Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability
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ABSTRACT:
PROVIDER: EGAS00001006377 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This dataset contains plasma WGS data from patients with stage IV colorectal cancer (CRC, n = 16) and healthy individuals (n = 21) used in the Pointy manuscript. Patients with CRC provided written consent and samples were collected as performed as described previously (Clinical-Trials.gov number NCT01876511; Georgiadis et al., 2019, Le et al., 2017). Plasma samples from 21 healthy control individuals were procured through BioIVT. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit. Libraries were sequenced on HiSeq2000/2500.
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Project description:Analysis of microRNA expression of tumoral and non-tumoral colonic tissues. The aim of this study was to analyze the global miRNA signatures in various groups of well-characterized CRCs based on the presence of microsatellite instability (MSI). Total RNA from formalin-fixed paraffin-embedded tissue blocks from 4 different groups (normal colonic mucosa, Lynch syndrome tumors, sporadic MSI tumors and MSS tumors) was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion) according to manufacturer instructions. MiRNA expression profiles were analyzed using miRNA microarray platform.
2011-11-22 | E-GEOD-30454 | biostudies-arrayexpress
Project description:We developed a new method to extract cfNA (containing cfDNA, cfRNA and viral RNA) from serum/plasma based on the adsorption of nucleic acids by MOF materials (Co-IRMOF-74-IV), and compared the extraction capability with commercial kit method. We conducted a comprehensive characterization of the cell-free RNA in a small number of clinical samples, including patients with HCC (n=14), CHB (n=17) and normal individuals (n=8). And then we build a model with 6 cfRNA signature to diagnose liver cancer, and indicated high diagnostic efficiency (AUC=0.905) in the independent validation cohort (HCC n=7, CHB n=4 and normal individuals n=8)
2023-08-01 | GSE210775 | GEO
Project description:Circulating nucleic acids are present in plasma and are derived from a range of cell types, mainly cells of hematopoietic origin, enabling their use as biomarkers for diseases involving these cell types. Using cell type-specific methylation markers, we determined that megakaryocytes are major contributors to cfDNA (~26%), while erythroblasts contribute 1-4% of cfDNA in healthy individuals. Additionally, we identified megakaryocyte-derived DNA within platelets, providing non-invasive access to the megakaryocyte genome and epigenome. Analysis of cfDNA in women who have received male platelet transfusions indicates that megakaryocyte-derived cfDNA does not originate from platelets but is rather released directly from megakaryocytes. The concentration of megakaryocyte-derived cfDNA is elevated in individuals with pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased by bone marrow suppression (due to chemotherapy), while erythrocyte progenitor cfDNA is elevated in patients with Thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns may serve as novel biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis.
2022-10-12 | GSE206818 | GEO
Project description:We performed all stimulatory experiments using THP1 cell line as a representative of primary human monocytes to show fundamental role of the cfDNA in healthy organisms. The experiments were conducted in duplicates using plasma containing cfDNA (NP) and the reference one with cfDNA removed by DNase (TP) to recognize unequivocally the effect of plasma cfDNA on transcriptome and proteome of monocytes. We used native human plasma samples obtained from healthy volunteers with no animal serum addition to cultivation medium in order to avoid the presence of uncharacterized animal cfDNA in the experiments.
2021-05-18 | PXD017285 | Pride
Project description:We aimed to clarify the cell-free DNA (cfDNA) physiological role. We exposed THP1 cells to plasma from healthy individuals with and without cfDNA and compared their transcriptomes and proteomes.
2020-12-01 | E-MTAB-8574 | biostudies-arrayexpress
Project description:The blood samples of eight lung cancer patients and one benign lung tumor patient are collected for this dataset. Blood samples were centrifuged first at 1,600 × g for 10 minutes, and then the plasma was transferred into new micro tubes and centrifuged at 16,000 × g for another 10 minutes. The plasma was collected and stored at -80⁰C. CfDNA was extracted from 5 ml plasma using the Qiagen QIAamp Circulating Nucleic Acids Kit and quantified by Qubit 3.0 Fluoromter (Thermo Fisher Scientific). Bisulfite conversion of cfDNA was performed by using EZ-DNA-Methylation-GOLD kit (Zymo Research). After that, Accel-NGS Methy-Seq DNA library kit (Swift Bioscience) was used to prepare the sequencing libraries. The DNA libraries were then sequenced with 150bp paired-end reads.
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Project description:The blood samples of four liver cancer patients and four healthy people, and the solid liver tumor samples of two liver cancer patients are collected for this dataset. Blood samples were centrifuged first at 1,600 × g for 10 minutes, and then the plasma was transferred into new micro tubes and centrifuged at 16,000 × g for another 10 minutes. The plasma was collected and stored at -80⁰C. CfDNA was extracted from 5 ml plasma using the Qiagen QIAamp Circulating Nucleic Acids Kit and quantified by Qubit 3.0 Fluoromter (Thermo Fisher Scientific). Bisulfite conversion of cfDNA was performed by using EZ-DNA-Methylation-GOLD kit (Zymo Research). After that, Accel-NGS Methy-Seq DNA library kit (Swift Bioscience) was used to prepare the sequencing libraries. The DNA libraries were then sequenced with 150bp paired-end reads.
| EGAD00001004317 | EGA
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
Project description:Colorectal cancers are among the most common cancers and a leading cause of cancer death. In our pursuit to discover molecular markers for better characterization and precision theranostics of these cancers, we first conducted global deep proteome analyses and identified maspin (serpin B5, peptidase inhibitor 5) as an upregulated protein in tumor tissue. We then validated its expression in a large cohort of 743 patients with colorectal cancers of all stages and found that both cytoplasmic and nuclear expression varied widely between different patients. Comparison with clinicopathological features revealed that maspin expression levels correlate significantly only with mismatch repair (MMR) status but not with other features. To elucidate the prognostic significance of maspin, we analyzed two outcome-annotated cohorts, one of 572 early stage cancer patients and another of 93 late stage cancer patients. Kaplan-Meier survival, univariate, and multivariate analyses revealed that maspin overexpression predicts longer overall and disease-free survival for early stage microsatellite instability (MSI) subtype colorectal cancer, but there is no correlation with survival for patients with early stage cancer of the microsatellite stability (MSS) subtype or late stage cancer. Our study identifies maspin expression as an independent prognostic marker for risk stratification of early stage MSI subtype colorectal cancer and may provide guidance for improved therapeutic management.
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