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Analysis of tumor DNA markers in the plasma of colorectal cancer patients by liquid biopsy

ABSTRACT: 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

DISEASE(S): Malignant Neoplasm Of Rectum,Malignant Neoplasm Of Colon

PROVIDER: 2433407 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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Towards clinical applications of blood-born miRNA signatures: The influence of the anticoagulant EDTA on miRNA abundance

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Comparison of collection strategies for germline analysis

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Somatic copy number variants in monozygotic twins and elderly single-born individuals

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The Extracellular RNA Quality Control (exRNAQC) study: Small RNA sequencing of blood collection tube study (exRNAQC013)

Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying Small RNA sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.

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The Extracellular RNA Quality Control (exRNAQC) study: RNA Exome sequencing of blood collection tube study (exRNAQC005)

Project description:To evaluate the impact of blood collection tubes on extracellular RNA (exRNA) sequencing, 10 different blood collection tubes were compared by applying RNA Exome sequencing (Illumina) to exRNA from human healthy donor plasma or serum. Three time spans between blood draw and downstream processing were evaluated for each of the tubes. Preservation tubes were processed immediately upon blood collection (T0), after 24 hours (T24), or after 72 hours (T72). Non-preservation plasma and serum tubes were processed immediately upon blood collection (T0), after 4 hours (T4), or after 16 hours (T16). Due to donor privacy concerns the raw data for this study have been submitted to the controlled-access archive EGA under the accession EGAS00001005263.

2021-06-10 | E-MTAB-10507 | biostudies-arrayexpress

Blood extracellular vesicle long RNA sequencing of human blood from pancreatic ductal adenocarcinoma (PDAC), chronic pancreatitis (CP) and healthy individuals

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2019-10-01 | GSE133684 | GEO

Somatic copy number variants in monozygotic twins and elderly single-born individuals

2011-12-16 | GSE34467 | GEO

Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

Project description:Background The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulfite-based cfDNA methylation profiling. Methods 15 tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulfite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. Results All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. Conclusion The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.

| EGAS00001004271 | EGA

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