasms., \"mammary neoplasm\" RELATED [], malignant tumor, Semen Donor, Malignant Neoplasms, male human body, Semen, Patient, breast cancer, Breast Tumors, Breast Cancer, ds DNA, Bra, Desoxyribonukleinsaeure, Breast Malignant Tumors, Cancer of Breast, assay, DNA, Ovum, Ovum Donors, Organ Donors, cancer, Females, Neoplasia, breast"],"pubmed_title_synonyms":["Plasma, Fresh, Fresh Frozen Plasmas, Fresh Frozen, Blood Plasma, thymus nucleic acid, Frozen Plasma, Materials, Genetic, DNS, Fresh Frozen Plasma, Genomes, (Deoxyribonucleotide)n, Deoxyribonucleic acids., Blood, DNAn+1, Gene, portion of plasma, Double Stranded, Deoxyribonucleic acid, whole genome, Double-Stranded, Cistrons, Plasmas, (Deoxyribonucleotide)n+m, Frozen Plasmas, Deoxyribonucleic Acid, Material, Blood Plasmas, ds DNA, Desoxyribonukleinsaeure, Genetic Materials, Cistron, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, DNAn, ds-DNA, desoxyribose nucleic acid, Genetic Material, plasma"],"pubmed_abstract_synonyms":["Materials, determination, Blood, Tumor, Medical Specialties, dmTAF[[II]]230, Classifications, Speciality, Polynucleosome, hierarchies, hierarchy, Extrinsic Pathway Apoptoses, Specialities, systematics, Transfer, Fresh Frozen Plasmas, Fresh Frozen, thymus nucleic acid, Insurance Medicine, TFIID TAF250, Genomes, cel, developmental field, Machine, nuclear nucleosome, Tissue, free, Intrinsic Pathway Apoptosis, medicine, malignant neoplasm, Classic, Classical Apoptosis, Medicine, Double-Stranded DNA, Tissue Donor, Malignancies, Medicines, deoxyribonucleic acids, DNAn, transcription from bacterial-type RNA polymerase promoter, plasma, Tumors, Specialties, dTAF[[II]]230, Frozen Plasma, Transplant Donor, Caspase-Dependent Apoptosis, Transplant, Learning, TAF200, Systematics, Semen Donors, RNA-seq, future organ, Double-Stranded, TAFII-250, TAF250/230, Plasmas, results, (Deoxyribonucleotide)n+m, Medical Speciality, Taxonomies, TAFII250, metastatic disease, Nucleosome, signaling (initiator) caspase activity, Benign, induction of apoptosis, Intrinsic Pathway, Extrinsic Pathway Apoptosis, Specialty, Genetic Materials, Donors, Caspase-Dependent, desoxyribose nucleic acid, Genetic Material, Dinucleosome, Deoxyribonucleic acids., Benign Neoplasms, INSDC_feature:gene, whole genome, CG17603, TAF[[II]], Semen Donor, Malignant Neoplasms, Intrinsic Pathway Apoptoses, Insurance Medicines, Semen, induction of apoptosis by p53, Taf250, Patient, Material, SR3-5, bacterial transcription, metastatic tumor, ds DNA, Extrinsic Pathway, Cistron, DNA, other neoplasm, Classical, Ovum, Ovum Donors, Organ Donors, Apoptoses, TAF230, Fresh, d230, DNS, Fresh Frozen Plasma, (Deoxyribonucleotide)n, taxonomy, Neoplasms, caspase-dependent programmed cell death, Benign Neoplasm, number, Caspase Dependent Apoptosis, Gene, dTAFII250, EfW1, Malignant, presence, Deoxyribonucleic acids, organ field, Medical Specialities, Deoxyribonucleic Acid, dmTAF1, Taf230, Whole Transcriptome Shotgun Sequencing, field, Type I, Medical, TAF250, Transfer Learning, Taf200, Blood Plasma, Taxonomy, dTAF[[II]]250, Genetic, Malignancy, cell, Double Stranded, Taf1p, Deoxyribonucleic acid, apoptosis activator activity, Transplant Donors, Neoplasias, dTAF250, drugs, Classic Apoptosis, Clients, Blood Plasmas, (Deoxyribonucleotide)m, Insurance, Ovum Donor, TAF, Apoptosis, Organ, Cancer, TAF[[II]]250, Malignant Neoplasm, Medical Specialty, DNAn+1, l(3)84Ab, BG:DS00004.13, Cistrons, Client, Cell, metastatic neoplasm, dTAF230, Frozen Plasmas, read, count in organism, MT, p230, Programmed Cell Death, chemical analysis, Neoplasm, TAF[[II]]250/230, TFIID, Donor, Polynucleosomes, ds-DNA, Taf[[II]]250, Plasma, primary cancer, TAF[[II]]230, apoptosis, Organ Donor, cytoplasmic nucleosome, portion of plasma, TAF[II]250, Cancers, malignant tumor, Dinucleosomes, Classic Apoptoses, DmelCG17603, cardinality, metastatic tumour, Desoxyribonukleinsaeure, commitment to apoptosis, assay, Neoplasia, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-MUG-24-06-2016-09:45:40:262-333 - samples","description":"Low coverage whole genome sequencing plasma DNA from 50 male, 54 female non-cancer donors. For the analysis of nucleosomal positioning all data from the non-cancer controls were merged. Furthermore, two patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00001002215","cross_references":{"TAXONOMY":["9606"],"pubmed":["27571261"],"EGA":["EGAC00001000072","EGAS00001001754"]}}