Pilot study comparing yield from 16srRNA sequencing from frozen tissue vs. formalin-fixed paraffin-embedded (FFPE) tissue from the ileum and colon. Colonpilot

Introduction: Next generation sequencing have made it possible to examine the microbiome of the GI tract without culture dependent methods. 16srRNA sequencing is currently the most frequently used sequencing method to examine the microbiome in the GI tract. As sequencing costs continues to decrease, thorough investigations of the microbiome in the GI tract is now easily accessible. However, several studies have shown large variation between the mucosal and fecal microbiome in humans. In inflammatory bowel disease (IBD), the mucosal microbiome is considered to be the most relevant for the pathogenesis. Mucosal tissue is only accessible during colonoscopy or surgery, and the availability of colon or ileum tissue is therefore the most important limiting factor in microbiome research in IBD. However the access to FFPE-tissue is immense compared to the availability of fresh tissue samples. Aims and methods: To compare the yield from 16srRNA sequencing on frozen tissue vs. FFPE from the same patient. Two patients scheduled for bowel resection because of cancer in the right hemicolon were included in this pilot study. Paired tissue biopsies were taken from the colon and ileum in both patients immediately after surgical bowel resection. One biopsy in the pair was frozen on liquid nitrogen and in -80 C and the other put on formalin for subsequent DNA isolation and sequencing analysis. DNA isolation were performed using Qiagen, QIAamp DNA mini kit for the frozen the tissue and Qiagen, QIAamp DNA FFPE tissue kit for FFPE tissue. 16srRNA sequencing, using Illumina Miseq platform were performed on both frozen tissue and FFPE tissue.