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Ena-DATASET-MUG-14-07-2016-11:57:14:452-1424 - samples

ABSTRACT: Single-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.

PROVIDER: EGAD00001002254 | EGA |

REPOSITORIES: EGA

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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 MR

Nature genetics 20160829 10

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, w ...[more]

PMID: 27571261

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