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Series GSE89570 Query DataSets for GSE89570
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
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)
GSM2383940 SHBPL000002CAC
GSM2383941 SHBPL000003CAC
GSM2383942 SHBPL000004CAC
SRA SRP080977

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Supplementary file Size Download File type/resource
GSE89570_Processed_Data.txt.gz 14.5 Mb (ftp)(http) TXT
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Processed data are available on Series record

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