EGAGenomicsIllumina MiSeq;https://ega-archive.org/datasets/EGAD000010022171EGA dataset EGAD00001002217EGAThe 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.Inferring expressed genes by whole-genome sequencing of plasma DNA.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 MRfalseena-DATASET-MUG-24-06-2016-10:36:41:861-335 - samplesMerged file of low-coverage WGS from 179 plasma DNA samples from non-cancer controls and cancer patients for assessment of size distribution of plasma nuclear DNA fragments.2017-07-26 15:39:27EGAD00001002217960627571261EGAC00001000072EGAS00001001754