GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE81314 Query DataSets for GSE81314
Status Public on Jul 13, 2017
Title Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary 5-Hydroxymethylcytosine (5hmC) is an important mammalian DNA epigenetic modification that has been linked to gene regulation and cancer pathogenesis. Here we explored the diagnostic potential of 5hmC in cell-free DNA (cfDNA), the circulating DNA found in human plasma which represents a noninvasive window into the health status of the body. We showed that the genome-wide 5hmC distribution in cfDNA can be reliably sequenced by chemical labeling-based 5hmC enrichment. We sequenced cell-free 5hmC from 49 patients of seven different cancer types and found distinct features that can be used for monitoring disease status and progression. Specifically, we discovered that lung cancer leads to a stage-dependent hypohydroxymethlation in cfDNA, whereas hepatocellular carcinoma (HCC) and pancreatic cancer lead to disease-specific changes in the cell-free hydroxymethylome. Our results demonstrate that cell-free 5hmC can be used not only to track the stage of cancer but also to identify tissue of origin in some solid tumors.
Overall design 79 samples were sequenced and 130 datasets were generated
Contributor(s) Xie D, Song C
BioProject PRJNA320940
Submission date May 11, 2016
Last update date May 15, 2019
Contact name Dan Xie
Organization name Sichuan University
Department West China Hospital
Lab State Key Laboratory of Biotherapy
Street address #17 Renmin Road
City Chengdu
State/province Sichuan
ZIP/Postal code 610041
Country China
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (126)
GSM2150136 healthy control 1
GSM2150137 healthy control 2
GSM2150138 healthy control 3
SRA SRP074577

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE81314_matrix.txt.gz 8.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap