Pilot_project_to_evaluate_bowel_preparation_and_sampling_procedure_for_microbiome_studies-sc-3415
Pilot_project_to_evaluate_bowel_preparation_and_sampling_procedure_for_microbiome_studies
We are proposing a pilot to study key factors about endoscopic sampling of the microbiome. These include sampling site, method and the "bowel preparation" typically done before endoscopy. To achieve this we will perform two separate procedures on a small number of IBD patients: one without standard bowel preparation, and another follow-up, with prep, a few days later. We plan to collect data from 10 subjects to examine inter-individual variation, and have planned for 16 samples per subject: -1 stool sample, for comparison to other published data, mostly stool based -lavage, brushing and biopsy samples from two sites (rectum & left colon) during the unprepared flexible sigmoidoscopy (i.e. the procedure without standard pre-colonoscopic bowel preparation) -lavage, brushing and biopsy samples from three sites (from the rectum, left side of the colon and from the furthest point of intubation - most often the ileum) during the follow-up colonoscopy DNA will be extracted, and we will perform shotgun metagenomic sequencing on all these samples. We can then analyze concordance by site, sampling method and with/without the preparation. These data will be used to plan our first main microbiome study.  This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
We are proposing a pilot to study key factors about endoscopic sampling of the microbiome. These include sampling site, method and the "bowel preparation" typically done before endoscopy. To achieve this we will perform two separate procedures on a small number of IBD patients: one without standard bowel preparation, and another follow-up, with prep, a few days later. We plan to collect data from 10 subjects to examine inter-individual variation, and have planned for 16 samples per subject: -1 stool sample, for comparison to other published data, mostly stool based -lavage, brushing and biopsy samples from two sites (rectum & left colon) during the unprepared flexible sigmoidoscopy (i.e. the procedure without standard pre-colonoscopic bowel preparation) -lavage, brushing and biopsy samples from three sites (from the rectum, left side of the colon and from the furthest point of intubation - most often the ileum) during the follow-up colonoscopy DNA will be extracted, and we will perform shotgun metagenomic sequencing on all these samples. We can then analyze concordance by site, sampling method and with/without the preparation. These data will be used to plan our first main microbiome study.