Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Data Access Committee - cfDNA fragmentation and personalized sequencing reveal ctDNA in urine and plasma of glioma patients

ABSTRACT: Data Access Committee EGAC00001001593

PROVIDER: EGAC00001001593 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients.

Project description: Not available

| S-EPMC8350897 | biostudies-literature

Fragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA

Project description:The unique chromatin structure at telomeres protects the ends of our chromosomes from being recognized as DNA damage and preserves genome integrity by preventing recombination. Here, we demonstrate that circulating cell-free DNA (cfDNA) from plasma can be used to map chromatin structure at telomeres. Using an alignment-free approach to overcome challenges in characterizing repetitive regions of DNA using sequencing, we find that the telomeric 6-mer repeats (TTAGGG/CCCTAA) are the most abundant circulating 6-mers in cfDNA. Telomeric sequences in cfDNA contain subnucleosomal footprints distinct from the rest of the genome, arising from specific cleavages in the C-rich strand. To map nucleosomal footprints from telomeric sequences in cfDNA, we performed long-read sequencing. We identified a nucleosome repeat length of 145 bp for telomeric sequences, which is significantly shorter than the repeat length of ~170 bp for the rest of the genome. The abundance of cfDNA telomeric footprints decreases with age, and this decline is exacerbated by Dyskeratosis Congenita (DC), a telomere biology disorder. DC also alters subtelomeric chromatin accessibility, as determined from cfDNA, allowing us to capture genome-wide effects of shortened telomeres non-invasively. Promoter subnucleosome enrichment (PSE) from cfDNA identifies DC-specific gene signatures that reflect disease states observed in transcriptomic studies. Notably, DC-specific gene signatures correlate with decreased cfDNA telomere footprint abundance and show enrichment of genes towards the ends of chromosomes. In summary, cfDNA provides an unexpected means to map telomere chromatin state and the impact of telomere shortening on the rest of the genome, offering a non-invasive way to track gene expression changes in DC.

2026-07-17 | GSE305882 | GEO

Cell-free DNA fragmentation patterns and personalized sequencing reveal circulating tumor DNA in urine and plasma of glioma patients

Project description:Glioma-derived cell-free DNA (cfDNA) is challenging to detect using liquid biopsy as levels in body fluids are low. We determined the glioma-derived DNA fractions in tumor biopsies, in cerebrospinal fluid (CSF), plasma and urine samples, using deep sequencing of personalized capture panels. By sequencing cfDNA across thousands of mutations identified individually in each patientÃ¢Â€Â™s matched tumor we detected tumor-derived DNA in plasma (10/12) and urine samples (8/11). The median tumor fraction was 6.4x10-3 in CSF, 3.1x10-5 in plasma and 4.7x10-5 in urine. We identified a shift in the size distribution for mutant cfDNA fragments in these body fluids. Next, we analyzed cfDNA fragment sizes with paired-end shallow whole genome sequencing (WGS) in urine samples from 35 patients with gliomas, 8 individuals with non-malignant brain disorders, and 26 controls (n=69 individuals, 96 samples). cfDNA in urine of glioma patients was significantly more fragmented compared to urine from patients with non-malignant brain disorders (t-test, p=1.7x10-2) and compared to urine of controls (t-test, p=5.2x10-9). The proportion of DNA fragments <60 bp was higher in glioma patients urine and could be used for classification (AUC=0.93). Machine learning models integrating fragment lengths could identify urine samples from glioma patients (AUC=0.97 in cross-validation).

| EGAS00001004355 | EGA

Optimization of Preanalytical Variables for cfDNA Processing and Detection of ctDNA in Archival Plasma Samples.

Project description: Not available

| S-EPMC8285169 | biostudies-literature

Plasma ctDNA enables early detection of temozolomide resistance mutations in glioma.

Project description: Not available

| S-EPMC11003533 | biostudies-literature

Plasma ctDNA liquid biopsy of IDH1, TERTp, and EGFRvIII mutations in glioma.

Project description: Not available

| S-EPMC10989869 | biostudies-literature

Fragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA

Project description:Fragmentation Patterns of Human Telomeric Chromatin in Plasma cfDNA