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Background  Colorectal cancer (CRC) is one of the most incident cancers, associated with significant morbidity and mortality, and usually classified into three main molecular pathways: chromosomal instability, microsatellite instability (MSI) and CpG island methylator phenotype (CIMP). Currently, available screening methods are either costly or of limited specificity, impairing global implementation. More cost-effective strategies, including DNA methylation-based tests, might prove advantageous. Although some are already available, its performance is suboptimal, entailing the need for better candidate biomarkers. Herein, we tested whether combined use of  APC ,  IGF2 ,  MGMT ,  RASSF1A , and  SEPT9  promoter methylation might accurately detect CRC irrespective of molecular subtype.    Methods  Selected genes were validated using formalin-fixed paraffin-embedded tissues from 214 CRC and 50 non-malignant colorectal mucosae (CRN). Promoter methylation levels were assessed using real-time quantitative methylation-specific PCR. MSI and CIMP status were determined. Molecular data were correlated with standard clinicopathological features. Diagnostic and prognostic performances were evaluated by receiver operator characteristics curve and survival analyses, respectively.    Results  Except for IGF2, promoter methylation levels were significantly higher in CRC compared to CRN. A three-gene panel ( MGMT ,  RASSF1A ,  SEPT9 ) identified malignancy with 96.6% sensitivity, 74.0% specificity and 91.5 positive predictive value (area under the curve: 0.97), independently of tumor location, stage, and molecular pathway.    Conclusions  Combined promoter methylation analysis of  MGMT / RASSF1A/SEPT9  displays a better performance than currently available epigenetic-based biomarkers for CRC, providing the basis for the development of a non-invasive assay to detect CRC irrespective of the molecular pathway.    Electronic supplementary material  The online version of this article (10.1186/s12967-018-1415-9) contains supplementary material, which is available to authorized users.

A novel DNA methylation panel accurately detects colorectal cancer independently of molecular pathway