EGAGenomicsIllumina MiSeq;https://ega-archive.org/datasets/EGAD000010022543EGA dataset EGAD00001002254EGAThe 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-14-07-2016-11:57:14:452-1424 - samplesSingle-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.2017-07-26 15:39:28EGAD00001002254960627571261EGAC00001000072EGAS00001001754