Abstract 5022: iGRAMMy: Cloud-based characterization of microbial landscape in colorectal cancers

Abstract

Abstract Many studies have identified pervasive tumor-infiltrating bacteria in colon, gastric, kidney, and other tumors. Infiltrating bacteria have functional significance, affecting the immune system state, affecting a tumor’s ability to metastasize, and modifying patient’s response to therapies. Only a few tools can infer infiltrating bacteria based on the RNA-and DNA-Seq data of tumor samples. These tools are not optimized for cloud-based computation, where large public datasets such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) now reside. Here, we present a novel cloud-based bioinformatics tool - iGRAMMy, that accurately, efficiently, and robustly estimate microbial relative abundance in sequenced tumor and matched normal samples. We developed iGRAMMy by integrating read filtering, remapping, and relative abundance estimation steps of whole genome (WGS-seq) and/or transcriptome (RNA-seq) based microbiome analysis. We validated iGRAMMy by comparing estimated abundance to positive and negative controls of a published dataset as golden standard. We applied iGRAMMy to study all colorectal cancer samples within the TCGA cohort and reported the microbial landscape of these tumors. We identified a significantly higher abundance of overall bacterial infiltration in tumor as compared to normal samples. We found species like Bacteroides fragilis, Bacteroides dorei and Fusobacterium nucleatum were significantly higher in tumors, which were corroborated by previous reports. We uniquely identified Bacteroides intestinalis was also significantly more abundant in tumor samples. We released iGRAMMy and the entire analysis as a workflow pipeline on cancer genomics cloud, where researchers can easily replicate the study and use the tool for their own data. Citation Format: Li C. Xia, Dongmei Ai, Man Guo, Hanlee Ji. iGRAMMy: Cloud-based characterization of microbial landscape in colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5022.