Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Clinical Study of Pan-cancer DNA Methylation Test in Plasma

ABSTRACT: We intend to establish an efficient method for plasma cfDNA extraction and Bisulfite transformation to facilitate the detection of DNA methylation status using multiplex fluorescence PCR. Meanwhile, we expect to identify several plasma methylation markers that can be highly sensitive for multi-cancer detection. Finally, we will provide a pan-cancer blood test that is easy to operate, low cost, accurate and easy to promote.

DISEASE(S): Ovarian Cancer,Lung Cancer,Esophageal Carcinoma,Cervical Cancer,Colorectal Cancer,Bladder Cancer,Pancreatic Cancer,Cancer

PROVIDER: 5068 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Expression data from human lung epithelial cells after amorphous silica nanoparticle exposure for 40 passages

Project description:Amorphous silica nanoparticles induce malignant transformation and tumorigenesis of human lung epithelial cells. We used microarrays to detail the global programme of gene expression underlying the cellular malignant transformation induced by amorphous silica nanoparticles and identified distinct classes of up-regulated and down-regulated genes during this process. The human lung epithelial cells, Beas-2B were continuously exposed to 5 Î¼g/mL amorphous silica nanoparticles for 40 passages, and named as BeasSiNPs-P40 (shortly as P40-5 during the further microarray detection). Meanwhile, the passage-matched control Beas-2B cells, named as Beas-P40 (shortly as NC during the further microarray detection).

2016-06-01 | E-GEOD-82062 | biostudies-arrayexpress

A multi-center study: the application value of plasma exosomal non-coding RNA in the early screening and clinical progress of colorectal cancer

Project description:Interventions: Gold Standard:Gastroscopy, colonoscopy, pathological diagnosis;Index test:Plasma exosome extraction: commercial plasma exosome extraction kit (EZB company) extraction. Extraction of plasma exosomal miRNA: Advanced probe method RT-qPCR extraction kit (Thermo Company). Primary outcome(s): exosome microRNA Study Design: Cohort study

| 40619 | ecrin-mdr-crc

Dynamic Monitoring of ctDNA Methylation to Predict Relapse in Colorectal Cancer After Radical Resection (POSTCA)

Project description:This is a prospective, multicenter, observational, single-blinded controlled study. Dynamic monitoring of patients with resectable colorectal cancer was performed using the previously established colorectal tumor-specific plasma ctDNA methylation markers (Multigene methylation detection). Dynamic monitoring of plasma ctDNA methylation before and after treatment and at regular follow-up in patients with colorectal cancer after radical resection of tumor, to explore the predictive effect of postoperative plasma ctDNA methylation on postoperative recurrence and whether dynamic monitoring of postoperative ctDNA methylation could be earlier than imaging examination to indicate tumor recurrence.

| 2289240 | ecrin-mdr-crc

Application of Polygenic Methylation Markers in Postoperative Recurrence Monitoring of Colorectal Cancer

Project description:This study dynamically monitored the prognosis of stage I-IV colorectal cancer patients who could receive radical surgical resection by detecting the levels of polygene methylation in plasma samples from patients with colorectal cancer. In patients with colorectal cancer feasible radical surgery, plasma ctDNA methylation detection was performed before and after surgical treatment and during regular follow-up to explore the predictive effect of plasma ctDNA methylation status at different time points on postoperative recurrence. To explore whether postoperative dynamic monitoring of plasma ctDNA methylation can be used for adjuvant chemotherapy efficacy evaluation and whether it can indicate tumor recurrence and metastasis earlier than imaging examination.

| 2739915 | ecrin-mdr-crc

A cell-free pipeline for recreating methylation patterns radically enhances DNA transformation in bacteria

Project description:The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic-biology chasses. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here we report IMPRINT, a generalized, rapid and scalable approach to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes cell-free systems to express DNA methyltransferases from the bacterial host’s restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the host DNA’s methylation pattern, circumventing restriction and enhancing transformation. Unlike established approaches, IMPRINT can be completed in under one day, readily accommodates all methyltransferase types, and avoids methylation-induced cytotoxicity. With IMPRINT, we efficiently multiplex DNA methylation and maximize plasmid transformation in gram-negative and gram-positive bacteria. We also developed a high-throughput pipeline that identifies the most consequential methyltransferases in one transformation. Overall, IMPRINT can vastly enhance DNA transformation, enabling use of increasingly sophisticated genetic manipulation tools across the bacterial world.

