HBC_raw_sequences_CM - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001009999 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Cell-free methylated DNA immunoprecipitation sequencing of plasma samples from patients with Li-Fraumeni syndrome.
| EGAD00001010013 | EGA
Project description:We analyzed the cell free DNA methylomes using 14 plasma samples from patients with mCRPC in the Barrier cohort. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.
| EGAD00001008712 | EGA
Project description:We analyzed the cell free DNA methylomes using 22 plasma samples from patients with mCRPC prostate cancer in the WCDT project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.
| EGAD00001008713 | EGA
Project description:We analyzed the cell free DNA methylomes using 67 plasma samples from patients with mCRPC prostate cancer in the VPC project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.
| EGAD00001008711 | EGA
Project description:We analyzed the cell free DNA methylomes using 30 plasma samples from patients with localized prostate cancer in the CPC-GENE project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.
| EGAD00001007972 | EGA
Project description:We analyzed the cell free DNA methylomes using 72 plasma samples from patients with mCRPC prostate cancer in the VPC project for validation. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology. Files from multiple lanes exists per sample.
| EGAD00001008737 | EGA
Project description:Using cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq), we analyzed methylation profiles in 93 plasma samples from 77 pediatric brain tumor patients and 16 non-neoplastic patients. Binomial GLMnet classifiers of tumor and tumor subtypes were built in training sets, and performance was evaluated in test sets. The methylation profiles from plasma cfMeDIP-seq discriminated tumor from non-tumor patients with 0.83 accuracy (precision = 0.93, sensitivity = 0.86, and specificity = 0.67). Among major tumor subtypes vs. nontumors, circumscribed astrocytic glioma showed an accuracy of 0.86 (precision = 0.88, sensitivity = 0.88, and specificity = 0.83), and glioneuronal tumors had an accuracy of 0.83 (precision, sensitivity, and specificity = 0.83). Circumscribed astrocytic glioma and glioneuronal tumors could be discriminated from other tumor subtypes with 0.79 and 0.82 accuracy, respectively.
2024-09-30 | GSE275598 | GEO
Project description:Interventions: Group 1: The project aims to:
Statistically compare the fragment length of cell-free DNA in the blood plasma of 80 patients with a confirmed diagnosis of colorectal carcinoma in stages I-IV with the cfDNA fragment lengths of 50 healthy subjects.
For this purpose, residual amounts of blood plasma samples are used, which are collected anyway as part of theroutine examinations.
Cell-free DNA was isolated from the blood plasma and the fragment lengths are measured using qPCR.
The project ends with the publication of the data.
Group 2: Statistically compare the fragment length of cell-free DNA in the blood plasma of 50 healthy subjects with 80 patients with a confirmed diagnosis of colorectal carcinoma in stages I-IV.
The plasma samples from healthy volunteers were purchased (Central Biohub GmbH).
Primary outcome(s): The aim of this study is: 1) to analyze total cfDNA concentration in CRC patients with different histopathological stages (UICC I-IV). 2) to address the question whether the integrity index of cfDNA increases in CRC patients as a result of elevated necrotic degradation processes. Therefore, we intended to quantify short and long fragments of cfDNA via qPCR independent from total cfDNA levels by using equal template concentrations for CRC patients and healthy individuals. This approach may help to understand whether previously described diagnostic markers are either increased, decreased or unaltered in blood plasma of CRC patients compared to healthy individuals.
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: basic science
| 2754663 | ecrin-mdr-crc
Project description:Non-invasive detection of aberrant DNA methylation could provide invaluable biomarkers for earlier detection of triple negative breast cancer (TNBC) which could help clinicians for easier and more efficient treatment options. We evaluated genome-wide DNA methylation data derived from TNBC and normal breast tissues, peripheral blood of TNBC cases and controls, and reference samples of sorted blood and mammary cells. Differentially methylated regions (DMRs) between TNBC and normal breast tissues were stringently selected, verified, and externally validated. A machine learning algorithm was applied to select the top DMRs, which then were evaluated on plasma-derived circulating cell-free DNA (cfDNA) samples of TNBC patients and healthy controls. We identified 23 DMRs accounting for the methylation profile of blood cells and reference mammary cells and then selected six top DMRs for cfDNA analysis. We quantified un-/methylated copies of these DMRs by droplet digital PCR analysis in a plasma test set from TNBC patients and healthy controls and confirmed our findings obtained on tissues. Differential cfDNA methylation was confirmed in an independent validation set of plasma samples. A methylation score combining signatures of the top three DMRs overlapping with the SPAG6, LINC10606, and TBCD/ZNF750 genes had the best capability to discriminate TNBC patients from controls (AUC=0.74 in test set and AUC=0.77 in validation set). Our findings demonstrate the usefulness of cfDNA-based methylation signatures as non-invasive liquid biopsy markers for diagnosis of TNBC.
2022-11-23 | GSE207998 | GEO
Project description:Interventions: Group 1: Blood and sputum samples as well as paraffin embedded tumour tissue from patients with microsatellite stable colorectal cancer shall be analysed before therapy and over time to establish and validate hotspot mutation and somatic copy number variant (SCNAs) analysis. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
- One sputum tube (only at study inclusion).
- FFPE tissue samples from the primary tumor (from initial surgery)
Group 2: Blood samples of tumor-free control persons shall be tested for hotspot mutations and somatic copy number variants (SCNAs) to identify technical artefacts and improve our protocols. We therefore need the following samples:
- Two Cell-Free DNA BCT CE Streck tubes with 8 ml blood per sampling for preparation of plasma-DNA.
Primary outcome(s): Identification of tumorspecific SCNAs in plasma samples of colorectal cancer patients
Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other
| 2433407 | ecrin-mdr-crc