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Background  Identifying gene mutation signatures will enable a better understanding for the occurrence and development of colorectal cancer (CRC), and provide some potential biomarkers for clinical practice. Currently, however, there is still few effective biomarkers for early diagnosis and prognostic judgment in CRC patients. The purpose was to identify novel mutation signatures for the diagnosis and prognosis of CRC.    Methods  Clinical information of 531 CRC patients and their sequencing data were downloaded from TCGA database (training group), and 53 clinical patients were collected and sequenced with targeted next generation sequencing (NGS) technology (validation group). The relationship between the mutation genes and the diagnosis, pathological type, stage and prognosis of CRC were compared to construct signatures for CRC, and then analyzed their relationship with RNA expression, immunocyte infiltration and tumor microenvironment (TME).    Results  Mutations of  TP53 ,  APC ,  KRAS ,  BRAF  and  ATM  covered 97.55% of TCGA population and 83.02% validation patients. Moreover, 57.14% validation samples and 22.06% TCGA samples indicated that patients with mucinous adenocarcinoma tended to have  BRAF  mutation, but no  TP53  mutation. Mutations of  TP53 ,  PIK3CA ,  FAT4 ,  FMN2  and  TRRAP  had a remarkable difference between I-II and III-IV stage patients ( P  < 0.0001). Besides, the combination of  PIK3CA ,  LRP1B ,  FAT4  and  ROS1  formed signatures for the prognosis and survival of CRC patients. The mutations of  TP53 ,  APC ,  KRAS ,  BRAF ,  ATM ,  PIK3CA ,  FAT4 ,  FMN2 ,  TRRAP ,  LRP1B , and  ROS1  formed the signatures for predicting diagnosis and prognosis of CRC. Among them, mutation of  TP53 ,  APC ,  KRAS ,  BRAF ,  ATM ,  PIK3CA ,  FAT4  and  TRRAP  significantly reduced their RNA expression level. Stromal score, immune score and ESTIMATE score were lower in patients with  TP53 ,  APC ,  KRAS ,  PIK3CA  mutation compared non-mutation patients. All the 11 gene mutations affected the distributions of immune cells.    Conclusion  This study constructed gene mutation signatures for the diagnosis, treatment and prognosis in CRC, and proved that their mutations affected RNA expression levels, TME and immunocyte infiltration. Our results put forward further insights into the genotype of CRC.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12885-021-08108-9.

Multi gene mutation signatures in colorectal cancer patients: predict for the diagnosis, pathological classification, staging and prognosis