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A Multi-center Study on Human Microecology Assisted Diagnosis of Colorectal Cancer

ABSTRACT: As for this research，we want to find whether the intestinal microecology (flora, peptidoglycan fragments) have certain distribution characteristics in colorectal diseases; whether it can predict the development of disease/as a prognostic indicator.

DISEASE(S): Human Microecology；colorectal Disease；auxiliary Diagnosis

PROVIDER: 70758 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

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Effects of Shenlingbaizhu powder on the efficacy of chemotherapy and the quality of life of patients with ovarian cancer based on intestinal microecology

Project description:Interventions: control group:Standard chemotherapy plus Bifid Triple Viable Capsules;Experiment group:Standard chemotherapy plus Shenlingbaizhu powder;Blank group:Standard chemotherapy, no Bifid Triple Viable Capsules Primary outcome(s): Distribution of intestinal flora;Immune function test;Efficacy evaluation Study Design: Parallel

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Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

Project description:Background: Cell free DNA (cfDNA) in plasma has received increasing attention and has been studied in a broad range of clinical conditions implicating inflammation, cancer, and aging. However, few studies have focused on mitochondrial DNA (mtDNA) in the cell free form. This study characterized the size distribution and sequence characteristics of plasma cell free mtDNA (cf mtDNA) in humans.Methods and Results: We optimized DNA isolation and next-generation sequencing library preparation protocols to better retain short DNA fragments from plasma, and applied these optimized methods to plasma samples from patients with sepsis. After massive parallel sequencing, we verified that our methods can retain substantially shorter DNA fragments than the standard isolation method, resulting in an average of 11.5 fold increase in short DNA fragments yield (DNA < 100bp). We report that cf mtDNA in plasma is highly enriched in short-size cfDNA (30 ~ 60 bp), which is much shorter than the value previously reported (~140 bp). Motivated by this unique size distribution, we size-selected short cfDNA fragments from the sequencing library, which further increased the mtDNA recovery rate by an average of 10.4 fold. Using this approach we detected mixtures of different mtDNA sequences, termed heteroplasmy, in plasma from 3 patients. In one patient who previously received bone marrow transplantation, different minor allele frequencies were observed between plasma and white blood cells (WBC) at heteroplasmic mtDNA sites, consistent with mixed-tissue origin for plasma DNA.Conclusion: mtDNA in plasma exists as very short fragments that exhibit mtDNA heteroplasmy distribution differences from that found in a single organ/tissue. This study is the first report of genome wide identification of mtDNA heteroplasmy in human plasma. Our optimized method can be used to investigate the potential utility of cf mtDNA fragments and heteroplasmy as biomarkers in various diseases.

2016-05-07 | GSE81178 | GEO

A multi-center study on human microecology assisted diagnosis of colorectal cancer

Project description:Interventions: CRC:None;NAP:None;CRA:None;IBD:None;IBS:None Primary outcome(s): microbiology;metabonomics Study Design: Case-Control study

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human gut metagenome

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Project description:Indicator indicator

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The gene expressional profiles between A172 glioma cells and the derived TMZ-resistance cells

Project description:We want to investigate whether there is an aquired resistance in glioma cells after TMZ treatment.

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The gene expressional profiles between U87MG glioma cells and the derived TMZ-resistance cells

Project description:We want to investigate whether there is an aquired resistance in glioma cells after TMZ treatment.

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LocusMasterTE: long-read assisted short-read TE quantification [short]

Project description:With an ability to compromise genome integrity, transposable elements (TEs) have significant associations with human diseases. Short-read sequencing has been used to study the expression of TEs; however, the highly repetitive nature of these elements makes multimapping a critical issue. Here we implement LocusMasterTE, an improved quantification method by integrating long-read sequencing. Introducing computed transcript per million(TPM) counts from long-read sequencing as prior distribution during Expectation-Maximization(EM) model in short-read TE quantification, multi-mapped reads are re-assigned to correct expression values. Based on simulated short reads, LocusMasterTE outperforms current quantitative approaches and is significantly favorable in capturing newly inserted TEs. We also verified that TEs quantified by LocusMasterTE clearly related to euchromatins and heterochromatins in cell line samples. With LocusMasterTE we anticipate that more accurate quantification can be performed, allowing novel functions of TEs to be uncovered.

2023-09-01 | GSE225380 | GEO

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