Project description:In this study we have sequenced the ctDNA of 28 Small Cell Lung Cancer patients in the TP53 gene, each sample has been sequenced twice.
Project description:This study aims to compared ctDNA methylation status induced by ionizing to different ograns. SD rats were irradiated with local radaition to brain, lung or skin. Serum was collected and subjiected to ctDNA extraction. ctDNA were then treated by methylation-sensive bisulfite and sequencing.
Project description:In this study we have sequenced the TP53 gene (exons) from circulating-tumor DNA of 125 controls samples. Each ctDNA samples was sequenced independently twice.
Project description:BAM files corresponding to sequencing of 28 circulating tumor DNA and matched tumor samples from SCC patients. Each ctDNA sample was sequenced twice.
Project description:To develop diagnostic and prognostic biomarkers, we compared methylation profiles of HCC tissues and normal blood by analyzing 485,000 CpG markers and identified a HCC enriched methylation marker panel compared to that of normal blood. We found there was a highly correlation of methylation profiles between DNA from HCC cancer tissue and matched plasma ctDNA within the same patient. We then selected 10 markers from this panel and created a combined diagnosis score (cd-score) which showed high diagnostic specificity and sensitivity in both a training cohort and an independent validation cohort. We also showed the cd-score correlate highly with tumor load, treatment response and stage and is superior to that by AFP. We also showed the cd-score correlate highly with tumor load, treatment response and stage and is superior to that by AFP. Additional, we generated 8 markers from unicox and LASSO-cox analysis and created a combined prognosis score (cp-score) which could predict prognosis and survival. Together, these findings demonstrated the utility of ctDNA methylation markers in the diagnosis, treatment evaluation and prognosis of HCC.
Project description:Patients with head and neck squamous cell carcinoma (HNSCC) have a poor prognosis due to the development of locoregional recurrences, distant metastases and second primary tumors. There is an urgent need for biomarkers that enable detection and monitoring of the disease to provide adequate therapeutic strategies. In this study we have investigated markers in peripheral blood cells (PBC) of 28 HNSCC patients who underwent surgery by means of expression profiling. Our hypothesis is that nucleated blood cells circulate continuously, also passing the tumor, and might change their expression profiles in response to tumor cell factors. For comparison, we enrolled a control group of 11 patients who underwent surgery in the head and neck region for non-HNSCC reasons. A set of 2,349 genes was found to be statistically different between the groups (p<0.05, false discovery rate-corrected) and the most prominently different pathways were EIF2 and mTOR signaling. These preliminary results are promising and warrant further studies on the definitive role of PBC gene expression as a biomarker for HNSCC detection and monitoring. Two-color experiment with each individual sample in a single channel. RNA of nucleated blood cells of humans was analysed. Case-control analysis, with 28 cases, patients with head and neck squamous cell carcinoma and 11 controls, without squamous cell carcinoma
Project description:BAM files corresponding to sequencing of 18 circulating tumor DNA and matched tumor samples from SCLC patients. Each ctDNA sample was sequenced twice.
