Foodomics strategies for the analysis of transgenic foods

•Potential of molecular profiling for study of genetically-modified organisms (GMOs).•Transcriptomics, proteomics and metabolomics in studying substantial equivalence.•Foodomics strategies for the investigation of unintended effects in GMOs.

Advanced tools in transcriptomics, proteomics, and metabolomics in combination with bioinformatics and chemometrics may provide chemical compositional data that may be helpful in studying any effects (intended or not) derived from genetic transformation. In this review, we critically discuss the use of the main omics technologies to characterize genetically-modified organisms at the transcriptome, proteome and metabolome levels.