2024-04-07 | GSE240651 | GEO

Tissue- and plasma-derived exosomal protein biomarkers define multiple human cancers

Project description:There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of exosomes in 426 human samples from tissue explants (TE), plasma and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, HSP90AB1 represent pan-exosomes/exomeres. Moreover, we identified novel pan-exosome/exomere markers (e.g., ACTB, MSN, RAP1B). As proof of principle that exosomes are ideal diagnostic tools, we analyzed the proteome of TE exosomes (n=151) or plasma-derived exosomes (n=120). Comparison of TE exosomes identified proteins (e.g., VCAN, TNC, THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machinelearning classification of plasma-derived exosomes revealed 95% sensitivity/90% specificity in identifying cancer-associated exosomes. Finally, we defined a panel of tumor-type specific exosomal proteins in TE and plasma, which may help classify tumors of unknown primary origin. Overall, exosomal proteins can serve as reliable biomarkers for cancer detection and for determining cancer type

2020-08-17 | PXD018301 | Pride

Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility

Project description:we reported the development of an accurate, easy-to-use and scalable system (SNuBar) for multiplexing single cell ATAC or multi-omics (ATAC&RNA) assays, and applied this method to multiplex therapy combinations in a lung cancer mouse model and macro-spatial regions of normal breast tissues and samples.

2021-10-20 | GSE162798 | GEO

Identification and validation of a novel 3-gene methylation classifier for HPV-based cervical screening on self-samples

Project description:Background: Offering self-sampling of cervico-vaginal material for human papillomavirus (HPV) testing is an effective method to increase the coverage in cervical screening programmes. Molecular triage directly on HPV-positive self-samples for colposcopy referral opens the way to full molecular cervical screening. Here, we set out to identify a methylation classifier for detection of precancer (CIN3) or cancer, applicable to self-samples obtained by different devices. Findings: Genome-wide DNA methylation profiling of HPV-positive self-samples revealed 12 methylation targets for CIN3 detection. Multiplex quantitative methylation-specific PCR of these targets yielded a 3-gene methylation classifier (ASCL1, LHX8 and ST6GALNAC5), showing a very good clinical performance for CIN3 detection in both lavage (AUC=0.88; sensitivity=74%; specificity=79%) and brush (AUC=0.90; sensitivity=88%; specificity=81%) self-samples in the validation set. All self-samples from women with cervical cancer scored methylation-positive. Conclusion: By genome-wide DNA methylation profiling on self-samples, we identified a highly effective 3-gene methylation classifier for direct triage on self-samples from HPV-positive women.

2018-01-01 | GSE99511 | GEO

Multiplex 5mC Marker Barcode Counting (MMBC-seq): A sensitive detection method for cell-free DNA methylation

Project description:The detection of hypermethylation markers on cell-free DNA (cfDNA) in biological fluids is a promising and non-invasive approach for early diagnosis and monitoring of human diseases. However, it is challenging to detect hypermethylation markers in a high-throughput, sensitive, and cost-effective manner. Here we presented a multiplex 5-methylcytosine marker barcode counting (MMBC-seq) technique and reported its clinical application for cfDNA from peripheral plasma samples. We identified an MMBC cancer detection panel and developed a scoring system to differentiate cancer versus healthy controls. In a multiple-cancer case-control study, the panel achieved a sensitivity and specificity of 80.2% and 95.7% respectively (AUC 0.906, 95% CI 0.846-0.948). The results suggest that MMBC-seq has great potential to realize non-invasive, flexible and clinically applicable cancer detection.

2022-01-07 | GSE124775 | GEO

Prediction of outcomes and response to treatments with an ultrasensitive method for assessing intratumor epigenetic heterogeneity in colorectal cancer

Project description:Primary outcome(s): The detection rates of epigenetic heterogeneity in primary tumor and plasma from colorectal cancer patients with Methylation-sensitive high resolution melt(MS-HRM).

| 2636460 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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