Abstract 6253: RNA-seq based somatic variant calling and gene expression analysis reveals tumor heterogeneity and metastatic potential in colorectal cancers

Abstract

Abstract Colorectal cancer (CRC) is the third common malignant tumor and the second most responsible for worldwide cancer deaths. Also, RNAseq technology has been used for two purposes: to find exonic regions on the genome and quantify the expression level of the gene. We tried to validate the pipeline for identifying somatic variants from RNA-seq data, mainly following GATK4 somatic calling pipelines with some optimizing modifications. It is intended to examine whether somatic mutations driven from RNAseq data are associated with the biological behaviors of the individual colorectal cancer cells. We found that key genes (i.e., tumor suppressor genes such as APC and p53) are mostly mutated by T to C (in the non-coding region) or C to T (in the coding region) transitions, so that causes missense and nonsense mutations. However, highly mutated genes did not show significant expressional changes compared to the normal tissue. Otherwise, genes related to the metastatic potentials were observed to have highly increased expression. Our results can substantially verify the reliability of the somatic mutation calling approach using RNAseq data to call cancer-driving mutation and confirm an increase of extracellular matrix metabolism in the CRC. Citation Format: Ji Won Choi, Kwangsung Ahn, Sangsoo Kim, Dong-Il Park, Soo-kyung Park. RNA-seq based somatic variant calling and gene expression analysis reveals tumor heterogeneity and metastatic potential in colorectal cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6253.