Project description:Interventions: Group 1: Surgical patients undergoing surgery for colorectal cancer: immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples perioperatively and during oncologic follow-up. Group 2: oncologic patients with chemo- / immune therapy without recent surgery: Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa and saliva samples during therapy and oncological follow-up. Group 3: healthy controls: Immunophenotyping by PBMCs and metagenomic analyses from stool, mucosa, and saliva samples at the time of screening colonoscopy. Primary outcome(s): Difference in the differential abundance of the colonic mucosa of patients with CRC vs. healthy controls for evaluation as diagnostic biomarkers based on metagenomic analyzes (microbial pattern) Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: diagnostic

| 2439680 | ecrin-mdr-crc

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.

2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress

HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): from reads to pathogens. A specific and exhaustive pipeline for handling metagenomic shotgun sequencing data.

2021-07-26 | E-MTAB-9191 | biostudies-arrayexpress

NeoM Study Metagenomic Samples

Project description:Metagenomic reads for the microbiota of premature infant faecal samples

| PRJEB24015 | ENA