Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1288126 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A Multivariate Cell-Based Liquid Biopsy for Lung Nodule Risk Stratification: Analytical Validation and Early Clinical Evaluation
| PRJNA1152596 | ENA
Project description:The Oxford Nanopore (ONT) platform provides portable and rapid genome sequencing, and its ability to natively profile DNA methylation without complex sample processing is attractive for clinical sequencing. We recently demonstrated ONT shallow whole-genome sequencing to detect copy number alterations (CNA) from the circulating tumor DNA (ctDNA) of cancer patients. Here, we show that cell-type and cancer-specific methylation changes can also be detected, as well as cancer-associated fragmentation signatures. This feasibility study suggests that ONT shallow WGS could be a powerful tool for liquid biopsy, especially real-time medical applications.
2022-04-27 | GSE185307 | GEO
Project description:Liver cancer is one of the most lethal cancers worldwide. Liquid biopsy provides a noninvasive approach in detecting and monitoring cancer biomarkers to overcome current limitations associated with tissue biopsies, comprising the analysis of circulating tumor-derived material. In this study, we profiled plasma cell-free RNA-seq to identify recurrently dysregulated RNA biomarkers for the liquid biopsy of cancer.
2020-09-30 | GSE142987 | GEO
Project description:Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. Given their functional and clinical relevance, small EVs have emerged as a promising target among the liquid biopsy approaches for cancer detection. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive. In this study, we established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC). By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitundial cohorts, we uncovered 28 EV-miRs for detecting mCRC, and 131 EV-miRs for long-term monitoring of tumor size progression. Among these candidates, we further pinpointed a 15-EV-miR signature with dual detection and monitoring functions for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker – aside from its diagnostic power, its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Furthermore, target spectrum of this 15-EV-miR signature of mCRC suggested an involvement of small EVs in programming the mesenchymal–epithelial transition (MET) transition for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche. Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in tumor therapeutic monitoring.
2022-09-14 | GSE188627 | GEO
Project description:Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive liquid biopsy. As such, Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.
2022-07-21 | GSE208596 | GEO
Project description:Genome-wide analysis of cell-free DNA (cfDNA) methylation profile has been recognized as a promising approach for sensitive and specific detection of many cancers. However, scaling such genome-wide assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We have shown that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbors the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that allows for focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable accurate tumor burden estimation with high sensitivity and quantitative tracking of colorectal cancer patient’s response to treatment, at much reduced sequencing cost suitable for frequent monitoring. We also show, for the first time, tumor epigenetic subtyping from cfDNA using Heatrich-BS, which could enable patient stratification from non-invasive liquid biopsy. As such, Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.
2022-05-13 | GSE202606 | GEO
Project description:Development of a novel machine learning guided ctDNA detection platform for use in liquid biopsy detection and therapeutic monitoring of solid tumors in several clinical contexts. Included are WGS alignments from our study.
| EGAS00001007306 | EGA
Project description:Purpose: Breast cancers with ESR1 mutations are resistant to antiestrogen therapy. We aimed to investigate the association of ESR1 mutations with resistance to CDK4/6 inhibitors (CDK4/6i) using real-world data analysis and experimental validation. Patients and Methods: A total of 3,958 patients with estrogen receptor-positive (ER+) metastatic breast cancer with DNA sequencing data were analyzed. Breast tumor DNA and circulating tumor (ct) DNA were sequenced using the Tempus xT tumor assay and Tempus xF liquid biopsy, respectively. Patients were stratified into either treated with CDK4/6i (breast tumors: 1,070; ctDNA: 1,885) or CDK4/6i naïve (breast tumors: 750; ctDNA: 253). Engineered MCF7 cells carrying ESR1 Y537S or D538G knock-in mutations were used to study antitumor efficacy of the CDK4/6i, palbociclib in vitro and in vivo. Results: In both xF and xT assays, ESR1 mutations were the only somatic alterations significantly more frequent in those who received CDK4/6i than those who did not. Knock-in of ESR1 Y537S or ESR1 D538G in MCF7 cells resulted in upregulation of cell cycle-related gene signatures upon treatment with CDK4/6i ± antiestrogen compared to cells with non-mutant ESR1. MCF7 xenografts harboring ESR1 Y537S and D538G mutations established in nude mice were resistant to palbociclib. Conclusions: We report herein real-world and preclinical evidence that ESR1 mutations, particularly Y537S and D538G, can drive resistance to CDK4/6 inhibitors.
2024-11-12 | GSE281302 | GEO
Project description:Interventions: Gold Standard:Clinical outcome;Index test:ctDNA methylated liquid biopsy
Primary outcome(s): ctDNA
Study Design: Sequential
| 2697935 | ecrin-mdr-crc