 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 05, 2017 |
| Title |
DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers​ |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
|
| Summary |
DNA modifications such as 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression, and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here genome-wide 5hmC profiling in circulating cell-free DNA (cfDNA) and paired tumor/adjacent tissues collected from a cohort of 90 healthy individuals and 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver, or thyroid cancer. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-specific epigenetic signatures in cfDNA were identified in different cancers. 5hmC-based biomarkers demonstrated highly accurate predictive value for patients with colorectal and gastric cancers versus healthy controls, superior to conventional biomarkers, and comparable to epigenetic biomarkers from tissue biopsies. This new strategy could lead to the development of an effective blood-based, minimally-invasive cancer diagnosis and prognosis approach.
|
| |
|
| Overall design |
A total of 421 + 11 individual (90 healthy individuals, 260 cancer patients, 71 patients with benign disease from China; 6 healthy individuals, 5 caner patients from the United States).
|
| |
|
| Contributor(s) |
He C, Liu J, Zhang W |
| Citation(s) |
28925386 |
| BioProject |
PRJNA336239 |
| |
| Submission date |
Nov 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xu Zhang |
| E-mail(s) |
xuzhangchicago@gmail.com
|
| Organization name |
University of Illinois at Chicago
|
| Street address |
820 South Wood St
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (604)
|
|
| Relations |
| SRA |
SRP080977 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89570_Processed_Data.txt.gz |
14.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...