Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circulating-free DNA Assessment as a Tool to Predict Colorectal Cancer in Subjects With a Positive Fecal Immunoassay.

ABSTRACT: Colorectal cancer (CRC): is one of the most frequent cancers, with almost 42152 new cases estimated in France for 2012. There are 3 levels of risk of developing CRC: moderate, high or very high. At each level of risk, appropriate follow-up recommendations are made. Immunological tests for fecal occult blood tests have emerged in recent years and have rapidly become established as benchmark tests in Europe and then in France (OC Sensor test) as part of mass screening. In the case of a positive immunological test, a diagnostic colonoscopy must be systematically organized in order to characterize the possible recto-colic cause of the digestive bleeding thus observed. Measurement of the DNA present in the circulating blood (circulating DNA or cfDNA): allowed a significant advance in the personalized management of cancers, as a non-invasive test capable of producing diagnostic, prognostic, theranostic, and of therapeutic follow-up type. The aim of the work is to measure the cfDNA concentration in subjects undergoing colonoscopy because of a positive immunological fecal test.

DISEASE(S): Colorectal Cancer,Colorectal Neoplasms

PROVIDER: 2307989 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Identification of fetal unmodified and 5-hydroxymethylated CGs in maternal cell-free DNA for non-invasive prenatal testing

Project description:Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of high cost. Building upon previous knowledge that placenta, the main source of fetal circulating DNA, is hypomethylated in comparison to maternal tissue counterparts of cfDNA, we propose that targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches fetal genetic material and reduces numbers of required analytical sequencing reads thereby decreasing cost of a test.

2020-10-20 | GSE148964 | GEO

Sensitivity of Fecal Immunochemical Test (FIT) for Colorectal Cancer (CRC) Screening

Project description:Fecal immunochemical test (FIT) was introduced in France late 2015, FIT has better diagnostic accuracy for colorectal cancers (CRCs) than previous screening tests. Our primary objective was to evaluate the sensitivity of FIT and the proportion of interval cancer.

| 2398790 | ecrin-mdr-crc

Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin

Project description: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.

2017-07-13 | GSE81314 | GEO

Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA

Project description:Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.

2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress

Genome-wide Mapping Implicates 5-Hydroxymethylcytosines in Diabetes and Alzheimer’s Disease

Project description:Background: Diabetes mellitus (DM) is a recognized risk factor for dementias, including AD, increasing its odds by two-fold. Because DM is potentially modifiable risk factor, a greater understanding of the mechanisms linking DM to the clinical expression of AD may provide insights into much needed dementia therapeutics. Epigenetics offers a novel approach, and previously under-investigated 5-hydroxymethylcytosines (5hmC) is now emerging as a promising measure to investigate in diabetes related conditions. Methods: Using 5hmC-Seal, a highly sensitive chemical labeling technique developed by our team, we performed genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and prefrontal cortex tissue from 80 individuals across four groups: AD, DM, DM and AD (AD+DM), and non-AD/non-DM controls. We used differential analysis and machine-learning to explore whether 5hmC and biological pathways might be implicated in DM-associated AD under a balanced design. Results: We uncovered distinct 5hmC genome-wide signatures and biological pathways associated with AD or AD+DM compared to non-AD/non-DM controls or DM alone. We further demonstrated potential diagnostic value of 5hmC profiling in circulating cfDNA through feature selection based on machine learning. Conclusions: Genome-wide 5hmC profiling uncovered genomic features and biological pathways linking DM to DM-associated AD. Our findings also demonstrate the potential of utilizing 5hmC in circulating cfDNA as diagnostic biomarkers or disease monitoring tools, with the ultimate goal of preventing or ameliorating DM-associated AD dementia and improving clinical outcomes.

2023-05-16 | GSE203337 | GEO

Data in support of Circulating neutrophil extracellular trap components including cell-free DNA are associated with neonatal sepsis and necrotizing enterocolitis in newborn, immature infants, pigs and mice

Project description:Preterm infants are highly susceptible to late-onset sepsis (LOS) and necrotizing enterocolitis (NEC) but specific biomarkers for diagnosis and effective treatment are lacking. Neutrophil extracellular traps (NETs) are related to sepsis in adults but not investigated in infant conditions. This is the first proteome study to document that circulating NETs are involved in neonatal LOS and NEC. cfDNA and NET proteins may provide new potential diagnostic markers for these diseases.

2018-03-05 | PXD004082 | Pride

CelFiE: Comprehensive cell type decomposition of circulating cell-free DNA

Project description:Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising non-invasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not rely on CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from rare cell types composing less than 1% of the total mixture. In a positive control of cfDNA extracted from pregnant and non-pregnant women, CelFiE correctly estimates a large placenta component specifically in pregnant women (p = 4.5x10^-5). In cfDNA from ALS patients and age-matched controls, we observed increased cfDNA concentrations in ALS patients (p = 5.0x10^-3), and CelFiE identified a corresponding increased skeletal muscle component (p = 2.4x10^-3), consistent with muscle impairment characterizing ALS. Together these results show CelFiE may be a useful tool for biomarker discovery and monitoring of degenerative disease progression.

2021-01-12 | GSE164600 | GEO

Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA

Project description:Current methods for mapping the tissue-of-origin of circulating cell-free DNA (cfDNA) are still insufficient. Here, we have extended a previously developed methylated CpG tandems amplification and sequencing (MCTA-Seq) method for quantitative analysis of tissue-of-origin of plasma cfDNA. By comparing paired plasma cfDNA and white blood cell genomic DNA, we have demonstrated that the liver is the major non-hematopoietic tissue contributing to plasma cfDNA in healthy adults, accounting for approximately 2%. Furthermore, we have detected changes in liver-derived DNA in patients with benign liver diseases and increases in pancreas-derived DNA in acute pancreatitis patients. Interestingly, our results suggest that DNA derived from pathological tissues makes a minor contribution to the increased cfDNA in many clinical cases. Finally, we have identified a tissue-specific hypermethylated cfDNA marker located in the intragenic regions of tissue-specifichighlyexpressed genes. This study represents valuable progress in the field of cfDNA and offers promise for clinical research and medical diagnostics using the described method.

2019-07-01 | GSE118690 | GEO

Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin

Project description:Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible. Sequencing of cfDNA libraries from healthy individuals, pooled healthy individuals and individuals with disease for the identification of nucleosomes and protection from other DNA binding proteins.

2015-11-04 | E-GEOD-71378 | biostudies-arrayexpress

Genome-wide plasma cell-free DNA methylation profiling in lung cancer patients using MeDIP-seq

Project description:As a non-invasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma is raising increasing interest due to its diagnostic and biology applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. Through enriching methylated cfDNA fragments with MeDIP followed by deep sequencing, we aimed to characterize cfDNA methylome in cancer patients. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. MEDIPS package was used for the identification of differentially methylated regions (DMRs) between patients and normal ones. Overall, we identified 330 differentially methylated regions (DMRs) in gene promoter regions, 33 hypermethylation and 297 hypomethylation respectively, by comparing lung cancer patients and healthy individuals as controls. The 33 hypermethylation regions represent 32 genes. Some of the genes had been previously reported to be associated with lung cancers, such as GAS7, AQP10, HLF, CHRNA9 and HOPX. Taken together, our study provided an alternative method of cfDNA methylation analysis in lung cancer patients with potential clinical applications.

2019-03-31 | E-MTAB-7163 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data